Starting phenix.real_space_refine on Sat May 17 17:06:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byy_45048/05_2025/9byy_45048_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byy_45048/05_2025/9byy_45048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9byy_45048/05_2025/9byy_45048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byy_45048/05_2025/9byy_45048.map" model { file = "/net/cci-nas-00/data/ceres_data/9byy_45048/05_2025/9byy_45048_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byy_45048/05_2025/9byy_45048_neut.cif" } resolution = 4.07 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: 9.04, per 1000 atoms: 0.56 Number of scatterers: 16038 At special positions: 0 Unit cell: (97.632, 124.074, 132.21, 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: 4.05 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: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.516A 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: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.665A 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: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.016A 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: 4.073A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.677A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.878A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A 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: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.567A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.668A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.427A 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: 8.393A 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: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.715A 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: 6.477A 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: 6.382A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.344A 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: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.44 Time building geometry restraints manager: 4.70 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: 4819 1.34 - 1.46: 3057 1.46 - 1.58: 8329 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 1.600 -0.060 1.25e-02 6.40e+03 2.29e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.039 1.20e-02 6.94e+03 1.06e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.574 -0.032 1.08e-02 8.57e+03 8.59e+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 7.50e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 7.07e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21577 2.09 - 4.18: 515 4.18 - 6.27: 37 6.27 - 8.36: 1 8.36 - 10.45: 4 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.63 -6.09 1.36e+00 5.41e-01 2.01e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.14 -4.43 1.15e+00 7.56e-01 1.48e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.20 -3.92 1.09e+00 8.42e-01 1.29e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.81 -4.31 1.23e+00 6.61e-01 1.23e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.68 -3.97 1.15e+00 7.56e-01 1.19e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 9468 35.81 - 71.62: 339 71.62 - 107.43: 37 107.43 - 143.24: 3 143.24 - 179.05: 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 -58.32 120.73 -179.05 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 301.68 151.20 150.48 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 31.91 148.06 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: 2144 0.093 - 0.186: 184 0.186 - 0.279: 27 0.279 - 0.372: 3 0.372 - 0.465: 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 5.42e+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 4.67e+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 2.16 0.35 2.00e-01 2.50e+01 3.01e+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 2.68e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.11e-02 2.14e+00 pdb=" CG PHE D 92 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 9.71e-03 1.88e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11557 3.11 - 3.70: 27052 3.70 - 4.30: 41529 4.30 - 4.90: 65421 Nonbonded interactions: 145688 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 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145683 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 37.200 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 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= 0.315 Angle : 0.740 10.449 22134 Z= 0.463 Chirality : 0.058 0.465 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.952 179.051 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.19 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: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 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 0.15421 ( 871) hydrogen bonds : angle 6.51807 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74007 (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 883 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 860 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8904 (mm) cc_final: 0.8699 (mm) REVERT: A 109 ASN cc_start: 0.8043 (m-40) cc_final: 0.7605 (p0) REVERT: A 116 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6842 (mt-10) REVERT: A 118 TYR cc_start: 0.8114 (t80) cc_final: 0.7878 (t80) REVERT: A 147 GLN cc_start: 0.8293 (mt0) cc_final: 0.7235 (mt0) REVERT: A 149 TYR cc_start: 0.8380 (t80) cc_final: 0.8006 (t80) REVERT: A 155 THR cc_start: 0.9239 (m) cc_final: 0.8917 (m) REVERT: A 162 LYS cc_start: 0.7625 (ttpt) cc_final: 0.7303 (ttmm) REVERT: A 190 MET cc_start: 0.8182 (mtt) cc_final: 0.7741 (mtt) REVERT: A 192 LEU cc_start: 0.9213 (mt) cc_final: 0.8696 (mt) REVERT: A 204 SER cc_start: 0.9231 (m) cc_final: 0.8697 (t) REVERT: A 227 MET cc_start: 0.8479 (mtp) cc_final: 0.8233 (mtp) REVERT: A 345 LYS cc_start: 0.8579 (tttt) cc_final: 0.8158 (tttt) REVERT: A 373 ILE cc_start: 0.8878 (mt) cc_final: 0.8624 (mt) REVERT: A 377 LYS cc_start: 0.8860 (mttt) cc_final: 0.8378 (mttp) REVERT: A 436 LEU cc_start: 0.8997 (mt) cc_final: 0.8614 (mm) REVERT: A 494 MET cc_start: 0.7832 (mtp) cc_final: 0.7622 (mtm) REVERT: A 588 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7280 (mm-40) REVERT: A 598 MET cc_start: 0.7525 (mtm) cc_final: 0.6983 (mtm) REVERT: A 606 TYR cc_start: 0.6927 (m-80) cc_final: 0.6628 (m-10) REVERT: A 634 MET cc_start: 0.8405 (mmp) cc_final: 0.8092 (mmm) REVERT: B 12 LEU cc_start: 0.8929 (mt) cc_final: 0.8447 (mt) REVERT: B 51 LEU cc_start: 0.8150 (tp) cc_final: 0.7908 (tp) REVERT: B 99 LYS cc_start: 0.9088 (mmtt) cc_final: 0.8645 (mmtt) REVERT: B 147 GLN cc_start: 0.8069 (mt0) cc_final: 0.7408 (mt0) REVERT: B 161 ARG cc_start: 0.7152 (mtt180) cc_final: 0.6949 (mtt180) REVERT: B 181 ASP cc_start: 0.8428 (m-30) cc_final: 0.8065 (m-30) REVERT: B 211 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7294 (mm-30) REVERT: B 264 THR cc_start: 0.8338 (p) cc_final: 0.8063 (p) REVERT: B 286 ASP cc_start: 0.6259 (OUTLIER) cc_final: 0.5869 (m-30) REVERT: B 288 PHE cc_start: 0.7851 (t80) cc_final: 0.7549 (t80) REVERT: B 319 MET cc_start: 0.8079 (tpp) cc_final: 0.7475 (tpp) REVERT: B 394 TYR cc_start: 0.8003 (m-80) cc_final: 0.7687 (m-80) REVERT: B 425 ILE cc_start: 0.9175 (mt) cc_final: 0.8901 (mt) REVERT: B 436 LEU cc_start: 0.9111 (mt) cc_final: 0.8899 (mt) REVERT: B 460 SER cc_start: 0.8467 (t) cc_final: 0.8141 (p) REVERT: B 570 MET cc_start: 0.7289 (mtm) cc_final: 0.6927 (mtm) REVERT: B 584 ILE cc_start: 0.8989 (tp) cc_final: 0.8770 (tp) REVERT: B 585 SER cc_start: 0.9094 (p) cc_final: 0.8615 (t) REVERT: B 588 GLN cc_start: 0.7635 (mm-40) cc_final: 0.6504 (mm-40) REVERT: B 589 SER cc_start: 0.7889 (m) cc_final: 0.7565 (m) REVERT: B 597 ILE cc_start: 0.9096 (pt) cc_final: 0.8873 (pt) REVERT: B 640 MET cc_start: 0.7717 (tpp) cc_final: 0.7083 (tpp) REVERT: B 644 ILE cc_start: 0.8889 (mt) cc_final: 0.8581 (mt) outliers start: 23 outliers final: 7 residues processed: 874 average time/residue: 0.3045 time to fit residues: 376.4581 Evaluate side-chains 584 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 576 time to evaluate : 1.769 ------------------------------------------------------------------------------- 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: 5.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 44 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 676 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 84 HIS C 210 GLN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.097847 restraints weight = 36714.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101124 restraints weight = 19082.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103491 restraints weight = 12037.660| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 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 : 0.005 0.066 16386 Z= 0.246 Angle : 0.691 13.080 22134 Z= 0.365 Chirality : 0.045 0.345 2360 Planarity : 0.004 0.047 2818 Dihedral : 11.490 173.362 2242 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.17 % Allowed : 2.86 % Favored : 96.97 % 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: 1.28 (0.19), residues: 1932 helix: 1.24 (0.15), residues: 1130 sheet: 0.34 (0.44), residues: 134 loop : 0.48 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 9 HIS 0.008 0.002 HIS A 255 PHE 0.031 0.002 PHE D 259 TYR 0.024 0.002 TYR A 522 ARG 0.009 0.001 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 871) hydrogen bonds : angle 5.08149 ( 2571) covalent geometry : bond 0.00536 (16386) covalent geometry : angle 0.69131 (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 679 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 676 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8846 (t80) cc_final: 0.8528 (t80) REVERT: A 99 LYS cc_start: 0.9147 (mmtt) cc_final: 0.8940 (mmtm) REVERT: A 117 ARG cc_start: 0.8454 (mtp85) cc_final: 0.8199 (mtp85) REVERT: A 131 ASN cc_start: 0.9037 (t0) cc_final: 0.8813 (t0) REVERT: A 147 GLN cc_start: 0.8796 (mt0) cc_final: 0.8529 (mt0) REVERT: A 164 ARG cc_start: 0.7304 (ptt90) cc_final: 0.7070 (ptt-90) REVERT: A 286 ASP cc_start: 0.8761 (m-30) cc_final: 0.8067 (m-30) REVERT: A 322 MET cc_start: 0.8726 (mmp) cc_final: 0.8353 (mmm) REVERT: A 362 ASP cc_start: 0.7162 (m-30) cc_final: 0.6752 (m-30) REVERT: A 444 ASP cc_start: 0.8317 (t0) cc_final: 0.7731 (t0) REVERT: A 446 ARG cc_start: 0.7885 (mmm160) cc_final: 0.6982 (mmt180) REVERT: A 458 MET cc_start: 0.9246 (mmm) cc_final: 0.8465 (mmm) REVERT: A 493 MET cc_start: 0.9041 (tmm) cc_final: 0.8578 (tmm) REVERT: A 494 MET cc_start: 0.8973 (mtp) cc_final: 0.8627 (mtp) REVERT: A 640 MET cc_start: 0.9116 (ttm) cc_final: 0.8611 (ttm) REVERT: B 8 LYS cc_start: 0.8820 (tptp) cc_final: 0.8187 (tppt) REVERT: B 12 LEU cc_start: 0.9530 (mt) cc_final: 0.9135 (mt) REVERT: B 96 SER cc_start: 0.9546 (m) cc_final: 0.9279 (p) REVERT: B 112 LYS cc_start: 0.8938 (pptt) cc_final: 0.8666 (pttm) REVERT: B 119 GLU cc_start: 0.8761 (mp0) cc_final: 0.8311 (mp0) REVERT: B 147 GLN cc_start: 0.8902 (mt0) cc_final: 0.8191 (mt0) REVERT: B 181 ASP cc_start: 0.8940 (m-30) cc_final: 0.8128 (m-30) REVERT: B 200 SER cc_start: 0.8963 (t) cc_final: 0.8695 (t) REVERT: B 253 ILE cc_start: 0.9551 (tt) cc_final: 0.9307 (tt) REVERT: B 263 ASP cc_start: 0.9040 (m-30) cc_final: 0.8687 (m-30) REVERT: B 276 LYS cc_start: 0.9272 (pttt) cc_final: 0.8870 (pttm) REVERT: B 288 PHE cc_start: 0.9326 (t80) cc_final: 0.8974 (t80) REVERT: B 291 LEU cc_start: 0.9455 (mt) cc_final: 0.8954 (mt) REVERT: B 316 GLU cc_start: 0.8709 (tt0) cc_final: 0.8390 (tt0) REVERT: B 348 MET cc_start: 0.7927 (tpt) cc_final: 0.7284 (tpp) REVERT: B 386 LEU cc_start: 0.9230 (mt) cc_final: 0.9019 (mt) REVERT: B 393 SER cc_start: 0.9490 (m) cc_final: 0.8997 (p) REVERT: B 394 TYR cc_start: 0.8916 (m-80) cc_final: 0.8014 (m-80) REVERT: B 413 SER cc_start: 0.8007 (p) cc_final: 0.6844 (t) REVERT: B 425 ILE cc_start: 0.9663 (mt) cc_final: 0.9450 (mt) REVERT: B 467 ASN cc_start: 0.9117 (t0) cc_final: 0.8872 (t0) REVERT: B 474 GLN cc_start: 0.9025 (mt0) cc_final: 0.8743 (mt0) REVERT: B 493 MET cc_start: 0.9434 (tmm) cc_final: 0.9212 (tmm) REVERT: B 526 GLU cc_start: 0.8119 (tp30) cc_final: 0.7804 (tp30) REVERT: B 550 MET cc_start: 0.7913 (mtp) cc_final: 0.7371 (ttm) REVERT: B 588 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8421 (mm-40) REVERT: B 602 GLU cc_start: 0.7949 (pt0) cc_final: 0.7749 (pt0) REVERT: B 640 MET cc_start: 0.9107 (tpp) cc_final: 0.8599 (tpp) REVERT: B 667 LEU cc_start: 0.9557 (tp) cc_final: 0.9340 (tp) REVERT: C 27 LYS cc_start: 0.8944 (mtmm) cc_final: 0.8641 (tptt) REVERT: C 53 ASP cc_start: 0.8153 (t0) cc_final: 0.7947 (t0) REVERT: C 212 ILE cc_start: 0.8537 (mm) cc_final: 0.8113 (mm) REVERT: C 247 TYR cc_start: 0.7951 (m-10) cc_final: 0.7547 (m-80) REVERT: D 23 ASN cc_start: 0.9262 (m110) cc_final: 0.9052 (m-40) REVERT: D 95 MET cc_start: 0.9321 (tmm) cc_final: 0.9120 (tmm) REVERT: D 96 MET cc_start: 0.8264 (mmm) cc_final: 0.8033 (tpt) REVERT: D 100 VAL cc_start: 0.7984 (t) cc_final: 0.7547 (t) REVERT: D 109 PHE cc_start: 0.6782 (m-80) cc_final: 0.6094 (m-80) REVERT: D 149 ASP cc_start: 0.8542 (m-30) cc_final: 0.8305 (m-30) REVERT: D 178 PHE cc_start: 0.8384 (m-80) cc_final: 0.8156 (m-80) REVERT: D 189 GLU cc_start: 0.7512 (tm-30) cc_final: 0.6747 (pt0) REVERT: D 259 PHE cc_start: 0.7955 (t80) cc_final: 0.7435 (t80) outliers start: 3 outliers final: 1 residues processed: 678 average time/residue: 0.2786 time to fit residues: 276.7812 Evaluate side-chains 527 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 526 time to evaluate : 1.690 ------------------------------------------------------------------------------- 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: 4.9990 chunk 168 optimal weight: 3.9990 chunk 175 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 338 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 645 GLN B 11 GLN B 61 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 233 ASN D 28 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN D 288 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.129568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.094231 restraints weight = 37451.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.097512 restraints weight = 19245.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.099810 restraints weight = 11722.409| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16386 Z= 0.228 Angle : 0.642 11.440 22134 Z= 0.340 Chirality : 0.044 0.302 2360 Planarity : 0.004 0.047 2818 Dihedral : 11.236 169.062 2242 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.12 % Allowed : 3.03 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.19), residues: 1932 helix: 1.18 (0.15), residues: 1131 sheet: 0.07 (0.44), residues: 134 loop : 0.46 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 124 HIS 0.008 0.001 HIS A 255 PHE 0.022 0.002 PHE A 129 TYR 0.026 0.002 TYR C 169 ARG 0.006 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 871) hydrogen bonds : angle 4.95969 ( 2571) covalent geometry : bond 0.00496 (16386) covalent geometry : angle 0.64202 (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 639 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 637 time to evaluate : 1.662 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 40 TYR cc_start: 0.8718 (t80) cc_final: 0.8092 (t80) REVERT: A 99 LYS cc_start: 0.9213 (mmtt) cc_final: 0.8913 (mmtp) REVERT: A 117 ARG cc_start: 0.8451 (mtp85) cc_final: 0.8186 (mtp85) REVERT: A 131 ASN cc_start: 0.9241 (t0) cc_final: 0.8953 (t0) REVERT: A 147 GLN cc_start: 0.8786 (mt0) cc_final: 0.8460 (mt0) REVERT: A 188 ILE cc_start: 0.9523 (mm) cc_final: 0.9315 (mm) REVERT: A 204 SER cc_start: 0.9290 (t) cc_final: 0.8929 (t) REVERT: A 286 ASP cc_start: 0.8775 (m-30) cc_final: 0.8173 (m-30) REVERT: A 290 GLU cc_start: 0.8373 (mp0) cc_final: 0.8173 (mp0) REVERT: A 362 ASP cc_start: 0.7244 (m-30) cc_final: 0.6571 (m-30) REVERT: A 399 GLU cc_start: 0.8915 (tp30) cc_final: 0.8688 (tp30) REVERT: A 458 MET cc_start: 0.9290 (mmm) cc_final: 0.8474 (mmm) REVERT: A 493 MET cc_start: 0.9011 (tmm) cc_final: 0.8642 (tmm) REVERT: A 494 MET cc_start: 0.8936 (mtp) cc_final: 0.8522 (mtp) REVERT: A 550 MET cc_start: 0.7647 (mtp) cc_final: 0.7258 (mtm) REVERT: A 552 ILE cc_start: 0.9464 (pt) cc_final: 0.9233 (mt) REVERT: B 65 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8153 (mm-30) REVERT: B 119 GLU cc_start: 0.8868 (mp0) cc_final: 0.8462 (mp0) REVERT: B 147 GLN cc_start: 0.8989 (mt0) cc_final: 0.8271 (mt0) REVERT: B 157 LEU cc_start: 0.9131 (tp) cc_final: 0.8786 (tp) REVERT: B 173 LEU cc_start: 0.9567 (mt) cc_final: 0.9345 (mt) REVERT: B 186 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9289 (mp) REVERT: B 211 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7486 (mm-30) REVERT: B 217 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7757 (tm-30) REVERT: B 238 ASP cc_start: 0.6840 (p0) cc_final: 0.5942 (p0) REVERT: B 263 ASP cc_start: 0.9047 (m-30) cc_final: 0.8737 (m-30) REVERT: B 288 PHE cc_start: 0.9374 (t80) cc_final: 0.9002 (t80) REVERT: B 316 GLU cc_start: 0.8735 (tt0) cc_final: 0.8489 (tt0) REVERT: B 348 MET cc_start: 0.8049 (tpt) cc_final: 0.7271 (tpp) REVERT: B 349 LEU cc_start: 0.9257 (mp) cc_final: 0.8940 (mt) REVERT: B 359 MET cc_start: 0.8605 (ttp) cc_final: 0.8388 (tmm) REVERT: B 373 ILE cc_start: 0.9691 (mt) cc_final: 0.9422 (mt) REVERT: B 393 SER cc_start: 0.9480 (m) cc_final: 0.8500 (p) REVERT: B 394 TYR cc_start: 0.9007 (m-80) cc_final: 0.8271 (m-80) REVERT: B 425 ILE cc_start: 0.9650 (mt) cc_final: 0.9374 (mt) REVERT: B 493 MET cc_start: 0.9459 (tmm) cc_final: 0.9123 (tmm) REVERT: B 526 GLU cc_start: 0.8062 (tp30) cc_final: 0.7616 (tp30) REVERT: B 550 MET cc_start: 0.8088 (mtp) cc_final: 0.7618 (ttm) REVERT: B 588 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8475 (mm-40) REVERT: B 590 SER cc_start: 0.9165 (p) cc_final: 0.8960 (p) REVERT: B 640 MET cc_start: 0.9189 (tpp) cc_final: 0.8596 (tpp) REVERT: B 644 ILE cc_start: 0.9640 (mt) cc_final: 0.9418 (mt) REVERT: B 667 LEU cc_start: 0.9513 (tp) cc_final: 0.9247 (tp) REVERT: C 27 LYS cc_start: 0.9035 (mtmm) cc_final: 0.8469 (tptp) REVERT: C 31 LEU cc_start: 0.9275 (mt) cc_final: 0.9062 (mt) REVERT: C 53 ASP cc_start: 0.8238 (t0) cc_final: 0.8012 (t0) REVERT: C 154 PHE cc_start: 0.8510 (t80) cc_final: 0.7831 (t80) REVERT: C 157 MET cc_start: 0.9212 (ptp) cc_final: 0.8972 (ptt) REVERT: C 212 ILE cc_start: 0.8613 (mm) cc_final: 0.8233 (mm) REVERT: C 247 TYR cc_start: 0.8045 (m-10) cc_final: 0.7672 (m-80) REVERT: D 42 LEU cc_start: 0.5916 (pp) cc_final: 0.5603 (pp) REVERT: D 46 TYR cc_start: 0.8462 (m-80) cc_final: 0.8169 (m-80) REVERT: D 56 MET cc_start: 0.6357 (mpp) cc_final: 0.5952 (mpp) REVERT: D 95 MET cc_start: 0.9341 (tmm) cc_final: 0.9139 (tmm) REVERT: D 149 ASP cc_start: 0.8510 (m-30) cc_final: 0.8269 (m-30) REVERT: D 189 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7212 (tm-30) REVERT: D 211 GLU cc_start: 0.9444 (tp30) cc_final: 0.9122 (mt-10) REVERT: D 224 LEU cc_start: 0.8710 (mt) cc_final: 0.8471 (mt) REVERT: D 259 PHE cc_start: 0.7961 (t80) cc_final: 0.7427 (t80) outliers start: 2 outliers final: 0 residues processed: 637 average time/residue: 0.2759 time to fit residues: 259.1227 Evaluate side-chains 546 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 545 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 645 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 313 HIS ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN D 23 ASN D 24 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.130590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.094975 restraints weight = 37554.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.098128 restraints weight = 19548.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100501 restraints weight = 11893.252| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16386 Z= 0.181 Angle : 0.604 9.490 22134 Z= 0.322 Chirality : 0.042 0.195 2360 Planarity : 0.004 0.044 2818 Dihedral : 10.942 165.571 2242 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.17 % Allowed : 3.26 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.19), residues: 1932 helix: 1.24 (0.15), residues: 1117 sheet: -0.24 (0.44), residues: 134 loop : 0.29 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 124 HIS 0.008 0.001 HIS A 255 PHE 0.029 0.002 PHE A 129 TYR 0.025 0.002 TYR A 118 ARG 0.006 0.001 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 871) hydrogen bonds : angle 4.85193 ( 2571) covalent geometry : bond 0.00397 (16386) covalent geometry : angle 0.60444 (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 636 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 633 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8727 (t80) cc_final: 0.8166 (t80) REVERT: A 107 LYS cc_start: 0.9072 (mtpp) cc_final: 0.8778 (mtpp) REVERT: A 117 ARG cc_start: 0.8398 (mtp85) cc_final: 0.8172 (mtp85) REVERT: A 131 ASN cc_start: 0.9134 (t0) cc_final: 0.8821 (t0) REVERT: A 147 GLN cc_start: 0.8711 (mt0) cc_final: 0.8385 (mt0) REVERT: A 150 GLN cc_start: 0.8938 (tp40) cc_final: 0.8671 (tp-100) REVERT: A 204 SER cc_start: 0.9165 (t) cc_final: 0.8835 (t) REVERT: A 286 ASP cc_start: 0.8824 (m-30) cc_final: 0.8231 (m-30) REVERT: A 290 GLU cc_start: 0.8508 (mp0) cc_final: 0.8265 (mp0) REVERT: A 360 PHE cc_start: 0.8669 (m-80) cc_final: 0.8429 (m-80) REVERT: A 362 ASP cc_start: 0.7245 (m-30) cc_final: 0.6685 (m-30) REVERT: A 399 GLU cc_start: 0.8975 (tp30) cc_final: 0.8764 (tp30) REVERT: A 443 THR cc_start: 0.9120 (m) cc_final: 0.8912 (t) REVERT: A 447 ASN cc_start: 0.8940 (m-40) cc_final: 0.8665 (m-40) REVERT: A 493 MET cc_start: 0.9030 (tmm) cc_final: 0.8626 (tmm) REVERT: A 494 MET cc_start: 0.8907 (mtp) cc_final: 0.8586 (mtp) REVERT: A 550 MET cc_start: 0.7583 (mtp) cc_final: 0.7320 (mtm) REVERT: A 597 ILE cc_start: 0.9056 (pt) cc_final: 0.8824 (pt) REVERT: A 640 MET cc_start: 0.9097 (ttm) cc_final: 0.8624 (ttm) REVERT: B 8 LYS cc_start: 0.8908 (tptp) cc_final: 0.8556 (tppt) REVERT: B 12 LEU cc_start: 0.9574 (mt) cc_final: 0.9250 (mt) REVERT: B 119 GLU cc_start: 0.8897 (mp0) cc_final: 0.8470 (mp0) REVERT: B 147 GLN cc_start: 0.8861 (mt0) cc_final: 0.8143 (mt0) REVERT: B 157 LEU cc_start: 0.9173 (tp) cc_final: 0.8756 (tp) REVERT: B 158 ASN cc_start: 0.8922 (m110) cc_final: 0.8626 (m-40) REVERT: B 173 LEU cc_start: 0.9568 (mt) cc_final: 0.9353 (mt) REVERT: B 186 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9260 (mp) REVERT: B 211 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7565 (mm-30) REVERT: B 217 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7839 (tm-30) REVERT: B 253 ILE cc_start: 0.9524 (tt) cc_final: 0.9319 (tt) REVERT: B 263 ASP cc_start: 0.9032 (m-30) cc_final: 0.8565 (m-30) REVERT: B 266 LYS cc_start: 0.9383 (mtpp) cc_final: 0.9094 (mttm) REVERT: B 288 PHE cc_start: 0.9294 (t80) cc_final: 0.8922 (t80) REVERT: B 316 GLU cc_start: 0.8689 (tt0) cc_final: 0.8486 (tt0) REVERT: B 348 MET cc_start: 0.7926 (tpt) cc_final: 0.7267 (tpp) REVERT: B 359 MET cc_start: 0.8728 (ttp) cc_final: 0.8247 (tmm) REVERT: B 361 GLN cc_start: 0.8934 (tp40) cc_final: 0.8632 (tp40) REVERT: B 373 ILE cc_start: 0.9648 (mt) cc_final: 0.8808 (mt) REVERT: B 393 SER cc_start: 0.9472 (m) cc_final: 0.8520 (p) REVERT: B 394 TYR cc_start: 0.9068 (m-80) cc_final: 0.8377 (m-80) REVERT: B 425 ILE cc_start: 0.9653 (mt) cc_final: 0.9403 (mt) REVERT: B 467 ASN cc_start: 0.9297 (t0) cc_final: 0.8915 (m-40) REVERT: B 493 MET cc_start: 0.9472 (tmm) cc_final: 0.9176 (tmm) REVERT: B 498 TYR cc_start: 0.8976 (m-80) cc_final: 0.8772 (m-80) REVERT: B 526 GLU cc_start: 0.7989 (tp30) cc_final: 0.7530 (tp30) REVERT: B 550 MET cc_start: 0.8163 (mtp) cc_final: 0.7915 (ttm) REVERT: B 588 GLN cc_start: 0.9163 (mm-40) cc_final: 0.8437 (mm-40) REVERT: B 590 SER cc_start: 0.9137 (p) cc_final: 0.8904 (p) REVERT: B 602 GLU cc_start: 0.7940 (pt0) cc_final: 0.7685 (pt0) REVERT: B 615 MET cc_start: 0.9419 (mmm) cc_final: 0.9086 (mmm) REVERT: B 640 MET cc_start: 0.9133 (tpp) cc_final: 0.8519 (tpp) REVERT: B 644 ILE cc_start: 0.9647 (mt) cc_final: 0.9407 (mt) REVERT: B 667 LEU cc_start: 0.9496 (tp) cc_final: 0.9171 (tp) REVERT: C 27 LYS cc_start: 0.9005 (mtmm) cc_final: 0.8567 (tptp) REVERT: C 53 ASP cc_start: 0.8222 (t0) cc_final: 0.7815 (t0) REVERT: C 154 PHE cc_start: 0.8446 (t80) cc_final: 0.7829 (t80) REVERT: C 157 MET cc_start: 0.9191 (ptp) cc_final: 0.8961 (ptt) REVERT: C 243 THR cc_start: 0.7221 (p) cc_final: 0.6614 (p) REVERT: C 247 TYR cc_start: 0.8065 (m-80) cc_final: 0.7706 (m-80) REVERT: D 20 MET cc_start: 0.8832 (ptp) cc_final: 0.8479 (ptp) REVERT: D 24 GLN cc_start: 0.8183 (mp-120) cc_final: 0.7686 (tp-100) REVERT: D 42 LEU cc_start: 0.5926 (pp) cc_final: 0.5636 (pp) REVERT: D 46 TYR cc_start: 0.8457 (m-80) cc_final: 0.8130 (m-80) REVERT: D 96 MET cc_start: 0.8464 (tpt) cc_final: 0.8083 (tpp) REVERT: D 100 VAL cc_start: 0.8397 (t) cc_final: 0.8016 (t) REVERT: D 149 ASP cc_start: 0.8383 (m-30) cc_final: 0.8112 (m-30) REVERT: D 185 MET cc_start: 0.7726 (mmm) cc_final: 0.6404 (pmm) REVERT: D 211 GLU cc_start: 0.9452 (tp30) cc_final: 0.9165 (mt-10) REVERT: D 235 LEU cc_start: 0.9110 (mt) cc_final: 0.8746 (pp) REVERT: D 259 PHE cc_start: 0.7753 (t80) cc_final: 0.7462 (t80) REVERT: D 288 ASN cc_start: 0.8780 (t0) cc_final: 0.8543 (t0) outliers start: 3 outliers final: 0 residues processed: 634 average time/residue: 0.2785 time to fit residues: 260.8407 Evaluate side-chains 515 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 514 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.132111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.096481 restraints weight = 37702.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099931 restraints weight = 19156.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.102144 restraints weight = 11656.024| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16386 Z= 0.165 Angle : 0.601 9.978 22134 Z= 0.319 Chirality : 0.042 0.294 2360 Planarity : 0.003 0.034 2818 Dihedral : 10.776 163.729 2242 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: 1.09 (0.19), residues: 1932 helix: 1.22 (0.15), residues: 1120 sheet: -0.26 (0.44), residues: 134 loop : 0.28 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 124 HIS 0.008 0.001 HIS A 255 PHE 0.035 0.002 PHE A 129 TYR 0.033 0.002 TYR C 174 ARG 0.006 0.001 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 871) hydrogen bonds : angle 4.83692 ( 2571) covalent geometry : bond 0.00369 (16386) covalent geometry : angle 0.60132 (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 618 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 618 time to evaluate : 1.815 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 10 ILE cc_start: 0.9654 (mm) cc_final: 0.9280 (mm) REVERT: A 40 TYR cc_start: 0.8774 (t80) cc_final: 0.8150 (t80) REVERT: A 107 LYS cc_start: 0.9045 (mtpp) cc_final: 0.8174 (mtpp) REVERT: A 131 ASN cc_start: 0.9173 (t0) cc_final: 0.8803 (t0) REVERT: A 147 GLN cc_start: 0.8698 (mt0) cc_final: 0.8369 (mt0) REVERT: A 164 ARG cc_start: 0.8006 (ptt90) cc_final: 0.7783 (ptt-90) REVERT: A 204 SER cc_start: 0.9307 (t) cc_final: 0.8847 (t) REVERT: A 214 LYS cc_start: 0.8743 (mmpt) cc_final: 0.8507 (mmtt) REVERT: A 286 ASP cc_start: 0.8804 (m-30) cc_final: 0.8369 (m-30) REVERT: A 322 MET cc_start: 0.8918 (mmp) cc_final: 0.7792 (tpp) REVERT: A 360 PHE cc_start: 0.8626 (m-80) cc_final: 0.8222 (m-80) REVERT: A 362 ASP cc_start: 0.7128 (m-30) cc_final: 0.6636 (m-30) REVERT: A 443 THR cc_start: 0.9092 (m) cc_final: 0.8829 (t) REVERT: A 447 ASN cc_start: 0.8822 (m-40) cc_final: 0.8521 (t0) REVERT: A 493 MET cc_start: 0.9037 (tmm) cc_final: 0.8584 (tmm) REVERT: B 71 LEU cc_start: 0.9499 (mm) cc_final: 0.9104 (mp) REVERT: B 95 MET cc_start: 0.9141 (tpp) cc_final: 0.8928 (mmm) REVERT: B 119 GLU cc_start: 0.8857 (mp0) cc_final: 0.8464 (mp0) REVERT: B 147 GLN cc_start: 0.8941 (mt0) cc_final: 0.8246 (mt0) REVERT: B 157 LEU cc_start: 0.9112 (tp) cc_final: 0.8728 (tp) REVERT: B 158 ASN cc_start: 0.8949 (m110) cc_final: 0.8657 (m-40) REVERT: B 173 LEU cc_start: 0.9505 (mt) cc_final: 0.9297 (mt) REVERT: B 211 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7516 (mm-30) REVERT: B 232 ASN cc_start: 0.8237 (t0) cc_final: 0.7870 (t0) REVERT: B 253 ILE cc_start: 0.9545 (tt) cc_final: 0.9317 (tt) REVERT: B 263 ASP cc_start: 0.9003 (m-30) cc_final: 0.8664 (m-30) REVERT: B 288 PHE cc_start: 0.9323 (t80) cc_final: 0.8892 (t80) REVERT: B 348 MET cc_start: 0.7925 (tpt) cc_final: 0.7452 (tpp) REVERT: B 373 ILE cc_start: 0.9543 (mt) cc_final: 0.9301 (mt) REVERT: B 394 TYR cc_start: 0.9087 (m-80) cc_final: 0.8447 (m-80) REVERT: B 425 ILE cc_start: 0.9636 (mt) cc_final: 0.9389 (mt) REVERT: B 493 MET cc_start: 0.9454 (tmm) cc_final: 0.9073 (tmm) REVERT: B 526 GLU cc_start: 0.8005 (tp30) cc_final: 0.7497 (tp30) REVERT: B 550 MET cc_start: 0.8262 (mtp) cc_final: 0.7916 (ttm) REVERT: B 588 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8520 (mm-40) REVERT: B 602 GLU cc_start: 0.7839 (pt0) cc_final: 0.7602 (pt0) REVERT: B 615 MET cc_start: 0.9399 (mmm) cc_final: 0.9126 (mmm) REVERT: B 635 PHE cc_start: 0.8924 (m-80) cc_final: 0.8513 (m-80) REVERT: B 640 MET cc_start: 0.9170 (tpp) cc_final: 0.8599 (tpp) REVERT: B 644 ILE cc_start: 0.9642 (mt) cc_final: 0.9402 (mt) REVERT: B 667 LEU cc_start: 0.9495 (tp) cc_final: 0.9183 (tp) REVERT: B 671 ASP cc_start: 0.8670 (m-30) cc_final: 0.8440 (m-30) REVERT: C 21 PHE cc_start: 0.9267 (m-10) cc_final: 0.8706 (m-80) REVERT: C 24 GLN cc_start: 0.8916 (pt0) cc_final: 0.8350 (pp30) REVERT: C 25 ASN cc_start: 0.9232 (m110) cc_final: 0.9026 (m110) REVERT: C 27 LYS cc_start: 0.9048 (mtmm) cc_final: 0.8647 (tptp) REVERT: C 154 PHE cc_start: 0.8398 (t80) cc_final: 0.7764 (t80) REVERT: C 157 MET cc_start: 0.9133 (ptp) cc_final: 0.8875 (ptt) REVERT: C 196 ARG cc_start: 0.8299 (ttp80) cc_final: 0.7571 (ptt-90) REVERT: C 313 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8670 (mt-10) REVERT: D 20 MET cc_start: 0.8838 (ptp) cc_final: 0.8438 (ptp) REVERT: D 24 GLN cc_start: 0.8400 (mp-120) cc_final: 0.7770 (tp-100) REVERT: D 42 LEU cc_start: 0.5976 (pp) cc_final: 0.5637 (pp) REVERT: D 46 TYR cc_start: 0.8467 (m-80) cc_final: 0.8187 (m-80) REVERT: D 56 MET cc_start: 0.6112 (mpp) cc_final: 0.5750 (mpp) REVERT: D 95 MET cc_start: 0.9230 (tmm) cc_final: 0.8865 (tmm) REVERT: D 96 MET cc_start: 0.8528 (tpt) cc_final: 0.7657 (mmm) REVERT: D 149 ASP cc_start: 0.8507 (m-30) cc_final: 0.8222 (m-30) REVERT: D 154 PHE cc_start: 0.8499 (t80) cc_final: 0.7903 (t80) REVERT: D 185 MET cc_start: 0.7927 (mmm) cc_final: 0.6467 (pmm) REVERT: D 224 LEU cc_start: 0.8790 (mt) cc_final: 0.8584 (mt) REVERT: D 235 LEU cc_start: 0.9069 (mt) cc_final: 0.8823 (pp) REVERT: D 259 PHE cc_start: 0.7839 (t80) cc_final: 0.7534 (t80) REVERT: D 288 ASN cc_start: 0.8819 (t0) cc_final: 0.8547 (t0) outliers start: 0 outliers final: 0 residues processed: 618 average time/residue: 0.2805 time to fit residues: 255.2956 Evaluate side-chains 511 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 511 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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: 3.9990 chunk 126 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 645 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.129939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.094513 restraints weight = 38054.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.097583 restraints weight = 19488.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099889 restraints weight = 12257.445| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.6113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16386 Z= 0.202 Angle : 0.639 11.865 22134 Z= 0.336 Chirality : 0.043 0.162 2360 Planarity : 0.003 0.033 2818 Dihedral : 10.793 163.177 2242 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.17 % Allowed : 2.10 % Favored : 97.73 % 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: 0.90 (0.19), residues: 1932 helix: 1.08 (0.15), residues: 1126 sheet: -0.37 (0.43), residues: 134 loop : 0.18 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 124 HIS 0.008 0.001 HIS A 255 PHE 0.027 0.002 PHE A 129 TYR 0.030 0.002 TYR C 174 ARG 0.006 0.001 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 871) hydrogen bonds : angle 4.90702 ( 2571) covalent geometry : bond 0.00445 (16386) covalent geometry : angle 0.63881 (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 610 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 607 time to evaluate : 1.727 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 28 LYS cc_start: 0.9022 (ttmt) cc_final: 0.8776 (ttpp) REVERT: A 40 TYR cc_start: 0.8811 (t80) cc_final: 0.8319 (t80) REVERT: A 107 LYS cc_start: 0.9058 (mtpp) cc_final: 0.8209 (mtpp) REVERT: A 131 ASN cc_start: 0.9238 (t0) cc_final: 0.8890 (t0) REVERT: A 147 GLN cc_start: 0.8823 (mt0) cc_final: 0.8451 (mt0) REVERT: A 204 SER cc_start: 0.9337 (t) cc_final: 0.8810 (t) REVERT: A 286 ASP cc_start: 0.8853 (m-30) cc_final: 0.8335 (m-30) REVERT: A 290 GLU cc_start: 0.8357 (mp0) cc_final: 0.8106 (mp0) REVERT: A 318 ASP cc_start: 0.8901 (t0) cc_final: 0.8390 (p0) REVERT: A 362 ASP cc_start: 0.7186 (m-30) cc_final: 0.6638 (m-30) REVERT: A 494 MET cc_start: 0.8886 (mtp) cc_final: 0.8567 (mtm) REVERT: A 584 ILE cc_start: 0.9234 (pt) cc_final: 0.9011 (pt) REVERT: B 8 LYS cc_start: 0.8914 (tptp) cc_final: 0.8524 (tppt) REVERT: B 12 LEU cc_start: 0.9610 (mt) cc_final: 0.9256 (mt) REVERT: B 60 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8450 (mp0) REVERT: B 95 MET cc_start: 0.9148 (tpp) cc_final: 0.8895 (mmm) REVERT: B 119 GLU cc_start: 0.8888 (mp0) cc_final: 0.8509 (mp0) REVERT: B 127 LEU cc_start: 0.9519 (mm) cc_final: 0.9291 (mm) REVERT: B 147 GLN cc_start: 0.8962 (mt0) cc_final: 0.8686 (mt0) REVERT: B 157 LEU cc_start: 0.9076 (tp) cc_final: 0.8677 (tp) REVERT: B 158 ASN cc_start: 0.8957 (m110) cc_final: 0.8637 (m-40) REVERT: B 180 ASN cc_start: 0.8282 (m110) cc_final: 0.8010 (t0) REVERT: B 211 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7590 (mm-30) REVERT: B 232 ASN cc_start: 0.8205 (t0) cc_final: 0.7864 (t0) REVERT: B 253 ILE cc_start: 0.9566 (tt) cc_final: 0.9323 (tt) REVERT: B 263 ASP cc_start: 0.8970 (m-30) cc_final: 0.8631 (m-30) REVERT: B 288 PHE cc_start: 0.9335 (t80) cc_final: 0.8984 (t80) REVERT: B 316 GLU cc_start: 0.8725 (tt0) cc_final: 0.8521 (tt0) REVERT: B 348 MET cc_start: 0.7770 (tpt) cc_final: 0.7294 (tpp) REVERT: B 373 ILE cc_start: 0.9592 (mt) cc_final: 0.8968 (mt) REVERT: B 393 SER cc_start: 0.9401 (m) cc_final: 0.8971 (m) REVERT: B 394 TYR cc_start: 0.9120 (m-80) cc_final: 0.8484 (m-80) REVERT: B 471 TYR cc_start: 0.9052 (t80) cc_final: 0.8652 (t80) REVERT: B 493 MET cc_start: 0.9443 (tmm) cc_final: 0.9039 (tmm) REVERT: B 526 GLU cc_start: 0.8048 (tp30) cc_final: 0.7527 (tp30) REVERT: B 595 MET cc_start: 0.8936 (mmm) cc_final: 0.8355 (mmm) REVERT: B 602 GLU cc_start: 0.7963 (pt0) cc_final: 0.7731 (pt0) REVERT: B 615 MET cc_start: 0.9442 (mmm) cc_final: 0.9191 (mmm) REVERT: B 635 PHE cc_start: 0.8941 (m-80) cc_final: 0.8616 (m-80) REVERT: B 640 MET cc_start: 0.9214 (tpp) cc_final: 0.8543 (tpp) REVERT: B 644 ILE cc_start: 0.9656 (mt) cc_final: 0.9429 (mt) REVERT: B 667 LEU cc_start: 0.9483 (tp) cc_final: 0.9181 (tp) REVERT: C 21 PHE cc_start: 0.9348 (m-10) cc_final: 0.9146 (m-10) REVERT: C 24 GLN cc_start: 0.8909 (pt0) cc_final: 0.8700 (pt0) REVERT: C 27 LYS cc_start: 0.9030 (mtmm) cc_final: 0.8648 (tptp) REVERT: C 154 PHE cc_start: 0.8395 (t80) cc_final: 0.7727 (t80) REVERT: C 157 MET cc_start: 0.9166 (ptp) cc_final: 0.8945 (ptt) REVERT: C 196 ARG cc_start: 0.8316 (ttp80) cc_final: 0.7577 (ptt-90) REVERT: C 243 THR cc_start: 0.7233 (p) cc_final: 0.6594 (p) REVERT: C 313 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8609 (mt-10) REVERT: D 20 MET cc_start: 0.8476 (ptp) cc_final: 0.8211 (ptp) REVERT: D 24 GLN cc_start: 0.8477 (mp-120) cc_final: 0.7774 (tp-100) REVERT: D 42 LEU cc_start: 0.5998 (pp) cc_final: 0.5617 (pp) REVERT: D 46 TYR cc_start: 0.8636 (m-80) cc_final: 0.8270 (m-80) REVERT: D 56 MET cc_start: 0.5745 (mpp) cc_final: 0.5339 (mpp) REVERT: D 95 MET cc_start: 0.9227 (tmm) cc_final: 0.8857 (tmm) REVERT: D 96 MET cc_start: 0.8528 (mmm) cc_final: 0.7522 (mmm) REVERT: D 138 ILE cc_start: 0.8917 (mm) cc_final: 0.8714 (mm) REVERT: D 149 ASP cc_start: 0.8470 (m-30) cc_final: 0.8210 (m-30) REVERT: D 154 PHE cc_start: 0.8286 (t80) cc_final: 0.7931 (t80) REVERT: D 185 MET cc_start: 0.7932 (mmm) cc_final: 0.6709 (pmm) REVERT: D 189 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7325 (pt0) REVERT: D 192 ASN cc_start: 0.8766 (t0) cc_final: 0.8187 (m-40) REVERT: D 224 LEU cc_start: 0.8848 (mt) cc_final: 0.8636 (mt) REVERT: D 233 ASN cc_start: 0.8691 (m110) cc_final: 0.8446 (m110) REVERT: D 241 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7401 (tm-30) REVERT: D 259 PHE cc_start: 0.7844 (t80) cc_final: 0.7479 (t80) outliers start: 3 outliers final: 1 residues processed: 608 average time/residue: 0.2756 time to fit residues: 250.7322 Evaluate side-chains 488 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 486 time to evaluate : 1.741 ------------------------------------------------------------------------------- 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: 0.5980 chunk 85 optimal weight: 6.9990 chunk 161 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN C 24 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.130178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.095122 restraints weight = 38091.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.098291 restraints weight = 19230.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.100733 restraints weight = 11654.040| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.6358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16386 Z= 0.212 Angle : 0.666 12.801 22134 Z= 0.352 Chirality : 0.044 0.235 2360 Planarity : 0.004 0.059 2818 Dihedral : 10.671 158.137 2242 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.19), residues: 1932 helix: 0.92 (0.15), residues: 1132 sheet: -0.50 (0.43), residues: 134 loop : 0.14 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP D 124 HIS 0.007 0.001 HIS A 255 PHE 0.036 0.002 PHE A 129 TYR 0.034 0.002 TYR A 118 ARG 0.011 0.001 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 871) hydrogen bonds : angle 5.07839 ( 2571) covalent geometry : bond 0.00467 (16386) covalent geometry : angle 0.66568 (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 606 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 606 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8664 (ttpp) REVERT: A 40 TYR cc_start: 0.8753 (t80) cc_final: 0.8253 (t80) REVERT: A 107 LYS cc_start: 0.9099 (mtpp) cc_final: 0.8272 (mtpp) REVERT: A 131 ASN cc_start: 0.9206 (t0) cc_final: 0.8955 (t0) REVERT: A 147 GLN cc_start: 0.8787 (mt0) cc_final: 0.8396 (mt0) REVERT: A 204 SER cc_start: 0.9318 (t) cc_final: 0.8822 (t) REVERT: A 286 ASP cc_start: 0.8909 (m-30) cc_final: 0.8490 (m-30) REVERT: A 290 GLU cc_start: 0.8484 (mp0) cc_final: 0.8278 (mp0) REVERT: A 318 ASP cc_start: 0.8611 (t0) cc_final: 0.8270 (p0) REVERT: A 360 PHE cc_start: 0.8431 (m-80) cc_final: 0.8139 (m-80) REVERT: A 362 ASP cc_start: 0.7064 (m-30) cc_final: 0.6518 (m-30) REVERT: A 493 MET cc_start: 0.9037 (tmm) cc_final: 0.8786 (tmm) REVERT: A 494 MET cc_start: 0.8902 (mtp) cc_final: 0.8504 (mtm) REVERT: A 599 GLU cc_start: 0.8498 (mp0) cc_final: 0.8181 (mp0) REVERT: A 602 GLU cc_start: 0.8553 (pm20) cc_final: 0.8340 (mp0) REVERT: A 640 MET cc_start: 0.9184 (ttm) cc_final: 0.8755 (ttm) REVERT: B 71 LEU cc_start: 0.9470 (mm) cc_final: 0.9136 (mp) REVERT: B 95 MET cc_start: 0.9129 (tpp) cc_final: 0.8883 (mmm) REVERT: B 119 GLU cc_start: 0.8906 (mp0) cc_final: 0.8517 (mp0) REVERT: B 147 GLN cc_start: 0.8998 (mt0) cc_final: 0.8729 (mt0) REVERT: B 157 LEU cc_start: 0.9103 (tp) cc_final: 0.8749 (tp) REVERT: B 211 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7524 (mm-30) REVERT: B 232 ASN cc_start: 0.8164 (t0) cc_final: 0.7859 (t0) REVERT: B 253 ILE cc_start: 0.9552 (tt) cc_final: 0.9291 (tt) REVERT: B 263 ASP cc_start: 0.8935 (m-30) cc_final: 0.8608 (m-30) REVERT: B 288 PHE cc_start: 0.9411 (t80) cc_final: 0.9042 (t80) REVERT: B 348 MET cc_start: 0.7835 (tpt) cc_final: 0.7404 (tpp) REVERT: B 373 ILE cc_start: 0.9630 (mt) cc_final: 0.9195 (mt) REVERT: B 393 SER cc_start: 0.9391 (m) cc_final: 0.9129 (m) REVERT: B 394 TYR cc_start: 0.9141 (m-80) cc_final: 0.8437 (m-80) REVERT: B 425 ILE cc_start: 0.9642 (mt) cc_final: 0.9398 (mt) REVERT: B 471 TYR cc_start: 0.9001 (t80) cc_final: 0.8713 (t80) REVERT: B 493 MET cc_start: 0.9437 (tmm) cc_final: 0.9023 (tmm) REVERT: B 526 GLU cc_start: 0.8116 (tp30) cc_final: 0.7627 (tp30) REVERT: B 612 TYR cc_start: 0.8075 (m-80) cc_final: 0.7400 (m-80) REVERT: B 615 MET cc_start: 0.9425 (mmm) cc_final: 0.9144 (mmm) REVERT: B 667 LEU cc_start: 0.9476 (tp) cc_final: 0.9142 (tp) REVERT: B 671 ASP cc_start: 0.8648 (m-30) cc_final: 0.8436 (m-30) REVERT: C 27 LYS cc_start: 0.9028 (mtmm) cc_final: 0.8653 (tptp) REVERT: C 154 PHE cc_start: 0.8405 (t80) cc_final: 0.7738 (t80) REVERT: C 157 MET cc_start: 0.9161 (ptp) cc_final: 0.8936 (ptt) REVERT: C 243 THR cc_start: 0.7390 (p) cc_final: 0.7043 (t) REVERT: C 313 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8606 (mt-10) REVERT: D 42 LEU cc_start: 0.6023 (pp) cc_final: 0.5638 (pp) REVERT: D 46 TYR cc_start: 0.8681 (m-80) cc_final: 0.8264 (m-80) REVERT: D 56 MET cc_start: 0.5583 (mpp) cc_final: 0.5225 (mpp) REVERT: D 95 MET cc_start: 0.9212 (tmm) cc_final: 0.8786 (tmm) REVERT: D 96 MET cc_start: 0.8493 (mmm) cc_final: 0.7296 (mmm) REVERT: D 149 ASP cc_start: 0.8408 (m-30) cc_final: 0.8132 (m-30) REVERT: D 185 MET cc_start: 0.8109 (mmm) cc_final: 0.6806 (pmm) REVERT: D 189 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7464 (pt0) REVERT: D 192 ASN cc_start: 0.8819 (t0) cc_final: 0.8296 (m-40) REVERT: D 205 VAL cc_start: 0.9482 (t) cc_final: 0.9219 (t) REVERT: D 224 LEU cc_start: 0.8896 (mt) cc_final: 0.8628 (mt) REVERT: D 233 ASN cc_start: 0.8656 (m110) cc_final: 0.8415 (m110) REVERT: D 259 PHE cc_start: 0.7894 (t80) cc_final: 0.7532 (t80) REVERT: D 282 ILE cc_start: 0.6200 (tp) cc_final: 0.5959 (tp) outliers start: 0 outliers final: 0 residues processed: 606 average time/residue: 0.2715 time to fit residues: 245.2530 Evaluate side-chains 485 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 1.859 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 180 optimal weight: 20.0000 chunk 108 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.135881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.100138 restraints weight = 37718.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.103558 restraints weight = 18994.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105912 restraints weight = 11571.522| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.6511 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= 0.148 Angle : 0.631 13.425 22134 Z= 0.332 Chirality : 0.043 0.259 2360 Planarity : 0.003 0.045 2818 Dihedral : 10.420 154.416 2242 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: 0.70 (0.19), residues: 1932 helix: 0.96 (0.15), residues: 1130 sheet: -0.68 (0.41), residues: 134 loop : 0.07 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP D 124 HIS 0.008 0.001 HIS A 255 PHE 0.039 0.002 PHE A 129 TYR 0.031 0.002 TYR A 118 ARG 0.007 0.001 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 871) hydrogen bonds : angle 4.97909 ( 2571) covalent geometry : bond 0.00331 (16386) covalent geometry : angle 0.63102 (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 629 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 629 time to evaluate : 1.862 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 8 LYS cc_start: 0.9053 (ttpp) cc_final: 0.8785 (tppt) REVERT: A 12 LEU cc_start: 0.9316 (mp) cc_final: 0.8658 (mp) REVERT: A 28 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8682 (ttpp) REVERT: A 107 LYS cc_start: 0.9070 (mtpp) cc_final: 0.8277 (mtpp) REVERT: A 131 ASN cc_start: 0.9155 (t0) cc_final: 0.8705 (p0) REVERT: A 147 GLN cc_start: 0.8687 (mt0) cc_final: 0.8329 (mt0) REVERT: A 204 SER cc_start: 0.9300 (t) cc_final: 0.8793 (t) REVERT: A 286 ASP cc_start: 0.8903 (m-30) cc_final: 0.8403 (m-30) REVERT: A 290 GLU cc_start: 0.8474 (mp0) cc_final: 0.8232 (mp0) REVERT: A 318 ASP cc_start: 0.8605 (t0) cc_final: 0.8267 (p0) REVERT: A 360 PHE cc_start: 0.8337 (m-80) cc_final: 0.8093 (m-80) REVERT: A 362 ASP cc_start: 0.6810 (m-30) cc_final: 0.6379 (m-30) REVERT: A 447 ASN cc_start: 0.8162 (t0) cc_final: 0.7764 (t0) REVERT: A 479 TYR cc_start: 0.9051 (t80) cc_final: 0.8325 (t80) REVERT: A 493 MET cc_start: 0.9011 (tmm) cc_final: 0.8721 (tmm) REVERT: A 640 MET cc_start: 0.9084 (ttm) cc_final: 0.8566 (ttm) REVERT: B 8 LYS cc_start: 0.8932 (tptp) cc_final: 0.8581 (tppt) REVERT: B 12 LEU cc_start: 0.9600 (mt) cc_final: 0.9301 (mt) REVERT: B 95 MET cc_start: 0.8997 (tpp) cc_final: 0.8782 (mmm) REVERT: B 111 LYS cc_start: 0.8917 (mptt) cc_final: 0.8682 (mmtt) REVERT: B 119 GLU cc_start: 0.8889 (mp0) cc_final: 0.8527 (mp0) REVERT: B 127 LEU cc_start: 0.9532 (mm) cc_final: 0.9297 (mm) REVERT: B 140 TYR cc_start: 0.9203 (m-10) cc_final: 0.8851 (m-10) REVERT: B 147 GLN cc_start: 0.9000 (mt0) cc_final: 0.8151 (mt0) REVERT: B 157 LEU cc_start: 0.9053 (tp) cc_final: 0.8749 (tp) REVERT: B 211 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7517 (mm-30) REVERT: B 253 ILE cc_start: 0.9579 (tt) cc_final: 0.9301 (tt) REVERT: B 259 ASN cc_start: 0.9123 (m-40) cc_final: 0.8628 (m-40) REVERT: B 263 ASP cc_start: 0.8939 (m-30) cc_final: 0.8602 (m-30) REVERT: B 288 PHE cc_start: 0.9342 (t80) cc_final: 0.8989 (t80) REVERT: B 348 MET cc_start: 0.7843 (tpt) cc_final: 0.7406 (tpp) REVERT: B 373 ILE cc_start: 0.9555 (mt) cc_final: 0.9354 (mt) REVERT: B 393 SER cc_start: 0.9412 (m) cc_final: 0.9134 (m) REVERT: B 394 TYR cc_start: 0.9103 (m-80) cc_final: 0.8440 (m-80) REVERT: B 414 LEU cc_start: 0.9450 (mt) cc_final: 0.9241 (mt) REVERT: B 471 TYR cc_start: 0.8897 (t80) cc_final: 0.8630 (t80) REVERT: B 493 MET cc_start: 0.9419 (tmm) cc_final: 0.8995 (tmm) REVERT: B 526 GLU cc_start: 0.7999 (tp30) cc_final: 0.7438 (tp30) REVERT: B 588 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8451 (mm-40) REVERT: B 667 LEU cc_start: 0.9493 (tp) cc_final: 0.9164 (tp) REVERT: C 27 LYS cc_start: 0.9021 (mtmm) cc_final: 0.8647 (tptp) REVERT: C 92 PHE cc_start: 0.8422 (t80) cc_final: 0.8183 (t80) REVERT: C 96 MET cc_start: 0.7063 (mmp) cc_final: 0.6627 (mmp) REVERT: C 154 PHE cc_start: 0.8345 (t80) cc_final: 0.7699 (t80) REVERT: C 157 MET cc_start: 0.9150 (ptp) cc_final: 0.8911 (ptt) REVERT: C 243 THR cc_start: 0.7318 (p) cc_final: 0.6888 (t) REVERT: D 42 LEU cc_start: 0.6086 (pp) cc_final: 0.5691 (pp) REVERT: D 46 TYR cc_start: 0.8656 (m-80) cc_final: 0.8204 (m-80) REVERT: D 56 MET cc_start: 0.5817 (mpp) cc_final: 0.5399 (mpp) REVERT: D 95 MET cc_start: 0.9243 (tmm) cc_final: 0.8686 (tmm) REVERT: D 96 MET cc_start: 0.8481 (mmm) cc_final: 0.7234 (mmm) REVERT: D 131 LEU cc_start: 0.8621 (tt) cc_final: 0.8304 (tt) REVERT: D 149 ASP cc_start: 0.8392 (m-30) cc_final: 0.8116 (m-30) REVERT: D 185 MET cc_start: 0.8186 (mmm) cc_final: 0.6928 (pmm) REVERT: D 192 ASN cc_start: 0.8744 (t0) cc_final: 0.8218 (m-40) REVERT: D 224 LEU cc_start: 0.8844 (mt) cc_final: 0.8642 (mt) REVERT: D 233 ASN cc_start: 0.8631 (m110) cc_final: 0.8405 (m110) REVERT: D 235 LEU cc_start: 0.9035 (mt) cc_final: 0.8762 (pp) REVERT: D 259 PHE cc_start: 0.7863 (t80) cc_final: 0.7257 (t80) REVERT: D 282 ILE cc_start: 0.6289 (tp) cc_final: 0.5712 (tp) outliers start: 0 outliers final: 0 residues processed: 629 average time/residue: 0.2644 time to fit residues: 248.8426 Evaluate side-chains 504 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.712 ------------------------------------------------------------------------------- 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: 0.5980 chunk 182 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 188 optimal weight: 5.9990 chunk 27 optimal weight: 0.0870 chunk 50 optimal weight: 1.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3787 r_free = 0.3787 target = 0.136085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100466 restraints weight = 37476.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103950 restraints weight = 18987.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106201 restraints weight = 11574.929| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 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 = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.6734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16386 Z= 0.141 Angle : 0.673 15.834 22134 Z= 0.351 Chirality : 0.043 0.171 2360 Planarity : 0.003 0.051 2818 Dihedral : 10.197 148.079 2242 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.06 % Allowed : 0.70 % Favored : 99.24 % 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: 0.59 (0.19), residues: 1932 helix: 0.86 (0.15), residues: 1137 sheet: -0.73 (0.42), residues: 134 loop : 0.03 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP D 124 HIS 0.004 0.001 HIS A 255 PHE 0.031 0.002 PHE A 129 TYR 0.025 0.001 TYR A 118 ARG 0.007 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 871) hydrogen bonds : angle 5.05684 ( 2571) covalent geometry : bond 0.00314 (16386) covalent geometry : angle 0.67339 (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 634 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 633 time to evaluate : 1.715 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 28 LYS cc_start: 0.8920 (ttmt) cc_final: 0.8699 (ttpp) REVERT: A 40 TYR cc_start: 0.8776 (t80) cc_final: 0.8368 (t80) REVERT: A 107 LYS cc_start: 0.8972 (mtpp) cc_final: 0.8511 (mtpp) REVERT: A 131 ASN cc_start: 0.9186 (t0) cc_final: 0.8745 (p0) REVERT: A 139 GLU cc_start: 0.8741 (mp0) cc_final: 0.8518 (mp0) REVERT: A 147 GLN cc_start: 0.8672 (mt0) cc_final: 0.8280 (mt0) REVERT: A 204 SER cc_start: 0.9312 (t) cc_final: 0.8753 (t) REVERT: A 274 ARG cc_start: 0.8162 (ttm110) cc_final: 0.7720 (ptp-110) REVERT: A 276 LYS cc_start: 0.9231 (pttp) cc_final: 0.8902 (ptpp) REVERT: A 286 ASP cc_start: 0.8847 (m-30) cc_final: 0.8514 (m-30) REVERT: A 290 GLU cc_start: 0.8545 (mp0) cc_final: 0.8292 (mp0) REVERT: A 361 GLN cc_start: 0.7985 (tp40) cc_final: 0.7677 (tp-100) REVERT: A 362 ASP cc_start: 0.6928 (m-30) cc_final: 0.6314 (m-30) REVERT: A 365 ASN cc_start: 0.8283 (m110) cc_final: 0.7766 (m110) REVERT: A 447 ASN cc_start: 0.7993 (t0) cc_final: 0.7725 (t0) REVERT: A 493 MET cc_start: 0.9012 (tmm) cc_final: 0.8744 (tmm) REVERT: A 640 MET cc_start: 0.9017 (ttm) cc_final: 0.8713 (ttm) REVERT: B 8 LYS cc_start: 0.8936 (tptp) cc_final: 0.8576 (tppt) REVERT: B 12 LEU cc_start: 0.9607 (mt) cc_final: 0.9294 (mt) REVERT: B 95 MET cc_start: 0.8963 (tpp) cc_final: 0.8685 (mmm) REVERT: B 119 GLU cc_start: 0.8689 (mp0) cc_final: 0.8425 (mp0) REVERT: B 127 LEU cc_start: 0.9538 (mm) cc_final: 0.9291 (mm) REVERT: B 140 TYR cc_start: 0.9202 (m-10) cc_final: 0.8843 (m-10) REVERT: B 147 GLN cc_start: 0.8960 (mt0) cc_final: 0.8104 (mt0) REVERT: B 157 LEU cc_start: 0.9033 (tp) cc_final: 0.8724 (tp) REVERT: B 211 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7443 (mm-30) REVERT: B 217 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7817 (tm-30) REVERT: B 253 ILE cc_start: 0.9535 (tt) cc_final: 0.9294 (tt) REVERT: B 259 ASN cc_start: 0.9086 (m-40) cc_final: 0.8620 (m-40) REVERT: B 263 ASP cc_start: 0.9037 (m-30) cc_final: 0.8721 (m-30) REVERT: B 288 PHE cc_start: 0.9326 (t80) cc_final: 0.9005 (t80) REVERT: B 348 MET cc_start: 0.7863 (tpt) cc_final: 0.7152 (tpp) REVERT: B 357 TYR cc_start: 0.8782 (m-10) cc_final: 0.8525 (m-10) REVERT: B 373 ILE cc_start: 0.9499 (mt) cc_final: 0.9261 (mt) REVERT: B 375 LYS cc_start: 0.8936 (mttm) cc_final: 0.8715 (mttm) REVERT: B 381 LEU cc_start: 0.8727 (tp) cc_final: 0.8457 (tp) REVERT: B 393 SER cc_start: 0.9363 (m) cc_final: 0.8999 (m) REVERT: B 394 TYR cc_start: 0.9133 (m-80) cc_final: 0.8484 (m-80) REVERT: B 425 ILE cc_start: 0.9648 (mt) cc_final: 0.9428 (mt) REVERT: B 493 MET cc_start: 0.9410 (tmm) cc_final: 0.8984 (tmm) REVERT: B 526 GLU cc_start: 0.7924 (tp30) cc_final: 0.7338 (tp30) REVERT: B 588 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8432 (mm-40) REVERT: B 595 MET cc_start: 0.8738 (mmm) cc_final: 0.8166 (mmm) REVERT: B 602 GLU cc_start: 0.8434 (pt0) cc_final: 0.8080 (pt0) REVERT: B 610 LYS cc_start: 0.8930 (tptp) cc_final: 0.8544 (tptp) REVERT: B 615 MET cc_start: 0.9407 (mmp) cc_final: 0.9115 (mmm) REVERT: B 667 LEU cc_start: 0.9501 (tp) cc_final: 0.9172 (tp) REVERT: B 683 TYR cc_start: 0.8245 (t80) cc_final: 0.7421 (t80) REVERT: C 24 GLN cc_start: 0.8843 (pt0) cc_final: 0.8519 (pp30) REVERT: C 27 LYS cc_start: 0.9035 (mtmm) cc_final: 0.8663 (tptp) REVERT: C 38 ASN cc_start: 0.3718 (m-40) cc_final: 0.3476 (m-40) REVERT: C 96 MET cc_start: 0.6866 (mmp) cc_final: 0.6507 (mmp) REVERT: C 154 PHE cc_start: 0.8343 (t80) cc_final: 0.7687 (t80) REVERT: C 157 MET cc_start: 0.9127 (ptp) cc_final: 0.8878 (ptt) REVERT: C 196 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7447 (ptt-90) REVERT: D 27 LYS cc_start: 0.9059 (ptpp) cc_final: 0.8844 (ptpt) REVERT: D 42 LEU cc_start: 0.6126 (pp) cc_final: 0.5684 (pp) REVERT: D 46 TYR cc_start: 0.8732 (m-80) cc_final: 0.8246 (m-80) REVERT: D 56 MET cc_start: 0.5783 (mpp) cc_final: 0.5383 (mpp) REVERT: D 95 MET cc_start: 0.9155 (tmm) cc_final: 0.8713 (tmm) REVERT: D 96 MET cc_start: 0.8534 (mmm) cc_final: 0.7883 (mpp) REVERT: D 131 LEU cc_start: 0.8544 (tt) cc_final: 0.8292 (tp) REVERT: D 149 ASP cc_start: 0.8390 (m-30) cc_final: 0.8130 (m-30) REVERT: D 185 MET cc_start: 0.8249 (mmm) cc_final: 0.7179 (pmm) REVERT: D 192 ASN cc_start: 0.8734 (t0) cc_final: 0.8173 (m-40) REVERT: D 205 VAL cc_start: 0.9470 (t) cc_final: 0.9172 (t) REVERT: D 233 ASN cc_start: 0.8612 (m110) cc_final: 0.8326 (m110) REVERT: D 235 LEU cc_start: 0.9009 (mt) cc_final: 0.8755 (pp) REVERT: D 259 PHE cc_start: 0.7889 (t80) cc_final: 0.7281 (t80) REVERT: D 282 ILE cc_start: 0.6181 (tp) cc_final: 0.5941 (tp) outliers start: 1 outliers final: 0 residues processed: 634 average time/residue: 0.2716 time to fit residues: 258.0547 Evaluate side-chains 509 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 1.804 ------------------------------------------------------------------------------- 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: 6.9990 chunk 0 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3771 r_free = 0.3771 target = 0.135140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099773 restraints weight = 37947.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.103219 restraints weight = 19247.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105463 restraints weight = 11695.866| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 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 = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16386 Z= 0.160 Angle : 0.683 14.248 22134 Z= 0.360 Chirality : 0.044 0.211 2360 Planarity : 0.004 0.063 2818 Dihedral : 10.158 145.854 2242 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.12 % Allowed : 0.64 % Favored : 99.24 % 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: 0.54 (0.19), residues: 1932 helix: 0.80 (0.15), residues: 1143 sheet: 0.03 (0.49), residues: 104 loop : -0.17 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP D 124 HIS 0.006 0.001 HIS A 255 PHE 0.028 0.002 PHE A 129 TYR 0.021 0.002 TYR C 174 ARG 0.007 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 871) hydrogen bonds : angle 5.02783 ( 2571) covalent geometry : bond 0.00361 (16386) covalent geometry : angle 0.68316 (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 608 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 606 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8943 (tptp) cc_final: 0.8658 (tppt) REVERT: A 12 LEU cc_start: 0.9190 (mp) cc_final: 0.8981 (mt) REVERT: A 28 LYS cc_start: 0.8902 (ttmt) cc_final: 0.8644 (ttpp) REVERT: A 40 TYR cc_start: 0.8778 (t80) cc_final: 0.8416 (t80) REVERT: A 107 LYS cc_start: 0.8981 (mtpp) cc_final: 0.8476 (mtpp) REVERT: A 131 ASN cc_start: 0.9167 (t0) cc_final: 0.8930 (t0) REVERT: A 139 GLU cc_start: 0.8751 (mp0) cc_final: 0.8545 (mp0) REVERT: A 147 GLN cc_start: 0.8790 (mt0) cc_final: 0.8444 (mt0) REVERT: A 204 SER cc_start: 0.9323 (t) cc_final: 0.8791 (t) REVERT: A 214 LYS cc_start: 0.8522 (mmpt) cc_final: 0.8313 (mmtt) REVERT: A 274 ARG cc_start: 0.8228 (ttm110) cc_final: 0.7796 (ptp-110) REVERT: A 286 ASP cc_start: 0.8828 (m-30) cc_final: 0.8421 (m-30) REVERT: A 361 GLN cc_start: 0.8014 (tp40) cc_final: 0.7741 (tp-100) REVERT: A 362 ASP cc_start: 0.6761 (m-30) cc_final: 0.6201 (m-30) REVERT: A 365 ASN cc_start: 0.8306 (m110) cc_final: 0.7805 (m110) REVERT: A 396 ASP cc_start: 0.7732 (p0) cc_final: 0.6767 (p0) REVERT: A 410 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.8057 (t160) REVERT: A 459 LYS cc_start: 0.9043 (mttp) cc_final: 0.8564 (ttmm) REVERT: A 493 MET cc_start: 0.8898 (tmm) cc_final: 0.8647 (tmm) REVERT: A 494 MET cc_start: 0.8861 (mtp) cc_final: 0.8566 (mmt) REVERT: A 597 ILE cc_start: 0.9008 (pt) cc_final: 0.8799 (pt) REVERT: A 640 MET cc_start: 0.8928 (ttm) cc_final: 0.8680 (ttm) REVERT: B 8 LYS cc_start: 0.8980 (tptp) cc_final: 0.8608 (tppt) REVERT: B 12 LEU cc_start: 0.9617 (mt) cc_final: 0.9301 (mt) REVERT: B 119 GLU cc_start: 0.8749 (mp0) cc_final: 0.8466 (mp0) REVERT: B 127 LEU cc_start: 0.9535 (mm) cc_final: 0.9290 (mm) REVERT: B 140 TYR cc_start: 0.9187 (m-10) cc_final: 0.8868 (m-10) REVERT: B 147 GLN cc_start: 0.8956 (mt0) cc_final: 0.8118 (mt0) REVERT: B 211 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7416 (mm-30) REVERT: B 217 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7766 (tm-30) REVERT: B 253 ILE cc_start: 0.9557 (tt) cc_final: 0.9280 (tt) REVERT: B 259 ASN cc_start: 0.9073 (m-40) cc_final: 0.8607 (m-40) REVERT: B 263 ASP cc_start: 0.9014 (m-30) cc_final: 0.8613 (m-30) REVERT: B 288 PHE cc_start: 0.9302 (t80) cc_final: 0.9006 (t80) REVERT: B 348 MET cc_start: 0.7921 (tpt) cc_final: 0.7204 (tpp) REVERT: B 357 TYR cc_start: 0.8761 (m-10) cc_final: 0.8521 (m-10) REVERT: B 373 ILE cc_start: 0.9532 (mt) cc_final: 0.9283 (mt) REVERT: B 381 LEU cc_start: 0.8684 (tp) cc_final: 0.8423 (tp) REVERT: B 394 TYR cc_start: 0.9111 (m-80) cc_final: 0.8303 (m-80) REVERT: B 425 ILE cc_start: 0.9654 (mt) cc_final: 0.9421 (mt) REVERT: B 493 MET cc_start: 0.9408 (tmm) cc_final: 0.9044 (tmm) REVERT: B 526 GLU cc_start: 0.7924 (tp30) cc_final: 0.7362 (tp30) REVERT: B 588 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8442 (mm-40) REVERT: B 595 MET cc_start: 0.8758 (mmm) cc_final: 0.8206 (mmm) REVERT: B 599 GLU cc_start: 0.8273 (pt0) cc_final: 0.7339 (pt0) REVERT: B 601 ILE cc_start: 0.9053 (mm) cc_final: 0.8845 (mm) REVERT: B 602 GLU cc_start: 0.8436 (pt0) cc_final: 0.8129 (pt0) REVERT: B 610 LYS cc_start: 0.8887 (tptp) cc_final: 0.8394 (tptp) REVERT: B 612 TYR cc_start: 0.7845 (m-80) cc_final: 0.6816 (m-80) REVERT: B 615 MET cc_start: 0.9405 (mmp) cc_final: 0.9104 (mmm) REVERT: B 628 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8178 (mm-30) REVERT: B 667 LEU cc_start: 0.9509 (tp) cc_final: 0.9173 (tp) REVERT: B 683 TYR cc_start: 0.8108 (t80) cc_final: 0.7198 (t80) REVERT: C 27 LYS cc_start: 0.9073 (mtmm) cc_final: 0.8721 (tptp) REVERT: C 137 MET cc_start: 0.5375 (mpp) cc_final: 0.4794 (mpp) REVERT: C 154 PHE cc_start: 0.8331 (t80) cc_final: 0.7684 (t80) REVERT: C 157 MET cc_start: 0.9133 (ptp) cc_final: 0.8893 (ptt) REVERT: D 42 LEU cc_start: 0.6203 (pp) cc_final: 0.5765 (pp) REVERT: D 46 TYR cc_start: 0.8768 (m-80) cc_final: 0.8314 (m-80) REVERT: D 74 MET cc_start: 0.7419 (tpp) cc_final: 0.6988 (ttp) REVERT: D 96 MET cc_start: 0.8355 (mmm) cc_final: 0.7879 (mpp) REVERT: D 131 LEU cc_start: 0.8591 (tt) cc_final: 0.8390 (tp) REVERT: D 137 MET cc_start: 0.7922 (ttt) cc_final: 0.7689 (ttt) REVERT: D 149 ASP cc_start: 0.8379 (m-30) cc_final: 0.8130 (m-30) REVERT: D 154 PHE cc_start: 0.8226 (t80) cc_final: 0.8022 (t80) REVERT: D 185 MET cc_start: 0.8363 (mmm) cc_final: 0.7382 (pmm) REVERT: D 192 ASN cc_start: 0.8768 (t0) cc_final: 0.8314 (m-40) REVERT: D 205 VAL cc_start: 0.9455 (t) cc_final: 0.9226 (t) REVERT: D 233 ASN cc_start: 0.8667 (m110) cc_final: 0.8360 (m-40) REVERT: D 259 PHE cc_start: 0.7918 (t80) cc_final: 0.7307 (t80) REVERT: D 282 ILE cc_start: 0.6308 (tp) cc_final: 0.6104 (tp) outliers start: 2 outliers final: 0 residues processed: 608 average time/residue: 0.2727 time to fit residues: 250.4461 Evaluate side-chains 496 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 495 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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: 7.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 179 optimal weight: 6.9990 chunk 190 optimal weight: 0.0770 chunk 58 optimal weight: 0.0170 chunk 180 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 338 ASN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 410 ASN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN C 24 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.103195 restraints weight = 37143.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.106767 restraints weight = 18840.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109048 restraints weight = 11320.177| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.7151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16386 Z= 0.139 Angle : 0.683 13.241 22134 Z= 0.359 Chirality : 0.044 0.236 2360 Planarity : 0.004 0.074 2818 Dihedral : 9.891 138.301 2242 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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: 0.38 (0.18), residues: 1932 helix: 0.72 (0.15), residues: 1133 sheet: -0.11 (0.47), residues: 100 loop : -0.30 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP D 124 HIS 0.005 0.001 HIS A 255 PHE 0.028 0.002 PHE A 129 TYR 0.036 0.001 TYR A 118 ARG 0.007 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 871) hydrogen bonds : angle 5.11838 ( 2571) covalent geometry : bond 0.00309 (16386) covalent geometry : angle 0.68270 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6283.71 seconds wall clock time: 110 minutes 52.16 seconds (6652.16 seconds total)