Starting phenix.real_space_refine on Sat May 17 16:39:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byx_45047/05_2025/9byx_45047_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byx_45047/05_2025/9byx_45047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9byx_45047/05_2025/9byx_45047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byx_45047/05_2025/9byx_45047.map" model { file = "/net/cci-nas-00/data/ceres_data/9byx_45047/05_2025/9byx_45047_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byx_45047/05_2025/9byx_45047_neut.cif" } resolution = 3.94 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: 9.50, per 1000 atoms: 0.59 Number of scatterers: 16038 At special positions: 0 Unit cell: (95.598, 132.21, 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: 3.71 Conformation dependent library (CDL) restraints added in 2.3 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A 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: 3.664A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A 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: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.393A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.676A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.878A 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: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A 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: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.668A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.876A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A 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: 7.799A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A 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: 5.01 Time building geometry restraints manager: 4.28 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: 4824 1.34 - 1.46: 3048 1.46 - 1.58: 8332 1.58 - 1.70: 26 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.38e+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 1.04e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.033 1.08e-02 8.57e+03 9.06e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.33e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.572 -0.032 1.25e-02 6.40e+03 6.67e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21570 2.09 - 4.18: 521 4.18 - 6.27: 38 6.27 - 8.37: 1 8.37 - 10.46: 4 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.61 -6.07 1.36e+00 5.41e-01 1.99e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.17 -4.46 1.15e+00 7.56e-01 1.50e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.89 -4.39 1.23e+00 6.61e-01 1.27e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.71 -4.00 1.15e+00 7.56e-01 1.21e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.52 3.67 1.06e+00 8.90e-01 1.20e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 9470 35.79 - 71.58: 337 71.58 - 107.37: 37 107.37 - 143.16: 3 143.16 - 178.94: 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 -58.32 120.63 -178.94 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 151.17 150.52 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: 2143 0.093 - 0.186: 182 0.186 - 0.279: 30 0.279 - 0.372: 3 0.372 - 0.464: 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 2.05 0.46 2.00e-01 2.50e+01 5.39e+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 4.64e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+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 4.14e-02 2.75e+00 pdb=" N PRO D 75 " 0.072 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 2.16e+00 pdb=" CG PHE D 92 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.009 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 9.81e-03 1.93e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11558 3.11 - 3.70: 27040 3.70 - 4.30: 41539 4.30 - 4.90: 65436 Nonbonded interactions: 145702 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145697 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.900 Find NCS groups from input model: 0.750 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: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16386 Z= 0.315 Angle : 0.740 10.457 22134 Z= 0.463 Chirality : 0.057 0.464 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.930 178.944 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.28 % Allowed : 15.27 % Favored : 83.45 % 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: 0.55 (0.18), residues: 1932 helix: 0.58 (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 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE D 92 TYR 0.020 0.002 TYR C 169 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15421 ( 871) hydrogen bonds : angle 6.51788 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.73993 (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 834 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 812 time to evaluate : 1.752 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: A 29 ASP cc_start: 0.8331 (t0) cc_final: 0.8120 (t70) REVERT: A 68 PHE cc_start: 0.8345 (p90) cc_final: 0.8035 (p90) REVERT: A 76 ASP cc_start: 0.7984 (m-30) cc_final: 0.7603 (m-30) REVERT: A 106 LEU cc_start: 0.8439 (tp) cc_final: 0.8026 (tp) REVERT: A 147 GLN cc_start: 0.8238 (mt0) cc_final: 0.8023 (mt0) REVERT: A 186 ILE cc_start: 0.9463 (mt) cc_final: 0.9097 (mt) REVERT: A 188 ILE cc_start: 0.8860 (mt) cc_final: 0.8617 (mt) REVERT: A 218 ASN cc_start: 0.7556 (t0) cc_final: 0.7301 (t0) REVERT: A 227 MET cc_start: 0.8028 (mtp) cc_final: 0.7613 (mtp) REVERT: A 284 ILE cc_start: 0.8838 (mt) cc_final: 0.8588 (mt) REVERT: A 345 LYS cc_start: 0.8439 (tttt) cc_final: 0.8021 (tttt) REVERT: A 362 ASP cc_start: 0.6722 (m-30) cc_final: 0.5940 (m-30) REVERT: A 367 VAL cc_start: 0.8979 (m) cc_final: 0.8741 (t) REVERT: A 405 LEU cc_start: 0.8674 (mt) cc_final: 0.8441 (mt) REVERT: A 468 LEU cc_start: 0.9021 (tp) cc_final: 0.8799 (tp) REVERT: A 598 MET cc_start: 0.7516 (mtm) cc_final: 0.7309 (mtp) REVERT: A 624 PHE cc_start: 0.6941 (t80) cc_final: 0.6583 (t80) REVERT: A 645 GLN cc_start: 0.7642 (tp40) cc_final: 0.7296 (tp40) REVERT: B 186 ILE cc_start: 0.9221 (mt) cc_final: 0.8999 (mt) REVERT: B 191 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8478 (mm-40) REVERT: B 232 ASN cc_start: 0.7705 (OUTLIER) cc_final: 0.7268 (m-40) REVERT: B 253 ILE cc_start: 0.8665 (tt) cc_final: 0.8420 (tt) REVERT: B 288 PHE cc_start: 0.8107 (t80) cc_final: 0.7845 (t80) REVERT: B 355 TYR cc_start: 0.8183 (m-80) cc_final: 0.7818 (m-10) REVERT: B 358 ILE cc_start: 0.9180 (mm) cc_final: 0.8910 (mm) REVERT: B 425 ILE cc_start: 0.8694 (mt) cc_final: 0.8362 (mt) REVERT: B 468 LEU cc_start: 0.9158 (tp) cc_final: 0.8856 (tp) REVERT: B 494 MET cc_start: 0.7656 (mtp) cc_final: 0.7441 (mtp) REVERT: B 522 TYR cc_start: 0.8262 (m-80) cc_final: 0.7979 (m-80) REVERT: B 626 TYR cc_start: 0.7099 (m-80) cc_final: 0.6869 (m-80) REVERT: B 658 LEU cc_start: 0.8613 (mt) cc_final: 0.8279 (mt) REVERT: B 686 ARG cc_start: 0.7706 (mtp85) cc_final: 0.7029 (mtp180) REVERT: C 101 HIS cc_start: 0.4240 (m170) cc_final: 0.3792 (m-70) REVERT: C 131 LEU cc_start: 0.5337 (OUTLIER) cc_final: 0.4936 (tp) REVERT: C 163 LEU cc_start: 0.5589 (tt) cc_final: 0.4977 (tt) REVERT: C 213 TYR cc_start: 0.2249 (t80) cc_final: 0.1172 (t80) outliers start: 22 outliers final: 5 residues processed: 823 average time/residue: 0.2910 time to fit residues: 344.3897 Evaluate side-chains 556 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 549 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 126 LYS 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: 10.0000 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 0.2980 chunk 112 optimal weight: 0.2980 chunk 174 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 239 GLN A 320 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN B 338 ASN B 390 GLN B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN D 71 ASN D 84 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.161438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.115698 restraints weight = 31894.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.119966 restraints weight = 15742.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122713 restraints weight = 9597.892| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16386 Z= 0.189 Angle : 0.671 9.552 22134 Z= 0.349 Chirality : 0.044 0.185 2360 Planarity : 0.004 0.039 2818 Dihedral : 11.410 173.879 2255 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.14 % Allowed : 18.01 % Favored : 77.86 % 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: 1.49 (0.19), residues: 1932 helix: 1.44 (0.15), residues: 1133 sheet: 0.33 (0.42), residues: 130 loop : 0.52 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 44 HIS 0.006 0.001 HIS B 438 PHE 0.036 0.002 PHE C 168 TYR 0.021 0.002 TYR C 169 ARG 0.008 0.001 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 871) hydrogen bonds : angle 5.07536 ( 2571) covalent geometry : bond 0.00414 (16386) covalent geometry : angle 0.67052 (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 630 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 559 time to evaluate : 1.781 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: A 76 ASP cc_start: 0.8931 (m-30) cc_final: 0.8484 (m-30) REVERT: A 116 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7765 (mt-10) REVERT: A 138 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8602 (mtpp) REVERT: A 147 GLN cc_start: 0.9309 (mt0) cc_final: 0.9009 (mt0) REVERT: A 202 ASN cc_start: 0.9201 (t0) cc_final: 0.8990 (t0) REVERT: A 218 ASN cc_start: 0.8828 (t0) cc_final: 0.8298 (t0) REVERT: A 232 ASN cc_start: 0.9355 (OUTLIER) cc_final: 0.9108 (m-40) REVERT: A 259 ASN cc_start: 0.8897 (m-40) cc_final: 0.8593 (m-40) REVERT: A 263 ASP cc_start: 0.8323 (m-30) cc_final: 0.8013 (m-30) REVERT: A 318 ASP cc_start: 0.8892 (t0) cc_final: 0.8486 (t0) REVERT: A 344 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8376 (mt-10) REVERT: A 362 ASP cc_start: 0.7916 (m-30) cc_final: 0.6968 (m-30) REVERT: A 384 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: A 411 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7758 (mp) REVERT: A 415 ASN cc_start: 0.8857 (t0) cc_final: 0.8522 (t0) REVERT: A 468 LEU cc_start: 0.9396 (tp) cc_final: 0.9138 (tp) REVERT: A 493 MET cc_start: 0.9026 (tmm) cc_final: 0.8813 (tmm) REVERT: A 494 MET cc_start: 0.8762 (mtp) cc_final: 0.8518 (mtp) REVERT: A 531 TYR cc_start: 0.8778 (m-80) cc_final: 0.8165 (m-80) REVERT: A 558 TRP cc_start: 0.9112 (m100) cc_final: 0.8312 (m100) REVERT: A 586 TYR cc_start: 0.8285 (m-80) cc_final: 0.8047 (m-80) REVERT: A 640 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8161 (tpp) REVERT: B 15 GLU cc_start: 0.8942 (tp30) cc_final: 0.8685 (tp30) REVERT: B 119 GLU cc_start: 0.8919 (mp0) cc_final: 0.8308 (mp0) REVERT: B 125 VAL cc_start: 0.9563 (t) cc_final: 0.9345 (m) REVERT: B 184 ARG cc_start: 0.9223 (tpp-160) cc_final: 0.8937 (tpp-160) REVERT: B 251 LEU cc_start: 0.9028 (tp) cc_final: 0.8826 (tp) REVERT: B 267 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8681 (mm) REVERT: B 288 PHE cc_start: 0.9206 (t80) cc_final: 0.8939 (t80) REVERT: B 321 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7847 (pp20) REVERT: B 322 MET cc_start: 0.9114 (mmm) cc_final: 0.8731 (mmm) REVERT: B 415 ASN cc_start: 0.9506 (t0) cc_final: 0.9253 (t0) REVERT: B 425 ILE cc_start: 0.9369 (mt) cc_final: 0.9054 (mt) REVERT: B 494 MET cc_start: 0.8983 (mtp) cc_final: 0.8576 (mtp) REVERT: B 550 MET cc_start: 0.7769 (mtm) cc_final: 0.7374 (mtm) REVERT: B 586 TYR cc_start: 0.8376 (m-80) cc_final: 0.7767 (m-80) REVERT: B 598 MET cc_start: 0.7986 (mtm) cc_final: 0.7649 (mtp) REVERT: B 604 ARG cc_start: 0.9007 (tpp80) cc_final: 0.8579 (mmt-90) REVERT: B 626 TYR cc_start: 0.8117 (m-80) cc_final: 0.7850 (m-80) REVERT: B 686 ARG cc_start: 0.8571 (mtp85) cc_final: 0.8340 (mtp-110) REVERT: C 41 LEU cc_start: 0.6828 (pp) cc_final: 0.6438 (mm) REVERT: C 56 MET cc_start: 0.4884 (ptt) cc_final: 0.4636 (ptt) REVERT: C 93 MET cc_start: 0.2080 (mtp) cc_final: 0.1814 (mtp) REVERT: C 141 LEU cc_start: 0.8694 (mt) cc_final: 0.8308 (pp) REVERT: C 162 TYR cc_start: 0.9202 (m-10) cc_final: 0.8709 (m-80) REVERT: C 237 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8275 (pp20) REVERT: C 242 TYR cc_start: 0.9241 (t80) cc_final: 0.8732 (t80) REVERT: C 281 ASP cc_start: 0.7253 (m-30) cc_final: 0.6620 (t0) REVERT: D 95 MET cc_start: 0.7567 (ttp) cc_final: 0.7234 (ptm) REVERT: D 138 ILE cc_start: 0.9160 (mm) cc_final: 0.8923 (tp) outliers start: 71 outliers final: 31 residues processed: 598 average time/residue: 0.2652 time to fit residues: 236.1788 Evaluate side-chains 504 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 467 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 0.8980 chunk 168 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 171 optimal weight: 10.0000 chunk 189 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 467 ASN B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN C 210 GLN D 201 HIS D 210 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.152781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.110966 restraints weight = 32255.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.114536 restraints weight = 15653.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.117080 restraints weight = 9491.463| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16386 Z= 0.161 Angle : 0.630 11.157 22134 Z= 0.328 Chirality : 0.044 0.188 2360 Planarity : 0.003 0.043 2818 Dihedral : 11.020 166.370 2247 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.03 % Allowed : 19.87 % Favored : 77.10 % 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: 1.39 (0.19), residues: 1932 helix: 1.48 (0.16), residues: 1130 sheet: 0.07 (0.42), residues: 134 loop : 0.31 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 44 HIS 0.008 0.001 HIS C 201 PHE 0.057 0.002 PHE C 168 TYR 0.028 0.002 TYR C 55 ARG 0.006 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 871) hydrogen bonds : angle 4.99291 ( 2571) covalent geometry : bond 0.00359 (16386) covalent geometry : angle 0.63016 (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 582 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 530 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.9002 (m-30) cc_final: 0.8766 (m-30) REVERT: A 116 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7729 (mt-10) REVERT: A 157 LEU cc_start: 0.9034 (tp) cc_final: 0.8682 (tp) REVERT: A 202 ASN cc_start: 0.9253 (t0) cc_final: 0.9032 (t0) REVERT: A 209 LYS cc_start: 0.8832 (ttmm) cc_final: 0.8583 (ttmm) REVERT: A 218 ASN cc_start: 0.8863 (t0) cc_final: 0.8366 (t0) REVERT: A 221 LYS cc_start: 0.8301 (mmtp) cc_final: 0.7616 (mmtp) REVERT: A 232 ASN cc_start: 0.9238 (OUTLIER) cc_final: 0.9011 (m110) REVERT: A 263 ASP cc_start: 0.8461 (m-30) cc_final: 0.8094 (m-30) REVERT: A 308 LYS cc_start: 0.9194 (mtpt) cc_final: 0.8608 (mtmm) REVERT: A 322 MET cc_start: 0.8584 (mmm) cc_final: 0.7543 (tpp) REVERT: A 362 ASP cc_start: 0.8011 (m-30) cc_final: 0.7584 (m-30) REVERT: A 381 LEU cc_start: 0.8869 (tp) cc_final: 0.8373 (pt) REVERT: A 384 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7388 (pm20) REVERT: A 411 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7791 (mp) REVERT: A 453 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8244 (ttt-90) REVERT: A 479 TYR cc_start: 0.8754 (t80) cc_final: 0.8165 (t80) REVERT: A 493 MET cc_start: 0.9054 (tmm) cc_final: 0.8762 (tmm) REVERT: A 498 TYR cc_start: 0.9104 (m-80) cc_final: 0.8771 (m-80) REVERT: A 505 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8212 (mt-10) REVERT: A 634 MET cc_start: 0.8475 (mmt) cc_final: 0.8234 (mmp) REVERT: A 640 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8065 (ttp) REVERT: A 668 ASN cc_start: 0.8603 (m110) cc_final: 0.8391 (m110) REVERT: B 15 GLU cc_start: 0.9001 (tp30) cc_final: 0.8656 (tp30) REVERT: B 108 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8181 (p) REVERT: B 119 GLU cc_start: 0.8930 (mp0) cc_final: 0.8265 (mp0) REVERT: B 147 GLN cc_start: 0.9144 (mt0) cc_final: 0.8521 (mm-40) REVERT: B 190 MET cc_start: 0.9226 (mtm) cc_final: 0.8933 (mtm) REVERT: B 232 ASN cc_start: 0.8969 (t0) cc_final: 0.8525 (m-40) REVERT: B 251 LEU cc_start: 0.9105 (tp) cc_final: 0.8855 (tp) REVERT: B 322 MET cc_start: 0.9145 (mmm) cc_final: 0.8866 (mmt) REVERT: B 415 ASN cc_start: 0.9408 (t0) cc_final: 0.9192 (t0) REVERT: B 425 ILE cc_start: 0.9384 (mt) cc_final: 0.9078 (mt) REVERT: B 494 MET cc_start: 0.9004 (mtp) cc_final: 0.8597 (mtp) REVERT: B 550 MET cc_start: 0.7745 (mtm) cc_final: 0.7449 (mtm) REVERT: B 586 TYR cc_start: 0.8449 (m-80) cc_final: 0.7785 (m-80) REVERT: B 604 ARG cc_start: 0.9088 (tpp80) cc_final: 0.8648 (mmt-90) REVERT: B 626 TYR cc_start: 0.8255 (m-80) cc_final: 0.7850 (m-80) REVERT: B 627 LYS cc_start: 0.8781 (tttt) cc_final: 0.8361 (ttpp) REVERT: C 41 LEU cc_start: 0.6881 (pp) cc_final: 0.6465 (mm) REVERT: C 93 MET cc_start: 0.3272 (mtp) cc_final: 0.3070 (mtp) REVERT: C 162 TYR cc_start: 0.9087 (m-10) cc_final: 0.8620 (m-80) REVERT: C 227 PHE cc_start: 0.8048 (t80) cc_final: 0.7803 (t80) REVERT: C 242 TYR cc_start: 0.9260 (t80) cc_final: 0.8767 (t80) REVERT: D 138 ILE cc_start: 0.9164 (mm) cc_final: 0.8927 (tp) outliers start: 52 outliers final: 34 residues processed: 554 average time/residue: 0.2572 time to fit residues: 214.7082 Evaluate side-chains 499 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 459 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 320 ASN B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 418 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN C 84 HIS ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.150007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107048 restraints weight = 32910.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.110793 restraints weight = 16289.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113292 restraints weight = 9938.646| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16386 Z= 0.237 Angle : 0.659 10.718 22134 Z= 0.345 Chirality : 0.045 0.201 2360 Planarity : 0.004 0.051 2818 Dihedral : 10.894 168.874 2245 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.79 % Allowed : 20.92 % Favored : 75.29 % 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: 1.14 (0.19), residues: 1932 helix: 1.27 (0.15), residues: 1130 sheet: -0.06 (0.42), residues: 134 loop : 0.21 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP D 44 HIS 0.007 0.001 HIS C 201 PHE 0.044 0.002 PHE C 168 TYR 0.025 0.002 TYR A 571 ARG 0.011 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 871) hydrogen bonds : angle 5.05322 ( 2571) covalent geometry : bond 0.00524 (16386) covalent geometry : angle 0.65883 (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 554 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 489 time to evaluate : 1.781 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: A 18 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8859 (mm) REVERT: A 31 GLU cc_start: 0.9096 (mp0) cc_final: 0.8685 (mp0) REVERT: A 41 ILE cc_start: 0.9181 (mm) cc_final: 0.8947 (mm) REVERT: A 76 ASP cc_start: 0.9048 (m-30) cc_final: 0.8829 (m-30) REVERT: A 139 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8289 (mt-10) REVERT: A 157 LEU cc_start: 0.9041 (tp) cc_final: 0.8804 (tp) REVERT: A 209 LYS cc_start: 0.8864 (ttmm) cc_final: 0.8633 (ttmm) REVERT: A 218 ASN cc_start: 0.8882 (t0) cc_final: 0.8384 (t0) REVERT: A 221 LYS cc_start: 0.8513 (mmtp) cc_final: 0.7823 (mmtp) REVERT: A 232 ASN cc_start: 0.9413 (m-40) cc_final: 0.8898 (m110) REVERT: A 263 ASP cc_start: 0.8378 (m-30) cc_final: 0.7956 (m-30) REVERT: A 286 ASP cc_start: 0.7812 (m-30) cc_final: 0.7588 (m-30) REVERT: A 346 LEU cc_start: 0.9540 (mp) cc_final: 0.9325 (mp) REVERT: A 362 ASP cc_start: 0.8054 (m-30) cc_final: 0.7494 (m-30) REVERT: A 375 LYS cc_start: 0.8894 (mttt) cc_final: 0.8666 (mtmm) REVERT: A 381 LEU cc_start: 0.8996 (tp) cc_final: 0.8418 (pt) REVERT: A 384 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7169 (pm20) REVERT: A 415 ASN cc_start: 0.9089 (t0) cc_final: 0.8351 (t0) REVERT: A 418 ASN cc_start: 0.9076 (m110) cc_final: 0.8610 (m-40) REVERT: A 420 MET cc_start: 0.8743 (mmm) cc_final: 0.8437 (mmm) REVERT: A 453 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8361 (ttt-90) REVERT: A 479 TYR cc_start: 0.8996 (t80) cc_final: 0.8588 (t80) REVERT: A 493 MET cc_start: 0.9010 (tmm) cc_final: 0.8589 (tmm) REVERT: A 498 TYR cc_start: 0.9123 (m-80) cc_final: 0.8759 (m-80) REVERT: A 505 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8261 (mt-10) REVERT: A 586 TYR cc_start: 0.8348 (m-80) cc_final: 0.8094 (m-80) REVERT: A 602 GLU cc_start: 0.7659 (pt0) cc_final: 0.6686 (pt0) REVERT: A 604 ARG cc_start: 0.8511 (tpp-160) cc_final: 0.8185 (tpp-160) REVERT: A 640 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8068 (tpp) REVERT: A 668 ASN cc_start: 0.8616 (m110) cc_final: 0.8357 (m110) REVERT: B 15 GLU cc_start: 0.8960 (tp30) cc_final: 0.8577 (tp30) REVERT: B 108 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8386 (p) REVERT: B 119 GLU cc_start: 0.8978 (mp0) cc_final: 0.8305 (mp0) REVERT: B 190 MET cc_start: 0.9242 (mtm) cc_final: 0.8958 (mtm) REVERT: B 232 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8337 (m-40) REVERT: B 288 PHE cc_start: 0.9414 (t80) cc_final: 0.9047 (t80) REVERT: B 375 LYS cc_start: 0.8982 (mmtm) cc_final: 0.8537 (mppt) REVERT: B 425 ILE cc_start: 0.9398 (mt) cc_final: 0.9177 (mt) REVERT: B 441 GLU cc_start: 0.8686 (pt0) cc_final: 0.8366 (pt0) REVERT: B 447 ASN cc_start: 0.8595 (m-40) cc_final: 0.8358 (m-40) REVERT: B 467 ASN cc_start: 0.9275 (m-40) cc_final: 0.9015 (m-40) REVERT: B 494 MET cc_start: 0.8964 (mtp) cc_final: 0.8565 (mtp) REVERT: B 571 TYR cc_start: 0.8361 (t80) cc_final: 0.8106 (t80) REVERT: B 586 TYR cc_start: 0.8445 (m-80) cc_final: 0.7736 (m-80) REVERT: B 604 ARG cc_start: 0.9087 (tpp80) cc_final: 0.8626 (mmt-90) REVERT: C 41 LEU cc_start: 0.7160 (pp) cc_final: 0.6604 (mm) REVERT: C 162 TYR cc_start: 0.9151 (m-10) cc_final: 0.8722 (m-80) REVERT: C 227 PHE cc_start: 0.8196 (t80) cc_final: 0.7989 (t80) REVERT: C 242 TYR cc_start: 0.9334 (t80) cc_final: 0.8503 (t80) REVERT: D 44 TRP cc_start: 0.8629 (t60) cc_final: 0.8411 (t60) REVERT: D 95 MET cc_start: 0.7743 (ptm) cc_final: 0.7512 (ppp) REVERT: D 96 MET cc_start: 0.7029 (mmp) cc_final: 0.6481 (tpt) REVERT: D 138 ILE cc_start: 0.9176 (mm) cc_final: 0.8958 (tp) REVERT: D 191 ILE cc_start: 0.0441 (pt) cc_final: 0.0198 (pt) outliers start: 65 outliers final: 43 residues processed: 520 average time/residue: 0.2606 time to fit residues: 203.0761 Evaluate side-chains 493 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 444 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 175 optimal weight: 9.9990 chunk 182 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN A 410 ASN ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.155548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.112421 restraints weight = 32982.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116307 restraints weight = 16148.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.118884 restraints weight = 9832.348| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16386 Z= 0.133 Angle : 0.627 12.484 22134 Z= 0.322 Chirality : 0.044 0.220 2360 Planarity : 0.003 0.039 2818 Dihedral : 10.567 175.587 2244 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.09 % Allowed : 23.14 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 1932 helix: 1.33 (0.15), residues: 1125 sheet: 0.70 (0.48), residues: 100 loop : 0.07 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 44 HIS 0.019 0.001 HIS C 201 PHE 0.044 0.002 PHE C 168 TYR 0.028 0.001 TYR A 571 ARG 0.007 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 871) hydrogen bonds : angle 4.91732 ( 2571) covalent geometry : bond 0.00297 (16386) covalent geometry : angle 0.62687 (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 540 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 487 time to evaluate : 1.730 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: A 31 GLU cc_start: 0.9076 (mp0) cc_final: 0.8872 (mp0) REVERT: A 64 TYR cc_start: 0.8569 (m-10) cc_final: 0.8286 (m-10) REVERT: A 69 LEU cc_start: 0.9396 (mt) cc_final: 0.9051 (pp) REVERT: A 138 LYS cc_start: 0.9098 (mtpt) cc_final: 0.8771 (mtmm) REVERT: A 139 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8289 (mt-10) REVERT: A 150 GLN cc_start: 0.9224 (tm-30) cc_final: 0.8735 (tm-30) REVERT: A 178 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8594 (p) REVERT: A 209 LYS cc_start: 0.8836 (ttmm) cc_final: 0.8594 (ttmm) REVERT: A 218 ASN cc_start: 0.8732 (t0) cc_final: 0.8203 (t0) REVERT: A 221 LYS cc_start: 0.8563 (mmtp) cc_final: 0.7831 (mmtp) REVERT: A 232 ASN cc_start: 0.9287 (m-40) cc_final: 0.8656 (m-40) REVERT: A 263 ASP cc_start: 0.8385 (m-30) cc_final: 0.7914 (m-30) REVERT: A 346 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9135 (mp) REVERT: A 375 LYS cc_start: 0.8902 (mttt) cc_final: 0.8619 (mtmm) REVERT: A 381 LEU cc_start: 0.8972 (tp) cc_final: 0.8439 (pt) REVERT: A 384 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7169 (pm20) REVERT: A 411 LEU cc_start: 0.8012 (mp) cc_final: 0.7684 (mt) REVERT: A 415 ASN cc_start: 0.8991 (t0) cc_final: 0.8316 (t0) REVERT: A 418 ASN cc_start: 0.8984 (m110) cc_final: 0.8500 (m-40) REVERT: A 420 MET cc_start: 0.8636 (mmm) cc_final: 0.8316 (mmm) REVERT: A 453 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8349 (ttt-90) REVERT: A 467 ASN cc_start: 0.9061 (t0) cc_final: 0.8828 (t0) REVERT: A 493 MET cc_start: 0.8964 (tmm) cc_final: 0.8683 (tmm) REVERT: A 494 MET cc_start: 0.8457 (mtp) cc_final: 0.8205 (ttm) REVERT: A 498 TYR cc_start: 0.9072 (m-80) cc_final: 0.8646 (m-80) REVERT: A 505 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8207 (mt-10) REVERT: A 561 LEU cc_start: 0.8635 (tp) cc_final: 0.8238 (tt) REVERT: A 583 SER cc_start: 0.8927 (m) cc_final: 0.8399 (t) REVERT: A 590 SER cc_start: 0.9311 (p) cc_final: 0.8816 (t) REVERT: A 602 GLU cc_start: 0.7495 (pt0) cc_final: 0.7062 (pt0) REVERT: A 604 ARG cc_start: 0.8409 (tpp-160) cc_final: 0.8205 (tpp-160) REVERT: A 640 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.7977 (tpp) REVERT: A 668 ASN cc_start: 0.8649 (m-40) cc_final: 0.8384 (m-40) REVERT: B 15 GLU cc_start: 0.9012 (tp30) cc_final: 0.8592 (tp30) REVERT: B 108 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8273 (p) REVERT: B 119 GLU cc_start: 0.8953 (mp0) cc_final: 0.8328 (mp0) REVERT: B 147 GLN cc_start: 0.9159 (mt0) cc_final: 0.8649 (mm-40) REVERT: B 194 LYS cc_start: 0.9374 (ttpt) cc_final: 0.9167 (ttpt) REVERT: B 232 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8275 (m-40) REVERT: B 321 GLU cc_start: 0.8299 (pp20) cc_final: 0.7951 (pp20) REVERT: B 322 MET cc_start: 0.8989 (mmm) cc_final: 0.8486 (mmm) REVERT: B 441 GLU cc_start: 0.8722 (pt0) cc_final: 0.8389 (pt0) REVERT: B 467 ASN cc_start: 0.9320 (t0) cc_final: 0.8759 (m-40) REVERT: B 494 MET cc_start: 0.8764 (mtp) cc_final: 0.8320 (mtp) REVERT: B 515 ASP cc_start: 0.8842 (m-30) cc_final: 0.8614 (m-30) REVERT: B 604 ARG cc_start: 0.8999 (tpp80) cc_final: 0.8566 (mmt-90) REVERT: C 41 LEU cc_start: 0.7282 (pp) cc_final: 0.6798 (mm) REVERT: C 141 LEU cc_start: 0.9144 (mt) cc_final: 0.8861 (pp) REVERT: C 162 TYR cc_start: 0.9132 (m-10) cc_final: 0.8686 (m-80) REVERT: C 242 TYR cc_start: 0.9298 (t80) cc_final: 0.8596 (t80) REVERT: D 96 MET cc_start: 0.6986 (mmp) cc_final: 0.6458 (tpt) REVERT: D 138 ILE cc_start: 0.9107 (mm) cc_final: 0.8870 (tp) REVERT: D 191 ILE cc_start: 0.0502 (pt) cc_final: 0.0286 (pt) outliers start: 53 outliers final: 32 residues processed: 513 average time/residue: 0.2583 time to fit residues: 199.9380 Evaluate side-chains 479 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 440 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 242 TYR 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: 0.9980 chunk 62 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 177 optimal weight: 0.8980 overall best weight: 1.5182 ------------------------------------------------------------------------------- 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 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN B 467 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN ** D 265 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 = 0.3949 r_free = 0.3949 target = 0.153771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.111206 restraints weight = 32967.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.114975 restraints weight = 16447.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.117527 restraints weight = 10071.490| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16386 Z= 0.164 Angle : 0.635 10.757 22134 Z= 0.328 Chirality : 0.044 0.199 2360 Planarity : 0.004 0.066 2818 Dihedral : 10.356 160.021 2243 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.79 % Allowed : 23.08 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.19), residues: 1932 helix: 1.31 (0.15), residues: 1130 sheet: -0.15 (0.41), residues: 134 loop : 0.12 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 44 HIS 0.018 0.001 HIS C 201 PHE 0.046 0.002 PHE D 109 TYR 0.022 0.001 TYR A 571 ARG 0.012 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 871) hydrogen bonds : angle 4.90317 ( 2571) covalent geometry : bond 0.00369 (16386) covalent geometry : angle 0.63493 (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 522 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 457 time to evaluate : 1.741 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: A 27 ASP cc_start: 0.8925 (p0) cc_final: 0.8085 (p0) REVERT: A 31 GLU cc_start: 0.9078 (mp0) cc_final: 0.8839 (mp0) REVERT: A 41 ILE cc_start: 0.9173 (mm) cc_final: 0.8943 (mm) REVERT: A 69 LEU cc_start: 0.9418 (mt) cc_final: 0.9076 (pp) REVERT: A 76 ASP cc_start: 0.8902 (m-30) cc_final: 0.8522 (m-30) REVERT: A 77 ILE cc_start: 0.9475 (pt) cc_final: 0.9170 (mp) REVERT: A 138 LYS cc_start: 0.9137 (mtpt) cc_final: 0.8894 (mtmm) REVERT: A 139 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8196 (mt-10) REVERT: A 150 GLN cc_start: 0.9249 (tm-30) cc_final: 0.8648 (tm-30) REVERT: A 178 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8684 (p) REVERT: A 209 LYS cc_start: 0.8853 (ttmm) cc_final: 0.8625 (ttmm) REVERT: A 218 ASN cc_start: 0.8693 (t0) cc_final: 0.8146 (t0) REVERT: A 221 LYS cc_start: 0.8594 (mmtp) cc_final: 0.7937 (mmtp) REVERT: A 232 ASN cc_start: 0.9285 (m-40) cc_final: 0.8769 (m110) REVERT: A 263 ASP cc_start: 0.8375 (m-30) cc_final: 0.7887 (m-30) REVERT: A 286 ASP cc_start: 0.7654 (m-30) cc_final: 0.7382 (m-30) REVERT: A 346 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9186 (mp) REVERT: A 359 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8019 (ttp) REVERT: A 362 ASP cc_start: 0.8007 (m-30) cc_final: 0.7527 (m-30) REVERT: A 375 LYS cc_start: 0.8842 (mttt) cc_final: 0.8547 (mtmm) REVERT: A 381 LEU cc_start: 0.8998 (tp) cc_final: 0.8452 (pt) REVERT: A 384 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: A 415 ASN cc_start: 0.9019 (t0) cc_final: 0.8249 (t0) REVERT: A 418 ASN cc_start: 0.9040 (m110) cc_final: 0.8560 (m-40) REVERT: A 420 MET cc_start: 0.8775 (mmm) cc_final: 0.8396 (mmm) REVERT: A 425 ILE cc_start: 0.9068 (tt) cc_final: 0.8694 (tt) REVERT: A 447 ASN cc_start: 0.8089 (m-40) cc_final: 0.7770 (m-40) REVERT: A 479 TYR cc_start: 0.8938 (t80) cc_final: 0.8632 (t80) REVERT: A 480 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8262 (mt-10) REVERT: A 493 MET cc_start: 0.8972 (tmm) cc_final: 0.8458 (tmm) REVERT: A 494 MET cc_start: 0.8369 (mtp) cc_final: 0.7937 (ttm) REVERT: A 505 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8224 (mt-10) REVERT: A 561 LEU cc_start: 0.8721 (tp) cc_final: 0.8371 (tt) REVERT: A 590 SER cc_start: 0.9306 (p) cc_final: 0.9095 (m) REVERT: A 640 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.7933 (tpp) REVERT: A 668 ASN cc_start: 0.8585 (m-40) cc_final: 0.8272 (m-40) REVERT: B 15 GLU cc_start: 0.9065 (tp30) cc_final: 0.8832 (tp30) REVERT: B 119 GLU cc_start: 0.8960 (mp0) cc_final: 0.8293 (mp0) REVERT: B 194 LYS cc_start: 0.9390 (ttpt) cc_final: 0.9149 (ttpt) REVERT: B 232 ASN cc_start: 0.8933 (t0) cc_final: 0.8432 (m-40) REVERT: B 355 TYR cc_start: 0.8548 (m-10) cc_final: 0.8314 (m-10) REVERT: B 441 GLU cc_start: 0.8712 (pt0) cc_final: 0.8371 (pt0) REVERT: B 494 MET cc_start: 0.8785 (mtp) cc_final: 0.8422 (mtp) REVERT: B 515 ASP cc_start: 0.8866 (m-30) cc_final: 0.8647 (m-30) REVERT: B 604 ARG cc_start: 0.8995 (tpp80) cc_final: 0.8599 (mmt-90) REVERT: B 627 LYS cc_start: 0.9168 (tttt) cc_final: 0.8686 (tttt) REVERT: C 141 LEU cc_start: 0.9136 (mt) cc_final: 0.8751 (pp) REVERT: C 242 TYR cc_start: 0.9312 (t80) cc_final: 0.8918 (t80) REVERT: D 138 ILE cc_start: 0.9072 (mm) cc_final: 0.8854 (tp) REVERT: D 191 ILE cc_start: 0.0406 (pt) cc_final: 0.0182 (pt) outliers start: 65 outliers final: 40 residues processed: 492 average time/residue: 0.2510 time to fit residues: 186.3230 Evaluate side-chains 473 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 428 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 318 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 184 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 147 GLN A 320 ASN ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.151007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.108606 restraints weight = 33148.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.112345 restraints weight = 16397.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.114770 restraints weight = 10026.363| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16386 Z= 0.215 Angle : 0.673 11.800 22134 Z= 0.349 Chirality : 0.045 0.201 2360 Planarity : 0.004 0.037 2818 Dihedral : 10.192 159.328 2243 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.55 % Allowed : 23.66 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.19), residues: 1932 helix: 1.25 (0.15), residues: 1125 sheet: -0.32 (0.40), residues: 134 loop : 0.11 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 44 HIS 0.014 0.001 HIS C 201 PHE 0.054 0.002 PHE D 109 TYR 0.027 0.002 TYR D 173 ARG 0.009 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 871) hydrogen bonds : angle 4.99908 ( 2571) covalent geometry : bond 0.00480 (16386) covalent geometry : angle 0.67257 (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 505 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 444 time to evaluate : 1.748 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: A 27 ASP cc_start: 0.8897 (p0) cc_final: 0.8228 (p0) REVERT: A 31 GLU cc_start: 0.9119 (mp0) cc_final: 0.8893 (mp0) REVERT: A 138 LYS cc_start: 0.9198 (mtpt) cc_final: 0.8998 (mtmm) REVERT: A 179 LEU cc_start: 0.9262 (tp) cc_final: 0.8916 (tt) REVERT: A 218 ASN cc_start: 0.8866 (t0) cc_final: 0.8252 (t0) REVERT: A 221 LYS cc_start: 0.8699 (mmtp) cc_final: 0.8028 (mmtp) REVERT: A 250 TYR cc_start: 0.8679 (m-80) cc_final: 0.8404 (m-80) REVERT: A 263 ASP cc_start: 0.8392 (m-30) cc_final: 0.7888 (m-30) REVERT: A 346 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9265 (mp) REVERT: A 375 LYS cc_start: 0.8906 (mttt) cc_final: 0.8649 (mtmm) REVERT: A 381 LEU cc_start: 0.9016 (tp) cc_final: 0.8456 (pt) REVERT: A 384 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7543 (pm20) REVERT: A 415 ASN cc_start: 0.9127 (t0) cc_final: 0.8274 (t0) REVERT: A 418 ASN cc_start: 0.9027 (m110) cc_final: 0.8466 (m-40) REVERT: A 420 MET cc_start: 0.8848 (mmm) cc_final: 0.8515 (mmm) REVERT: A 447 ASN cc_start: 0.7928 (m-40) cc_final: 0.7473 (t0) REVERT: A 493 MET cc_start: 0.8980 (tmm) cc_final: 0.8480 (tmm) REVERT: A 505 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8255 (mt-10) REVERT: A 640 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8860 (tmm) REVERT: A 668 ASN cc_start: 0.8629 (m-40) cc_final: 0.8321 (m-40) REVERT: A 686 ARG cc_start: 0.7827 (ttm110) cc_final: 0.7528 (mtp-110) REVERT: B 186 ILE cc_start: 0.9717 (mp) cc_final: 0.9484 (mp) REVERT: B 190 MET cc_start: 0.9220 (mtm) cc_final: 0.8989 (mtm) REVERT: B 375 LYS cc_start: 0.8833 (mmtm) cc_final: 0.8559 (mppt) REVERT: B 494 MET cc_start: 0.8778 (mtp) cc_final: 0.8551 (mtp) REVERT: B 515 ASP cc_start: 0.8942 (m-30) cc_final: 0.8715 (m-30) REVERT: B 604 ARG cc_start: 0.9028 (tpp80) cc_final: 0.8573 (mmt-90) REVERT: B 662 MET cc_start: 0.8335 (ptp) cc_final: 0.8060 (mpp) REVERT: C 141 LEU cc_start: 0.9269 (mt) cc_final: 0.8897 (pp) REVERT: C 242 TYR cc_start: 0.9326 (t80) cc_final: 0.8915 (t80) REVERT: D 96 MET cc_start: 0.7499 (mmp) cc_final: 0.7004 (tpp) outliers start: 61 outliers final: 42 residues processed: 471 average time/residue: 0.2549 time to fit residues: 180.5589 Evaluate side-chains 464 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 419 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 318 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 159 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 183 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.154800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.112648 restraints weight = 32643.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.116442 restraints weight = 16021.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119015 restraints weight = 9821.844| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16386 Z= 0.149 Angle : 0.673 14.616 22134 Z= 0.345 Chirality : 0.045 0.214 2360 Planarity : 0.003 0.062 2818 Dihedral : 9.593 147.421 2243 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.80 % Allowed : 24.30 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.19), residues: 1932 helix: 1.25 (0.15), residues: 1127 sheet: -0.31 (0.41), residues: 134 loop : 0.08 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP C 124 HIS 0.008 0.001 HIS D 80 PHE 0.058 0.002 PHE D 109 TYR 0.025 0.001 TYR D 173 ARG 0.010 0.001 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 871) hydrogen bonds : angle 4.91474 ( 2571) covalent geometry : bond 0.00344 (16386) covalent geometry : angle 0.67328 (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 508 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 460 time to evaluate : 1.673 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: A 27 ASP cc_start: 0.8836 (p0) cc_final: 0.8589 (p0) REVERT: A 31 GLU cc_start: 0.9060 (mp0) cc_final: 0.8690 (mp0) REVERT: A 112 LYS cc_start: 0.8684 (ptpp) cc_final: 0.8380 (ptpp) REVERT: A 150 GLN cc_start: 0.9277 (tm-30) cc_final: 0.8647 (tm-30) REVERT: A 179 LEU cc_start: 0.9130 (tp) cc_final: 0.8841 (tt) REVERT: A 218 ASN cc_start: 0.8657 (t0) cc_final: 0.8093 (t0) REVERT: A 221 LYS cc_start: 0.8669 (mmtp) cc_final: 0.8261 (mmtp) REVERT: A 250 TYR cc_start: 0.8637 (m-80) cc_final: 0.8319 (m-80) REVERT: A 263 ASP cc_start: 0.8420 (m-30) cc_final: 0.7922 (m-30) REVERT: A 312 GLN cc_start: 0.8166 (tp-100) cc_final: 0.7961 (tp-100) REVERT: A 346 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9137 (mp) REVERT: A 359 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7968 (ttp) REVERT: A 362 ASP cc_start: 0.7904 (m-30) cc_final: 0.7605 (m-30) REVERT: A 375 LYS cc_start: 0.8846 (mttt) cc_final: 0.8611 (mtmm) REVERT: A 381 LEU cc_start: 0.8958 (tp) cc_final: 0.8408 (pt) REVERT: A 384 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7599 (pm20) REVERT: A 415 ASN cc_start: 0.9068 (t0) cc_final: 0.8260 (t0) REVERT: A 418 ASN cc_start: 0.9028 (m110) cc_final: 0.8489 (m-40) REVERT: A 420 MET cc_start: 0.8793 (mmm) cc_final: 0.8462 (mmm) REVERT: A 479 TYR cc_start: 0.8942 (t80) cc_final: 0.8690 (t80) REVERT: A 493 MET cc_start: 0.8967 (tmm) cc_final: 0.8461 (tmm) REVERT: A 505 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8315 (mt-10) REVERT: A 561 LEU cc_start: 0.8695 (tp) cc_final: 0.8289 (tt) REVERT: A 626 TYR cc_start: 0.8466 (m-80) cc_final: 0.8255 (m-80) REVERT: A 640 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.7914 (tpp) REVERT: A 668 ASN cc_start: 0.8562 (m-40) cc_final: 0.8149 (m-40) REVERT: B 108 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.7927 (p) REVERT: B 180 ASN cc_start: 0.7834 (OUTLIER) cc_final: 0.7549 (m110) REVERT: B 186 ILE cc_start: 0.9707 (mp) cc_final: 0.9480 (mp) REVERT: B 384 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.6818 (pm20) REVERT: B 396 ASP cc_start: 0.8316 (m-30) cc_final: 0.7880 (m-30) REVERT: B 494 MET cc_start: 0.8757 (mtp) cc_final: 0.8401 (mtp) REVERT: B 515 ASP cc_start: 0.8847 (m-30) cc_final: 0.8623 (m-30) REVERT: B 586 TYR cc_start: 0.8302 (m-80) cc_final: 0.7945 (m-80) REVERT: B 604 ARG cc_start: 0.8926 (tpp80) cc_final: 0.8563 (mmt-90) REVERT: B 662 MET cc_start: 0.8271 (ptp) cc_final: 0.8003 (mpp) REVERT: C 141 LEU cc_start: 0.9316 (mt) cc_final: 0.8912 (pp) REVERT: C 149 ASP cc_start: 0.8318 (t0) cc_final: 0.7710 (m-30) REVERT: C 242 TYR cc_start: 0.9358 (t80) cc_final: 0.9083 (t80) outliers start: 48 outliers final: 30 residues processed: 482 average time/residue: 0.2605 time to fit residues: 189.8684 Evaluate side-chains 474 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 437 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 115 optimal weight: 0.0170 chunk 127 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- 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 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.154901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.113525 restraints weight = 32267.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.117298 restraints weight = 15999.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119426 restraints weight = 9748.043| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.6292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16386 Z= 0.141 Angle : 0.691 14.766 22134 Z= 0.355 Chirality : 0.045 0.196 2360 Planarity : 0.003 0.056 2818 Dihedral : 9.257 138.555 2243 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.62 % Allowed : 24.94 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.19), residues: 1932 helix: 1.20 (0.15), residues: 1128 sheet: -0.44 (0.41), residues: 134 loop : 0.09 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 44 HIS 0.015 0.001 HIS D 80 PHE 0.060 0.002 PHE D 109 TYR 0.048 0.001 TYR B 36 ARG 0.008 0.001 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 871) hydrogen bonds : angle 4.92201 ( 2571) covalent geometry : bond 0.00326 (16386) covalent geometry : angle 0.69053 (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 507 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 462 time to evaluate : 1.688 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: A 27 ASP cc_start: 0.8819 (p0) cc_final: 0.8569 (p0) REVERT: A 31 GLU cc_start: 0.9064 (mp0) cc_final: 0.8669 (mp0) REVERT: A 150 GLN cc_start: 0.9256 (tm-30) cc_final: 0.8732 (tm-30) REVERT: A 179 LEU cc_start: 0.9122 (tp) cc_final: 0.8859 (tt) REVERT: A 218 ASN cc_start: 0.8751 (t0) cc_final: 0.8210 (t0) REVERT: A 221 LYS cc_start: 0.8674 (mmtp) cc_final: 0.8244 (mmtp) REVERT: A 228 LYS cc_start: 0.9183 (mttp) cc_final: 0.8922 (mmtt) REVERT: A 263 ASP cc_start: 0.8408 (m-30) cc_final: 0.7916 (m-30) REVERT: A 346 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9107 (mp) REVERT: A 359 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7947 (ttp) REVERT: A 362 ASP cc_start: 0.7659 (m-30) cc_final: 0.7305 (t0) REVERT: A 375 LYS cc_start: 0.8801 (mttt) cc_final: 0.8564 (mtmm) REVERT: A 381 LEU cc_start: 0.8980 (tp) cc_final: 0.8467 (pt) REVERT: A 384 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7595 (pm20) REVERT: A 415 ASN cc_start: 0.8818 (t0) cc_final: 0.8135 (t0) REVERT: A 418 ASN cc_start: 0.8962 (m110) cc_final: 0.8446 (m-40) REVERT: A 420 MET cc_start: 0.8772 (mmm) cc_final: 0.8327 (mmm) REVERT: A 493 MET cc_start: 0.8925 (tmm) cc_final: 0.8507 (tmm) REVERT: A 505 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8119 (mt-10) REVERT: A 561 LEU cc_start: 0.8717 (tp) cc_final: 0.8317 (tt) REVERT: A 626 TYR cc_start: 0.8446 (m-80) cc_final: 0.8234 (m-80) REVERT: A 640 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.7848 (tpp) REVERT: A 668 ASN cc_start: 0.8573 (m-40) cc_final: 0.8220 (m-40) REVERT: B 109 ASN cc_start: 0.9308 (m-40) cc_final: 0.8988 (m-40) REVERT: B 291 LEU cc_start: 0.9458 (mt) cc_final: 0.8932 (mt) REVERT: B 322 MET cc_start: 0.8892 (mmm) cc_final: 0.8630 (mmm) REVERT: B 348 MET cc_start: 0.8671 (ptt) cc_final: 0.8255 (tpt) REVERT: B 384 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.6770 (pm20) REVERT: B 494 MET cc_start: 0.8708 (mtp) cc_final: 0.8364 (mtp) REVERT: B 515 ASP cc_start: 0.8833 (m-30) cc_final: 0.8618 (m-30) REVERT: B 586 TYR cc_start: 0.8328 (m-80) cc_final: 0.7785 (m-80) REVERT: B 604 ARG cc_start: 0.8869 (tpp80) cc_final: 0.8549 (mmt-90) REVERT: B 640 MET cc_start: 0.9084 (tpp) cc_final: 0.8283 (tpp) REVERT: C 141 LEU cc_start: 0.9413 (mt) cc_final: 0.9031 (pp) REVERT: C 149 ASP cc_start: 0.8322 (t0) cc_final: 0.7746 (m-30) REVERT: C 242 TYR cc_start: 0.9264 (t80) cc_final: 0.8982 (t80) REVERT: D 96 MET cc_start: 0.7386 (mmp) cc_final: 0.7018 (tpp) REVERT: D 256 VAL cc_start: 0.8317 (m) cc_final: 0.8017 (p) outliers start: 45 outliers final: 34 residues processed: 481 average time/residue: 0.2631 time to fit residues: 190.2338 Evaluate side-chains 468 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 429 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 120 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- 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 232 ASN A 447 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.154285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.113385 restraints weight = 32637.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.116836 restraints weight = 16137.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119289 restraints weight = 10040.403| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.6426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16386 Z= 0.156 Angle : 0.732 14.362 22134 Z= 0.374 Chirality : 0.045 0.234 2360 Planarity : 0.004 0.059 2818 Dihedral : 9.159 138.849 2243 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.62 % Allowed : 26.17 % Favored : 71.21 % 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: 0.88 (0.19), residues: 1932 helix: 1.11 (0.15), residues: 1126 sheet: -0.45 (0.42), residues: 134 loop : 0.07 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 44 HIS 0.005 0.001 HIS C 201 PHE 0.061 0.002 PHE D 109 TYR 0.042 0.001 TYR B 36 ARG 0.008 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 871) hydrogen bonds : angle 5.03561 ( 2571) covalent geometry : bond 0.00365 (16386) covalent geometry : angle 0.73184 (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 494 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 449 time to evaluate : 1.689 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: A 27 ASP cc_start: 0.8794 (p0) cc_final: 0.8525 (p0) REVERT: A 31 GLU cc_start: 0.9005 (mp0) cc_final: 0.8726 (mp0) REVERT: A 109 ASN cc_start: 0.8945 (m110) cc_final: 0.8560 (p0) REVERT: A 150 GLN cc_start: 0.9245 (tm-30) cc_final: 0.8687 (tm-30) REVERT: A 179 LEU cc_start: 0.9133 (tp) cc_final: 0.8925 (tt) REVERT: A 218 ASN cc_start: 0.8686 (t0) cc_final: 0.8136 (t0) REVERT: A 221 LYS cc_start: 0.8675 (mmtp) cc_final: 0.8223 (mmtp) REVERT: A 228 LYS cc_start: 0.9189 (mttp) cc_final: 0.8559 (mttp) REVERT: A 232 ASN cc_start: 0.9050 (m-40) cc_final: 0.8240 (m110) REVERT: A 263 ASP cc_start: 0.8425 (m-30) cc_final: 0.7935 (m-30) REVERT: A 312 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7601 (tp-100) REVERT: A 346 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9152 (mp) REVERT: A 359 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8008 (ttp) REVERT: A 362 ASP cc_start: 0.7630 (m-30) cc_final: 0.7424 (t0) REVERT: A 375 LYS cc_start: 0.8807 (mttt) cc_final: 0.8580 (mtmm) REVERT: A 381 LEU cc_start: 0.8995 (tp) cc_final: 0.8475 (pt) REVERT: A 384 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7609 (pm20) REVERT: A 415 ASN cc_start: 0.8792 (t0) cc_final: 0.8164 (t0) REVERT: A 418 ASN cc_start: 0.9067 (m110) cc_final: 0.8633 (m-40) REVERT: A 420 MET cc_start: 0.8744 (mmm) cc_final: 0.8326 (mmm) REVERT: A 493 MET cc_start: 0.8904 (tmm) cc_final: 0.8498 (tmm) REVERT: A 505 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8123 (mt-10) REVERT: A 561 LEU cc_start: 0.8704 (tp) cc_final: 0.8306 (tt) REVERT: A 626 TYR cc_start: 0.8482 (m-80) cc_final: 0.8274 (m-80) REVERT: A 640 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.7857 (tpp) REVERT: A 668 ASN cc_start: 0.8552 (m-40) cc_final: 0.8189 (m-40) REVERT: B 109 ASN cc_start: 0.9343 (m-40) cc_final: 0.9130 (m-40) REVERT: B 190 MET cc_start: 0.8898 (mtm) cc_final: 0.8683 (mpp) REVERT: B 232 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.7880 (m110) REVERT: B 322 MET cc_start: 0.8959 (mmm) cc_final: 0.8617 (mmm) REVERT: B 348 MET cc_start: 0.8677 (ptt) cc_final: 0.8315 (tpt) REVERT: B 384 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.7382 (pm20) REVERT: B 494 MET cc_start: 0.8694 (mtp) cc_final: 0.8389 (mtp) REVERT: B 515 ASP cc_start: 0.8832 (m-30) cc_final: 0.8599 (m-30) REVERT: B 586 TYR cc_start: 0.8353 (m-80) cc_final: 0.7806 (m-80) REVERT: B 604 ARG cc_start: 0.8845 (tpp80) cc_final: 0.8568 (mmt-90) REVERT: C 141 LEU cc_start: 0.9505 (mt) cc_final: 0.9169 (pp) REVERT: C 149 ASP cc_start: 0.8346 (t0) cc_final: 0.7745 (m-30) REVERT: C 242 TYR cc_start: 0.9244 (t80) cc_final: 0.8970 (t80) REVERT: D 96 MET cc_start: 0.7628 (mmp) cc_final: 0.7275 (tpp) REVERT: D 256 VAL cc_start: 0.8312 (m) cc_final: 0.8041 (p) outliers start: 45 outliers final: 32 residues processed: 470 average time/residue: 0.2619 time to fit residues: 186.4441 Evaluate side-chains 476 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 438 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 180 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.155487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.113363 restraints weight = 32889.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.117179 restraints weight = 16328.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.119604 restraints weight = 9929.143| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 16386 Z= 0.185 Angle : 0.746 14.146 22134 Z= 0.383 Chirality : 0.046 0.194 2360 Planarity : 0.004 0.060 2818 Dihedral : 9.152 139.412 2243 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.56 % Allowed : 26.34 % Favored : 71.10 % 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: 0.80 (0.19), residues: 1932 helix: 1.05 (0.16), residues: 1125 sheet: -0.49 (0.42), residues: 138 loop : 0.06 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 44 HIS 0.004 0.001 HIS C 201 PHE 0.062 0.002 PHE D 109 TYR 0.038 0.002 TYR B 36 ARG 0.008 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 871) hydrogen bonds : angle 5.11274 ( 2571) covalent geometry : bond 0.00430 (16386) covalent geometry : angle 0.74591 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5858.83 seconds wall clock time: 103 minutes 30.77 seconds (6210.77 seconds total)