Starting phenix.real_space_refine on Sat Jun 14 07:22:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byx_45047/06_2025/9byx_45047_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byx_45047/06_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_45047/06_2025/9byx_45047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byx_45047/06_2025/9byx_45047.map" model { file = "/net/cci-nas-00/data/ceres_data/9byx_45047/06_2025/9byx_45047_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byx_45047/06_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-5710/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 12.98, per 1000 atoms: 0.81 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: 4.33 Conformation dependent library (CDL) restraints added in 2.2 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 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: 5.07 Time building geometry restraints manager: 5.09 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 41.170 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.000 ------------------------------------------------------------------------------- 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 : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.7601 (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: 0.3039 time to fit residues: 361.9494 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 : 1.908 ------------------------------------------------------------------------------- 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.161094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.115421 restraints weight = 32000.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.119632 restraints weight = 15913.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.122366 restraints weight = 9692.164| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 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 = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.184 Angle : 0.668 9.374 22134 Z= 0.347 Chirality : 0.044 0.177 2360 Planarity : 0.004 0.037 2818 Dihedral : 11.398 173.765 2255 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.20 % Allowed : 17.83 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.19), residues: 1932 helix: 1.43 (0.15), residues: 1133 sheet: 0.34 (0.42), residues: 130 loop : 0.52 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 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 0.009 0.001 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 871) hydrogen bonds : angle 5.07444 ( 2571) covalent geometry : bond 0.00406 (16386) covalent geometry : angle 0.66765 (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 632 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 560 time to evaluate : 2.065 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 76 ASP cc_start: 0.8941 (m-30) cc_final: 0.8613 (m-30) REVERT: A 138 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8715 (mtpp) REVERT: A 147 GLN cc_start: 0.9305 (mt0) cc_final: 0.9015 (mt0) REVERT: A 202 ASN cc_start: 0.9198 (t0) cc_final: 0.8983 (t0) REVERT: A 218 ASN cc_start: 0.8822 (t0) cc_final: 0.8295 (t0) REVERT: A 232 ASN cc_start: 0.9355 (OUTLIER) cc_final: 0.9111 (m-40) REVERT: A 259 ASN cc_start: 0.8901 (m-40) cc_final: 0.8605 (m110) REVERT: A 263 ASP cc_start: 0.8327 (m-30) cc_final: 0.8023 (m-30) REVERT: A 344 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8363 (mt-10) REVERT: A 362 ASP cc_start: 0.7911 (m-30) cc_final: 0.7070 (m-30) REVERT: A 384 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7668 (pm20) REVERT: A 411 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7743 (mp) REVERT: A 415 ASN cc_start: 0.8854 (t0) cc_final: 0.8539 (t0) REVERT: A 468 LEU cc_start: 0.9396 (tp) cc_final: 0.9130 (tp) REVERT: A 494 MET cc_start: 0.8736 (mtp) cc_final: 0.8521 (mtp) REVERT: A 586 TYR cc_start: 0.8283 (m-80) cc_final: 0.8046 (m-80) REVERT: A 640 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8159 (tpp) REVERT: A 654 PHE cc_start: 0.9195 (t80) cc_final: 0.8994 (t80) REVERT: B 15 GLU cc_start: 0.8930 (tp30) cc_final: 0.8675 (tp30) REVERT: B 119 GLU cc_start: 0.8909 (mp0) cc_final: 0.8331 (mp0) REVERT: B 125 VAL cc_start: 0.9567 (t) cc_final: 0.9354 (m) REVERT: B 184 ARG cc_start: 0.9226 (tpp-160) cc_final: 0.8943 (tpp-160) REVERT: B 267 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8693 (mm) REVERT: B 288 PHE cc_start: 0.9197 (t80) cc_final: 0.8934 (t80) REVERT: B 321 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7833 (pp20) REVERT: B 322 MET cc_start: 0.9103 (mmm) cc_final: 0.8717 (mmm) REVERT: B 415 ASN cc_start: 0.9500 (t0) cc_final: 0.9258 (t0) REVERT: B 494 MET cc_start: 0.8969 (mtp) cc_final: 0.8614 (mtp) REVERT: B 586 TYR cc_start: 0.8369 (m-80) cc_final: 0.7768 (m-80) REVERT: B 598 MET cc_start: 0.7979 (mtm) cc_final: 0.7642 (mtp) REVERT: B 604 ARG cc_start: 0.8988 (tpp80) cc_final: 0.8573 (mmt-90) REVERT: B 626 TYR cc_start: 0.8101 (m-80) cc_final: 0.7837 (m-80) REVERT: B 686 ARG cc_start: 0.8568 (mtp85) cc_final: 0.8338 (mtp-110) REVERT: C 41 LEU cc_start: 0.6825 (pp) cc_final: 0.6437 (mm) REVERT: C 56 MET cc_start: 0.4959 (ptt) cc_final: 0.4704 (ptt) REVERT: C 93 MET cc_start: 0.2187 (mtp) cc_final: 0.1960 (mtp) REVERT: C 141 LEU cc_start: 0.8708 (mt) cc_final: 0.8326 (pp) REVERT: C 162 TYR cc_start: 0.9201 (m-10) cc_final: 0.8706 (m-80) REVERT: C 237 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8309 (pp20) REVERT: C 242 TYR cc_start: 0.9261 (t80) cc_final: 0.8755 (t80) REVERT: C 281 ASP cc_start: 0.7256 (m-30) cc_final: 0.6621 (t0) REVERT: D 138 ILE cc_start: 0.9158 (mm) cc_final: 0.8920 (tp) outliers start: 72 outliers final: 33 residues processed: 598 average time/residue: 0.2706 time to fit residues: 243.1376 Evaluate side-chains 509 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 470 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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 321 GLU 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 117 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: 0.9980 chunk 168 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 57 optimal weight: 0.0770 chunk 52 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 320 ASN A 410 ASN ** 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 313 HIS ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 467 ASN B 645 GLN ** 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 210 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.152106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.109828 restraints weight = 32276.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113538 restraints weight = 15637.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115867 restraints weight = 9413.690| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16386 Z= 0.176 Angle : 0.639 11.157 22134 Z= 0.332 Chirality : 0.044 0.187 2360 Planarity : 0.003 0.042 2818 Dihedral : 11.029 166.657 2247 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.26 % Allowed : 19.58 % Favored : 77.16 % 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: 1.41 (0.19), residues: 1932 helix: 1.48 (0.15), residues: 1130 sheet: 0.08 (0.42), residues: 134 loop : 0.33 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 44 HIS 0.009 0.001 HIS C 201 PHE 0.056 0.002 PHE C 168 TYR 0.028 0.002 TYR C 55 ARG 0.007 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 871) hydrogen bonds : angle 4.99997 ( 2571) covalent geometry : bond 0.00394 (16386) covalent geometry : angle 0.63936 (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 588 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 532 time to evaluate : 1.859 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 76 ASP cc_start: 0.9025 (m-30) cc_final: 0.8795 (m-30) REVERT: A 161 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7966 (mtp85) REVERT: A 202 ASN cc_start: 0.9304 (t0) cc_final: 0.9092 (t0) REVERT: A 209 LYS cc_start: 0.8825 (ttmm) cc_final: 0.8574 (ttmm) REVERT: A 218 ASN cc_start: 0.8901 (t0) cc_final: 0.8425 (t0) REVERT: A 221 LYS cc_start: 0.8328 (mmtp) cc_final: 0.7659 (mmtp) REVERT: A 232 ASN cc_start: 0.9253 (OUTLIER) cc_final: 0.8997 (m110) REVERT: A 263 ASP cc_start: 0.8452 (m-30) cc_final: 0.8068 (m-30) REVERT: A 322 MET cc_start: 0.8565 (mmm) cc_final: 0.7824 (tpp) REVERT: A 362 ASP cc_start: 0.8039 (m-30) cc_final: 0.7573 (m-30) REVERT: A 381 LEU cc_start: 0.8925 (tp) cc_final: 0.8400 (pt) REVERT: A 384 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7301 (pm20) REVERT: A 411 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7798 (mp) REVERT: A 453 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8270 (ttt-90) REVERT: A 468 LEU cc_start: 0.9370 (tp) cc_final: 0.9167 (tp) REVERT: A 479 TYR cc_start: 0.8815 (t80) cc_final: 0.8432 (t80) REVERT: A 498 TYR cc_start: 0.9120 (m-80) cc_final: 0.8813 (m-80) REVERT: A 505 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8217 (mt-10) REVERT: A 526 GLU cc_start: 0.8424 (mp0) cc_final: 0.8140 (mp0) REVERT: A 640 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8087 (tpp) REVERT: A 668 ASN cc_start: 0.8633 (m110) cc_final: 0.8398 (m110) REVERT: B 15 GLU cc_start: 0.9012 (tp30) cc_final: 0.8639 (tp30) REVERT: B 108 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8203 (p) REVERT: B 119 GLU cc_start: 0.8932 (mp0) cc_final: 0.8286 (mp0) REVERT: B 147 GLN cc_start: 0.9168 (mt0) cc_final: 0.8528 (mm-40) REVERT: B 232 ASN cc_start: 0.8969 (t0) cc_final: 0.8544 (m-40) REVERT: B 322 MET cc_start: 0.9138 (mmm) cc_final: 0.8818 (mmt) REVERT: B 415 ASN cc_start: 0.9441 (t0) cc_final: 0.9231 (t0) REVERT: B 425 ILE cc_start: 0.9326 (mt) cc_final: 0.9087 (mt) REVERT: B 494 MET cc_start: 0.8941 (mtp) cc_final: 0.8552 (mtp) REVERT: B 586 TYR cc_start: 0.8468 (m-80) cc_final: 0.7813 (m-80) REVERT: B 604 ARG cc_start: 0.9109 (tpp80) cc_final: 0.8654 (mmt-90) REVERT: B 626 TYR cc_start: 0.8319 (m-80) cc_final: 0.7903 (m-80) REVERT: B 627 LYS cc_start: 0.8799 (tttt) cc_final: 0.8393 (ttpp) REVERT: B 686 ARG cc_start: 0.8659 (mtp85) cc_final: 0.8455 (mtp-110) REVERT: C 41 LEU cc_start: 0.6920 (pp) cc_final: 0.6507 (mm) REVERT: C 162 TYR cc_start: 0.9097 (m-10) cc_final: 0.8633 (m-80) REVERT: C 227 PHE cc_start: 0.8073 (t80) cc_final: 0.7822 (t80) REVERT: C 242 TYR cc_start: 0.9277 (t80) cc_final: 0.8770 (t80) REVERT: D 138 ILE cc_start: 0.9167 (mm) cc_final: 0.8936 (tp) outliers start: 56 outliers final: 35 residues processed: 557 average time/residue: 0.2653 time to fit residues: 222.4989 Evaluate side-chains 513 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 472 time to evaluate : 1.695 ------------------------------------------------------------------------------- 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 320 ASN 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 317 MET Chi-restraints excluded: chain B residue 336 LYS 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 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: 6.9990 chunk 99 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 25 GLN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN A 320 ASN ** 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 410 ASN B 418 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 107 ASN D 263 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.142359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103416 restraints weight = 33845.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105202 restraints weight = 18466.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.108555 restraints weight = 10725.654| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 16386 Z= 0.414 Angle : 0.793 10.440 22134 Z= 0.419 Chirality : 0.049 0.202 2360 Planarity : 0.004 0.052 2818 Dihedral : 11.309 178.993 2245 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.49 % Allowed : 20.92 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 1932 helix: 0.88 (0.15), residues: 1123 sheet: -0.07 (0.42), residues: 134 loop : 0.10 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 30 HIS 0.012 0.002 HIS C 201 PHE 0.034 0.003 PHE C 168 TYR 0.026 0.002 TYR A 571 ARG 0.013 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.04769 ( 871) hydrogen bonds : angle 5.37776 ( 2571) covalent geometry : bond 0.00900 (16386) covalent geometry : angle 0.79258 (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 543 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 466 time to evaluate : 1.691 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: A 31 GLU cc_start: 0.9143 (mp0) cc_final: 0.8715 (mp0) REVERT: A 51 LEU cc_start: 0.9250 (tp) cc_final: 0.8997 (mt) REVERT: A 104 TYR cc_start: 0.9278 (m-80) cc_final: 0.9048 (m-80) REVERT: A 157 LEU cc_start: 0.9050 (tp) cc_final: 0.8682 (tp) REVERT: A 161 ARG cc_start: 0.8034 (mtp85) cc_final: 0.7748 (mtp85) REVERT: A 218 ASN cc_start: 0.8957 (t0) cc_final: 0.8596 (t0) REVERT: A 221 LYS cc_start: 0.8633 (mmtp) cc_final: 0.8011 (mmtp) REVERT: A 232 ASN cc_start: 0.9307 (OUTLIER) cc_final: 0.9057 (m110) REVERT: A 263 ASP cc_start: 0.8432 (m-30) cc_final: 0.8040 (m-30) REVERT: A 375 LYS cc_start: 0.8909 (mttt) cc_final: 0.8625 (mtmm) REVERT: A 384 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7098 (pm20) REVERT: A 415 ASN cc_start: 0.9047 (t0) cc_final: 0.8307 (t0) REVERT: A 418 ASN cc_start: 0.9120 (m110) cc_final: 0.8590 (m-40) REVERT: A 420 MET cc_start: 0.8932 (mmm) cc_final: 0.8672 (mmm) REVERT: A 445 ILE cc_start: 0.9268 (mp) cc_final: 0.9038 (mm) REVERT: A 453 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8587 (ttt-90) REVERT: A 498 TYR cc_start: 0.9165 (m-80) cc_final: 0.8770 (m-80) REVERT: A 505 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8376 (mt-10) REVERT: A 588 GLN cc_start: 0.8986 (mm110) cc_final: 0.8611 (mm-40) REVERT: A 604 ARG cc_start: 0.8518 (tpp-160) cc_final: 0.8223 (tpp-160) REVERT: A 640 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8451 (tpp) REVERT: A 684 TYR cc_start: 0.7735 (OUTLIER) cc_final: 0.7290 (m-10) REVERT: B 108 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8526 (p) REVERT: B 184 ARG cc_start: 0.9235 (tpp-160) cc_final: 0.8860 (tpp-160) REVERT: B 190 MET cc_start: 0.9358 (mtm) cc_final: 0.9096 (mtm) REVERT: B 250 TYR cc_start: 0.8931 (m-80) cc_final: 0.8702 (m-80) REVERT: B 274 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6679 (ttm170) REVERT: B 322 MET cc_start: 0.9157 (mmm) cc_final: 0.8801 (mmm) REVERT: B 375 LYS cc_start: 0.9104 (mmtm) cc_final: 0.8697 (mppt) REVERT: B 415 ASN cc_start: 0.9422 (t0) cc_final: 0.9197 (t0) REVERT: B 441 GLU cc_start: 0.8780 (pt0) cc_final: 0.8444 (pt0) REVERT: B 447 ASN cc_start: 0.8683 (m-40) cc_final: 0.8392 (m-40) REVERT: B 494 MET cc_start: 0.9040 (mtp) cc_final: 0.8759 (mtp) REVERT: B 515 ASP cc_start: 0.9073 (m-30) cc_final: 0.8799 (m-30) REVERT: B 586 TYR cc_start: 0.8503 (m-80) cc_final: 0.7755 (m-80) REVERT: B 686 ARG cc_start: 0.8704 (mtp85) cc_final: 0.8468 (mtp-110) REVERT: C 162 TYR cc_start: 0.9265 (m-10) cc_final: 0.8876 (m-80) REVERT: C 242 TYR cc_start: 0.9432 (t80) cc_final: 0.8590 (t80) REVERT: D 44 TRP cc_start: 0.8681 (t60) cc_final: 0.8404 (t60) outliers start: 77 outliers final: 51 residues processed: 505 average time/residue: 0.2706 time to fit residues: 204.7341 Evaluate side-chains 490 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 432 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 116 GLU 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 321 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 499 SER 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 A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 124 ILE 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 231 ASP Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 408 SER 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 587 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 141 LEU 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: 0.8980 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 175 optimal weight: 8.9990 chunk 182 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN C 91 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN D 107 ASN D 186 GLN D 238 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.151800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.109164 restraints weight = 33041.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112998 restraints weight = 16393.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.115518 restraints weight = 10019.634| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16386 Z= 0.140 Angle : 0.643 12.595 22134 Z= 0.330 Chirality : 0.044 0.213 2360 Planarity : 0.003 0.035 2818 Dihedral : 10.474 156.658 2245 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.74 % Allowed : 23.43 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.19), residues: 1932 helix: 1.11 (0.15), residues: 1131 sheet: -0.20 (0.41), residues: 134 loop : 0.12 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 44 HIS 0.006 0.001 HIS C 201 PHE 0.038 0.002 PHE C 168 TYR 0.022 0.001 TYR D 173 ARG 0.007 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 871) hydrogen bonds : angle 5.00446 ( 2571) covalent geometry : bond 0.00314 (16386) covalent geometry : angle 0.64311 (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 547 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 500 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8951 (p0) cc_final: 0.8431 (p0) REVERT: A 31 GLU cc_start: 0.9101 (mp0) cc_final: 0.8802 (mp0) REVERT: A 69 LEU cc_start: 0.9481 (mt) cc_final: 0.9082 (pp) REVERT: A 76 ASP cc_start: 0.8993 (m-30) cc_final: 0.8561 (t70) REVERT: A 139 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8251 (mt-10) REVERT: A 150 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8682 (tm-30) REVERT: A 178 SER cc_start: 0.8750 (OUTLIER) cc_final: 0.8531 (p) REVERT: A 218 ASN cc_start: 0.8803 (t0) cc_final: 0.8326 (t0) REVERT: A 221 LYS cc_start: 0.8678 (mmtp) cc_final: 0.8258 (mmtp) REVERT: A 232 ASN cc_start: 0.9316 (m-40) cc_final: 0.8610 (m110) REVERT: A 259 ASN cc_start: 0.9110 (m-40) cc_final: 0.8676 (m110) REVERT: A 263 ASP cc_start: 0.8378 (m-30) cc_final: 0.7923 (m-30) REVERT: A 350 ARG cc_start: 0.8429 (mtp85) cc_final: 0.8212 (mtp-110) REVERT: A 362 ASP cc_start: 0.8011 (m-30) cc_final: 0.7474 (m-30) REVERT: A 375 LYS cc_start: 0.8911 (mttt) cc_final: 0.8647 (mtmm) REVERT: A 381 LEU cc_start: 0.8980 (tp) cc_final: 0.8361 (pt) REVERT: A 384 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7556 (pm20) REVERT: A 411 LEU cc_start: 0.8107 (mp) cc_final: 0.7842 (mt) REVERT: A 415 ASN cc_start: 0.8912 (t0) cc_final: 0.8370 (t0) REVERT: A 418 ASN cc_start: 0.9036 (m110) cc_final: 0.8693 (m-40) REVERT: A 420 MET cc_start: 0.8676 (mmm) cc_final: 0.8333 (mmm) REVERT: A 479 TYR cc_start: 0.8914 (t80) cc_final: 0.8613 (t80) REVERT: A 494 MET cc_start: 0.8431 (mtp) cc_final: 0.8178 (ttm) REVERT: A 505 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8281 (mt-10) REVERT: A 561 LEU cc_start: 0.8746 (tp) cc_final: 0.8348 (tt) REVERT: A 583 SER cc_start: 0.8912 (m) cc_final: 0.8383 (t) REVERT: A 590 SER cc_start: 0.9269 (p) cc_final: 0.8901 (t) REVERT: A 604 ARG cc_start: 0.8345 (tpp-160) cc_final: 0.8081 (tpp-160) REVERT: A 640 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.7946 (tpp) REVERT: A 645 GLN cc_start: 0.8805 (tp-100) cc_final: 0.8485 (tp-100) REVERT: A 668 ASN cc_start: 0.8652 (m-40) cc_final: 0.8333 (m-40) REVERT: B 15 GLU cc_start: 0.9018 (tp30) cc_final: 0.8684 (tp30) REVERT: B 71 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9166 (mp) REVERT: B 108 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8382 (p) REVERT: B 112 LYS cc_start: 0.9532 (OUTLIER) cc_final: 0.9317 (ptmm) REVERT: B 190 MET cc_start: 0.9175 (mtm) cc_final: 0.8896 (mtm) REVERT: B 194 LYS cc_start: 0.9384 (ttpt) cc_final: 0.9173 (ttpt) REVERT: B 232 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8208 (m-40) REVERT: B 374 SER cc_start: 0.9290 (t) cc_final: 0.8988 (p) REVERT: B 375 LYS cc_start: 0.9027 (mmtm) cc_final: 0.8615 (mppt) REVERT: B 384 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.6870 (pm20) REVERT: B 467 ASN cc_start: 0.9202 (t0) cc_final: 0.8854 (m-40) REVERT: B 494 MET cc_start: 0.8704 (mtp) cc_final: 0.8337 (mtp) REVERT: B 515 ASP cc_start: 0.8967 (m-30) cc_final: 0.8697 (m-30) REVERT: B 586 TYR cc_start: 0.8339 (m-80) cc_final: 0.7654 (m-80) REVERT: B 626 TYR cc_start: 0.8386 (m-80) cc_final: 0.7769 (m-80) REVERT: C 41 LEU cc_start: 0.7342 (pp) cc_final: 0.6807 (mm) REVERT: C 157 MET cc_start: 0.9187 (mtt) cc_final: 0.8981 (mtt) REVERT: C 162 TYR cc_start: 0.9168 (m-10) cc_final: 0.8623 (m-80) REVERT: C 242 TYR cc_start: 0.9325 (t80) cc_final: 0.8644 (t80) REVERT: D 93 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7196 (mtp) outliers start: 47 outliers final: 26 residues processed: 523 average time/residue: 0.2610 time to fit residues: 206.4588 Evaluate side-chains 482 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 447 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 384 GLU 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 653 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 112 LYS 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 384 GLU 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 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain D residue 93 MET 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: 1.9990 chunk 126 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 177 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 232 ASN B 320 ASN ** B 387 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 238 ASN ** 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 = 0.3933 r_free = 0.3933 target = 0.151325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109213 restraints weight = 32951.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112891 restraints weight = 16161.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115137 restraints weight = 9755.284| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16386 Z= 0.168 Angle : 0.660 11.291 22134 Z= 0.336 Chirality : 0.044 0.208 2360 Planarity : 0.004 0.066 2818 Dihedral : 9.865 149.900 2243 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.21 % Allowed : 23.95 % Favored : 72.84 % 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: 0.95 (0.19), residues: 1932 helix: 1.16 (0.15), residues: 1130 sheet: -0.27 (0.41), residues: 138 loop : 0.10 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 44 HIS 0.007 0.001 HIS D 80 PHE 0.043 0.002 PHE C 166 TYR 0.027 0.002 TYR A 571 ARG 0.011 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 871) hydrogen bonds : angle 4.96129 ( 2571) covalent geometry : bond 0.00381 (16386) covalent geometry : angle 0.66008 (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: 55 poor density : 467 time to evaluate : 1.968 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 27 ASP cc_start: 0.8915 (p0) cc_final: 0.8038 (t0) REVERT: A 31 GLU cc_start: 0.9104 (mp0) cc_final: 0.8479 (mp0) REVERT: A 69 LEU cc_start: 0.9493 (mt) cc_final: 0.9069 (pp) REVERT: A 76 ASP cc_start: 0.8961 (m-30) cc_final: 0.8543 (t70) REVERT: A 150 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8682 (tm-30) REVERT: A 179 LEU cc_start: 0.9234 (tp) cc_final: 0.8933 (tt) REVERT: A 209 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8221 (ttmm) REVERT: A 218 ASN cc_start: 0.8819 (t0) cc_final: 0.8323 (t0) REVERT: A 221 LYS cc_start: 0.8797 (mmtp) cc_final: 0.8501 (mmtp) REVERT: A 263 ASP cc_start: 0.8398 (m-30) cc_final: 0.7922 (m-30) REVERT: A 312 GLN cc_start: 0.8023 (tp-100) cc_final: 0.7734 (tp-100) REVERT: A 317 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7829 (mpp) REVERT: A 362 ASP cc_start: 0.7851 (m-30) cc_final: 0.7468 (m-30) REVERT: A 375 LYS cc_start: 0.8886 (mttt) cc_final: 0.8661 (mtmm) REVERT: A 381 LEU cc_start: 0.8999 (tp) cc_final: 0.8423 (pt) REVERT: A 384 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7535 (pm20) REVERT: A 411 LEU cc_start: 0.8217 (mp) cc_final: 0.7975 (mt) REVERT: A 415 ASN cc_start: 0.8963 (t0) cc_final: 0.8584 (t0) REVERT: A 420 MET cc_start: 0.8774 (mmm) cc_final: 0.8433 (mmm) REVERT: A 494 MET cc_start: 0.8438 (mtp) cc_final: 0.8206 (ttm) REVERT: A 505 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8244 (mt-10) REVERT: A 604 ARG cc_start: 0.8361 (tpp-160) cc_final: 0.8157 (tpp-160) REVERT: A 640 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.7922 (tpp) REVERT: A 668 ASN cc_start: 0.8620 (m-40) cc_final: 0.8315 (m-40) REVERT: A 686 ARG cc_start: 0.7791 (ttm110) cc_final: 0.7461 (mtp-110) REVERT: B 15 GLU cc_start: 0.9040 (tp30) cc_final: 0.8701 (tp30) REVERT: B 71 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9200 (mp) REVERT: B 119 GLU cc_start: 0.9022 (mp0) cc_final: 0.8369 (mp0) REVERT: B 186 ILE cc_start: 0.9725 (mp) cc_final: 0.9481 (mp) REVERT: B 190 MET cc_start: 0.9197 (mtm) cc_final: 0.8927 (mtm) REVERT: B 191 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8603 (mm-40) REVERT: B 194 LYS cc_start: 0.9378 (ttpt) cc_final: 0.9021 (ttpt) REVERT: B 274 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.7029 (ttm170) REVERT: B 341 LYS cc_start: 0.9118 (mmtm) cc_final: 0.8773 (mmmm) REVERT: B 375 LYS cc_start: 0.8966 (mmtm) cc_final: 0.8536 (mppt) REVERT: B 384 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: B 466 MET cc_start: 0.8897 (ptt) cc_final: 0.8636 (ptt) REVERT: B 494 MET cc_start: 0.8779 (mtp) cc_final: 0.8413 (mtp) REVERT: B 515 ASP cc_start: 0.8956 (m-30) cc_final: 0.8711 (m-30) REVERT: B 626 TYR cc_start: 0.8519 (m-80) cc_final: 0.7879 (m-80) REVERT: C 141 LEU cc_start: 0.9225 (mt) cc_final: 0.8889 (pp) REVERT: C 166 PHE cc_start: 0.8189 (m-80) cc_final: 0.7599 (m-80) REVERT: C 242 TYR cc_start: 0.9282 (t80) cc_final: 0.8840 (t80) outliers start: 55 outliers final: 32 residues processed: 494 average time/residue: 0.2599 time to fit residues: 194.0317 Evaluate side-chains 482 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 444 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 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 653 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 71 LEU 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 274 ARG Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 384 GLU 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 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 C residue 55 TYR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 230 ASP 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: 0.5980 chunk 85 optimal weight: 0.9990 chunk 161 optimal weight: 0.1980 chunk 23 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 chunk 119 optimal weight: 0.8980 chunk 175 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** 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 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 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 = 0.3941 r_free = 0.3941 target = 0.150870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109287 restraints weight = 32810.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112863 restraints weight = 16091.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115178 restraints weight = 10139.046| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.6034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16386 Z= 0.155 Angle : 0.662 13.900 22134 Z= 0.336 Chirality : 0.044 0.194 2360 Planarity : 0.003 0.060 2818 Dihedral : 9.463 140.163 2243 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.74 % Allowed : 24.77 % Favored : 72.49 % 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: 0.94 (0.19), residues: 1932 helix: 1.17 (0.15), residues: 1128 sheet: -0.37 (0.41), residues: 138 loop : 0.08 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP C 124 HIS 0.008 0.001 HIS C 201 PHE 0.038 0.002 PHE C 168 TYR 0.023 0.001 TYR D 173 ARG 0.008 0.001 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 871) hydrogen bonds : angle 4.91986 ( 2571) covalent geometry : bond 0.00350 (16386) covalent geometry : angle 0.66162 (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 520 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 473 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: A 27 ASP cc_start: 0.8840 (p0) cc_final: 0.8586 (p0) REVERT: A 31 GLU cc_start: 0.9070 (mp0) cc_final: 0.8693 (mp0) REVERT: A 76 ASP cc_start: 0.8961 (m-30) cc_final: 0.8565 (t70) REVERT: A 139 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8204 (mt-10) REVERT: A 150 GLN cc_start: 0.9208 (tm-30) cc_final: 0.8669 (tm-30) REVERT: A 178 SER cc_start: 0.8881 (OUTLIER) cc_final: 0.8665 (p) REVERT: A 209 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8310 (ttmm) REVERT: A 218 ASN cc_start: 0.8699 (t0) cc_final: 0.8218 (t0) REVERT: A 221 LYS cc_start: 0.8800 (mmtp) cc_final: 0.8487 (mmtp) REVERT: A 263 ASP cc_start: 0.8376 (m-30) cc_final: 0.7905 (m-30) REVERT: A 312 GLN cc_start: 0.8160 (tp-100) cc_final: 0.7941 (tp-100) REVERT: A 317 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7868 (mpp) REVERT: A 375 LYS cc_start: 0.8831 (mttt) cc_final: 0.8615 (mtmm) REVERT: A 381 LEU cc_start: 0.8981 (tp) cc_final: 0.8403 (pt) REVERT: A 384 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7546 (pm20) REVERT: A 415 ASN cc_start: 0.9011 (t0) cc_final: 0.8404 (t0) REVERT: A 420 MET cc_start: 0.8766 (mmm) cc_final: 0.8469 (mmm) REVERT: A 427 LYS cc_start: 0.9196 (mmmm) cc_final: 0.8952 (mmmt) REVERT: A 446 ARG cc_start: 0.7712 (mmm160) cc_final: 0.7419 (mmm160) REVERT: A 479 TYR cc_start: 0.8933 (t80) cc_final: 0.8667 (t80) REVERT: A 494 MET cc_start: 0.8508 (mtp) cc_final: 0.8199 (mtp) REVERT: A 640 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.7921 (tpp) REVERT: A 645 GLN cc_start: 0.8564 (tp-100) cc_final: 0.8188 (tp40) REVERT: A 668 ASN cc_start: 0.8563 (m-40) cc_final: 0.8185 (m-40) REVERT: B 15 GLU cc_start: 0.9021 (tp30) cc_final: 0.8776 (tp30) REVERT: B 71 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9183 (mp) REVERT: B 119 GLU cc_start: 0.8951 (mp0) cc_final: 0.8335 (mp0) REVERT: B 186 ILE cc_start: 0.9733 (mp) cc_final: 0.9501 (mp) REVERT: B 190 MET cc_start: 0.9246 (mtm) cc_final: 0.9005 (mtm) REVERT: B 274 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7115 (ttm170) REVERT: B 341 LYS cc_start: 0.9118 (mmtm) cc_final: 0.8792 (mmmm) REVERT: B 375 LYS cc_start: 0.8953 (mmtm) cc_final: 0.8534 (mppt) REVERT: B 384 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.6886 (pm20) REVERT: B 494 MET cc_start: 0.8721 (mtp) cc_final: 0.8384 (mtp) REVERT: B 515 ASP cc_start: 0.8910 (m-30) cc_final: 0.8649 (m-30) REVERT: B 604 ARG cc_start: 0.8934 (tpp80) cc_final: 0.8419 (mmt-90) REVERT: B 626 TYR cc_start: 0.8410 (m-80) cc_final: 0.7871 (m-80) REVERT: B 639 ASP cc_start: 0.8690 (m-30) cc_final: 0.8426 (m-30) REVERT: C 74 MET cc_start: 0.6564 (mmm) cc_final: 0.6061 (mmm) REVERT: C 141 LEU cc_start: 0.9299 (mt) cc_final: 0.8914 (pp) REVERT: C 242 TYR cc_start: 0.9308 (t80) cc_final: 0.8995 (t80) outliers start: 47 outliers final: 32 residues processed: 492 average time/residue: 0.2696 time to fit residues: 197.6834 Evaluate side-chains 482 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 443 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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 167 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 317 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 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 71 LEU 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 274 ARG Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 384 GLU 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 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 672 LEU Chi-restraints excluded: chain C residue 131 LEU 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 167 LEU Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 159 optimal weight: 30.0000 chunk 72 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 180 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS ** B 150 GLN ** 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 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 = 0.3943 r_free = 0.3943 target = 0.153004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.111733 restraints weight = 32682.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.115422 restraints weight = 15915.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.117690 restraints weight = 9605.486| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 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 = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16386 Z= 0.159 Angle : 0.682 14.489 22134 Z= 0.347 Chirality : 0.044 0.194 2360 Planarity : 0.003 0.036 2818 Dihedral : 9.310 139.247 2243 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.09 % Allowed : 25.35 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 1932 helix: 1.16 (0.15), residues: 1124 sheet: -0.49 (0.41), residues: 138 loop : 0.08 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 44 HIS 0.007 0.001 HIS A 647 PHE 0.038 0.002 PHE D 109 TYR 0.025 0.001 TYR D 173 ARG 0.009 0.001 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 871) hydrogen bonds : angle 4.90610 ( 2571) covalent geometry : bond 0.00358 (16386) covalent geometry : angle 0.68238 (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 511 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 458 time to evaluate : 2.190 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: A 31 GLU cc_start: 0.9084 (mp0) cc_final: 0.8787 (mp0) REVERT: A 76 ASP cc_start: 0.8967 (m-30) cc_final: 0.8577 (t70) REVERT: A 139 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8196 (mt-10) REVERT: A 150 GLN cc_start: 0.9214 (tm-30) cc_final: 0.8682 (tm-30) REVERT: A 209 LYS cc_start: 0.8808 (ttmm) cc_final: 0.8377 (ttmm) REVERT: A 218 ASN cc_start: 0.8697 (t0) cc_final: 0.8207 (t0) REVERT: A 221 LYS cc_start: 0.8821 (mmtp) cc_final: 0.8416 (mmtp) REVERT: A 232 ASN cc_start: 0.9163 (m-40) cc_final: 0.8279 (m110) REVERT: A 263 ASP cc_start: 0.8416 (m-30) cc_final: 0.7939 (m-30) REVERT: A 375 LYS cc_start: 0.8840 (mttt) cc_final: 0.8618 (mtmm) REVERT: A 381 LEU cc_start: 0.8999 (tp) cc_final: 0.8425 (pt) REVERT: A 384 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7536 (pm20) REVERT: A 420 MET cc_start: 0.8814 (mmm) cc_final: 0.8476 (mmm) REVERT: A 427 LYS cc_start: 0.9180 (mmmm) cc_final: 0.8950 (mmmt) REVERT: A 446 ARG cc_start: 0.7722 (mmm160) cc_final: 0.7143 (mmm160) REVERT: A 447 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7760 (t0) REVERT: A 479 TYR cc_start: 0.8936 (t80) cc_final: 0.8680 (t80) REVERT: A 493 MET cc_start: 0.8857 (tmm) cc_final: 0.8522 (tmm) REVERT: A 571 TYR cc_start: 0.8868 (t80) cc_final: 0.8537 (t80) REVERT: A 640 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.7869 (tpp) REVERT: A 668 ASN cc_start: 0.8577 (m-40) cc_final: 0.8164 (m-40) REVERT: B 15 GLU cc_start: 0.9037 (tp30) cc_final: 0.8815 (tp30) REVERT: B 87 LYS cc_start: 0.8978 (mmmt) cc_final: 0.8758 (tppt) REVERT: B 109 ASN cc_start: 0.9389 (m-40) cc_final: 0.8995 (m-40) REVERT: B 119 GLU cc_start: 0.8936 (mp0) cc_final: 0.8335 (mp0) REVERT: B 186 ILE cc_start: 0.9708 (mp) cc_final: 0.9468 (mp) REVERT: B 190 MET cc_start: 0.9315 (mtm) cc_final: 0.9091 (mtm) REVERT: B 232 ASN cc_start: 0.9004 (m-40) cc_final: 0.8353 (m110) REVERT: B 274 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7131 (ttm170) REVERT: B 341 LYS cc_start: 0.9150 (mmtm) cc_final: 0.8826 (mmmm) REVERT: B 375 LYS cc_start: 0.8972 (mmtm) cc_final: 0.8561 (mppt) REVERT: B 384 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.6919 (pm20) REVERT: B 494 MET cc_start: 0.8783 (mtp) cc_final: 0.8408 (mtp) REVERT: B 586 TYR cc_start: 0.8295 (m-80) cc_final: 0.7606 (m-80) REVERT: B 604 ARG cc_start: 0.8912 (tpp80) cc_final: 0.8503 (mmt-90) REVERT: B 626 TYR cc_start: 0.8447 (m-80) cc_final: 0.7857 (m-80) REVERT: B 639 ASP cc_start: 0.8710 (m-30) cc_final: 0.8427 (m-30) REVERT: C 141 LEU cc_start: 0.9424 (mt) cc_final: 0.9083 (pp) REVERT: C 149 ASP cc_start: 0.8310 (t0) cc_final: 0.7739 (m-30) REVERT: C 242 TYR cc_start: 0.9329 (t80) cc_final: 0.8972 (t80) REVERT: D 96 MET cc_start: 0.7523 (mmp) cc_final: 0.7093 (tpt) outliers start: 53 outliers final: 39 residues processed: 480 average time/residue: 0.2744 time to fit residues: 197.1698 Evaluate side-chains 476 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 432 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 167 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 270 ASP 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 447 ASN 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 598 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 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 274 ARG Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 384 GLU 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 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 131 LEU 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 167 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 238 ASN 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: 0.9980 chunk 182 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 96 optimal weight: 0.2980 chunk 115 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 469 HIS ** 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 ** 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** C 263 ASN D 25 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.153234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.111960 restraints weight = 32808.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.115617 restraints weight = 15982.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.117975 restraints weight = 9667.393| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 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 = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.6347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16386 Z= 0.163 Angle : 0.693 15.091 22134 Z= 0.354 Chirality : 0.045 0.204 2360 Planarity : 0.004 0.082 2818 Dihedral : 9.261 139.509 2243 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.74 % Allowed : 25.82 % Favored : 71.45 % 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: 1.14 (0.15), residues: 1118 sheet: -0.70 (0.40), residues: 152 loop : 0.13 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 44 HIS 0.006 0.001 HIS A 647 PHE 0.050 0.002 PHE D 109 TYR 0.021 0.001 TYR D 173 ARG 0.009 0.001 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 871) hydrogen bonds : angle 4.93800 ( 2571) covalent geometry : bond 0.00367 (16386) covalent geometry : angle 0.69328 (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 501 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 454 time to evaluate : 1.774 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 27 ASP cc_start: 0.8789 (p0) cc_final: 0.8434 (p0) REVERT: A 31 GLU cc_start: 0.9019 (mp0) cc_final: 0.8778 (mp0) REVERT: A 76 ASP cc_start: 0.8954 (m-30) cc_final: 0.8563 (t70) REVERT: A 150 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8677 (tm-30) REVERT: A 209 LYS cc_start: 0.8824 (ttmm) cc_final: 0.8368 (ttmm) REVERT: A 218 ASN cc_start: 0.8663 (t0) cc_final: 0.8160 (t0) REVERT: A 221 LYS cc_start: 0.8833 (mmtp) cc_final: 0.8434 (mmtp) REVERT: A 228 LYS cc_start: 0.9228 (mttp) cc_final: 0.8571 (mttt) REVERT: A 232 ASN cc_start: 0.9098 (m-40) cc_final: 0.8293 (m110) REVERT: A 263 ASP cc_start: 0.8389 (m-30) cc_final: 0.7907 (m-30) REVERT: A 375 LYS cc_start: 0.8839 (mttt) cc_final: 0.8616 (mtmm) REVERT: A 381 LEU cc_start: 0.9003 (tp) cc_final: 0.8441 (pt) REVERT: A 384 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7539 (pm20) REVERT: A 418 ASN cc_start: 0.9168 (m-40) cc_final: 0.8558 (m110) REVERT: A 420 MET cc_start: 0.8791 (mmm) cc_final: 0.8441 (mmm) REVERT: A 427 LYS cc_start: 0.9225 (mmmm) cc_final: 0.8938 (mmmm) REVERT: A 446 ARG cc_start: 0.7527 (mmm160) cc_final: 0.7267 (mmm160) REVERT: A 479 TYR cc_start: 0.8948 (t80) cc_final: 0.8654 (t80) REVERT: A 493 MET cc_start: 0.8840 (tmm) cc_final: 0.8526 (tmm) REVERT: A 626 TYR cc_start: 0.8682 (m-80) cc_final: 0.8334 (m-80) REVERT: A 640 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.7869 (tpp) REVERT: A 668 ASN cc_start: 0.8557 (m-40) cc_final: 0.8148 (m-40) REVERT: B 15 GLU cc_start: 0.9010 (tp30) cc_final: 0.8806 (tp30) REVERT: B 87 LYS cc_start: 0.8953 (mmmt) cc_final: 0.8726 (tppt) REVERT: B 108 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8612 (p) REVERT: B 119 GLU cc_start: 0.8957 (mp0) cc_final: 0.8353 (mp0) REVERT: B 186 ILE cc_start: 0.9708 (mp) cc_final: 0.9483 (mp) REVERT: B 232 ASN cc_start: 0.9027 (m-40) cc_final: 0.8012 (m110) REVERT: B 235 ARG cc_start: 0.8357 (ttm-80) cc_final: 0.8082 (ttm110) REVERT: B 274 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7068 (ttm170) REVERT: B 341 LYS cc_start: 0.9118 (mmtm) cc_final: 0.8812 (mmmm) REVERT: B 375 LYS cc_start: 0.8972 (mmtm) cc_final: 0.8554 (mppt) REVERT: B 384 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.7499 (pm20) REVERT: B 467 ASN cc_start: 0.9461 (OUTLIER) cc_final: 0.9169 (m110) REVERT: B 494 MET cc_start: 0.8745 (mtp) cc_final: 0.8378 (mtp) REVERT: B 586 TYR cc_start: 0.8303 (m-80) cc_final: 0.7606 (m-80) REVERT: B 604 ARG cc_start: 0.8886 (tpp80) cc_final: 0.8472 (mmt-90) REVERT: B 626 TYR cc_start: 0.8365 (m-80) cc_final: 0.7847 (m-80) REVERT: B 639 ASP cc_start: 0.8663 (m-30) cc_final: 0.8399 (m-30) REVERT: C 141 LEU cc_start: 0.9430 (mt) cc_final: 0.9074 (pp) REVERT: C 149 ASP cc_start: 0.8324 (t0) cc_final: 0.7695 (m-30) REVERT: C 237 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8320 (pp20) REVERT: C 242 TYR cc_start: 0.9336 (t80) cc_final: 0.8985 (t80) outliers start: 47 outliers final: 35 residues processed: 472 average time/residue: 0.2643 time to fit residues: 188.8191 Evaluate side-chains 486 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 445 time to evaluate : 1.891 ------------------------------------------------------------------------------- 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 167 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 584 ILE Chi-restraints excluded: chain A residue 590 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 A residue 667 LEU 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 274 ARG Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 384 GLU 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 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 679 ILE Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 226 GLU 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 167 LEU Chi-restraints excluded: chain D residue 176 LEU 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: 0.0970 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 469 HIS ** 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 ** 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 234 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.154042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.112575 restraints weight = 32856.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.116395 restraints weight = 16051.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118680 restraints weight = 9707.521| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 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 = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.6520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16386 Z= 0.154 Angle : 0.706 15.376 22134 Z= 0.358 Chirality : 0.045 0.284 2360 Planarity : 0.004 0.063 2818 Dihedral : 9.161 139.837 2243 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.91 % Allowed : 25.58 % Favored : 71.50 % 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: 0.83 (0.19), residues: 1932 helix: 1.11 (0.15), residues: 1122 sheet: -0.76 (0.39), residues: 152 loop : 0.10 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 44 HIS 0.007 0.001 HIS A 647 PHE 0.049 0.002 PHE D 109 TYR 0.020 0.001 TYR D 173 ARG 0.009 0.001 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 871) hydrogen bonds : angle 4.90294 ( 2571) covalent geometry : bond 0.00351 (16386) covalent geometry : angle 0.70608 (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 509 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 459 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9054 (mp0) cc_final: 0.8762 (mp0) REVERT: A 76 ASP cc_start: 0.8955 (m-30) cc_final: 0.8567 (t70) REVERT: A 139 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8196 (mt-10) REVERT: A 150 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8661 (tm-30) REVERT: A 179 LEU cc_start: 0.9089 (tp) cc_final: 0.8841 (tt) REVERT: A 209 LYS cc_start: 0.8823 (ttmm) cc_final: 0.8381 (ttmm) REVERT: A 218 ASN cc_start: 0.8708 (t0) cc_final: 0.8226 (t0) REVERT: A 221 LYS cc_start: 0.8794 (mmtp) cc_final: 0.8411 (mmtp) REVERT: A 228 LYS cc_start: 0.9218 (mttp) cc_final: 0.8481 (mttt) REVERT: A 232 ASN cc_start: 0.9125 (m-40) cc_final: 0.8747 (m110) REVERT: A 259 ASN cc_start: 0.9151 (m-40) cc_final: 0.8646 (m110) REVERT: A 263 ASP cc_start: 0.8403 (m-30) cc_final: 0.7920 (m-30) REVERT: A 375 LYS cc_start: 0.8829 (mttt) cc_final: 0.8602 (mtmm) REVERT: A 381 LEU cc_start: 0.9011 (tp) cc_final: 0.8444 (pt) REVERT: A 384 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7511 (pm20) REVERT: A 418 ASN cc_start: 0.9165 (m-40) cc_final: 0.8778 (m110) REVERT: A 420 MET cc_start: 0.8769 (mmm) cc_final: 0.8403 (mmm) REVERT: A 427 LYS cc_start: 0.9182 (mmmm) cc_final: 0.8902 (mmmm) REVERT: A 446 ARG cc_start: 0.7393 (mmm160) cc_final: 0.7126 (mmm160) REVERT: A 479 TYR cc_start: 0.8966 (t80) cc_final: 0.8746 (t80) REVERT: A 493 MET cc_start: 0.8901 (tmm) cc_final: 0.8580 (tmm) REVERT: A 570 MET cc_start: 0.9153 (mtp) cc_final: 0.8920 (mtp) REVERT: A 626 TYR cc_start: 0.8653 (m-80) cc_final: 0.8335 (m-80) REVERT: A 640 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.7891 (tpp) REVERT: A 668 ASN cc_start: 0.8571 (m-40) cc_final: 0.8157 (m-40) REVERT: B 15 GLU cc_start: 0.9029 (tp30) cc_final: 0.8802 (tp30) REVERT: B 87 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8680 (tppt) REVERT: B 108 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8325 (p) REVERT: B 119 GLU cc_start: 0.8948 (mp0) cc_final: 0.8329 (mp0) REVERT: B 190 MET cc_start: 0.8997 (mtm) cc_final: 0.8632 (mtm) REVERT: B 274 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.7118 (ttm170) REVERT: B 341 LYS cc_start: 0.9175 (mmtm) cc_final: 0.8797 (mmmm) REVERT: B 375 LYS cc_start: 0.8954 (mmtm) cc_final: 0.8547 (mppt) REVERT: B 384 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.6856 (pm20) REVERT: B 467 ASN cc_start: 0.9322 (OUTLIER) cc_final: 0.9000 (m110) REVERT: B 494 MET cc_start: 0.8710 (mtp) cc_final: 0.8309 (mtp) REVERT: B 586 TYR cc_start: 0.8276 (m-80) cc_final: 0.7800 (m-80) REVERT: B 604 ARG cc_start: 0.8875 (tpp80) cc_final: 0.8463 (mmt-90) REVERT: B 626 TYR cc_start: 0.8344 (m-80) cc_final: 0.7825 (m-80) REVERT: B 627 LYS cc_start: 0.9171 (tttt) cc_final: 0.8768 (tttt) REVERT: B 639 ASP cc_start: 0.8696 (m-30) cc_final: 0.8383 (m-30) REVERT: C 141 LEU cc_start: 0.9474 (mt) cc_final: 0.9133 (pp) REVERT: C 149 ASP cc_start: 0.8329 (t0) cc_final: 0.7723 (m-30) REVERT: C 237 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8315 (pp20) REVERT: C 242 TYR cc_start: 0.9345 (t80) cc_final: 0.9034 (t80) REVERT: D 79 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6759 (mm-30) REVERT: D 96 MET cc_start: 0.7592 (mmp) cc_final: 0.7111 (tpp) outliers start: 50 outliers final: 33 residues processed: 481 average time/residue: 0.2981 time to fit residues: 216.5165 Evaluate side-chains 481 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 442 time to evaluate : 1.930 ------------------------------------------------------------------------------- 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 167 LEU Chi-restraints excluded: chain A residue 226 VAL 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 584 ILE 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 A residue 667 LEU 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 274 ARG Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 384 GLU 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 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 679 ILE Chi-restraints excluded: chain C residue 131 LEU 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 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: 4.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 179 optimal weight: 20.0000 chunk 190 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 469 HIS ** 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 ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.152657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.111455 restraints weight = 32390.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115124 restraints weight = 16067.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117493 restraints weight = 9797.027| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 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 = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.6623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16386 Z= 0.161 Angle : 0.724 15.453 22134 Z= 0.367 Chirality : 0.045 0.234 2360 Planarity : 0.004 0.057 2818 Dihedral : 9.103 139.993 2243 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.80 % Allowed : 25.99 % 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: 0.79 (0.19), residues: 1932 helix: 1.05 (0.15), residues: 1120 sheet: -0.36 (0.45), residues: 118 loop : -0.01 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 44 HIS 0.008 0.001 HIS D 80 PHE 0.047 0.002 PHE D 109 TYR 0.031 0.001 TYR D 173 ARG 0.009 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 871) hydrogen bonds : angle 4.98449 ( 2571) covalent geometry : bond 0.00370 (16386) covalent geometry : angle 0.72409 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6195.26 seconds wall clock time: 108 minutes 35.47 seconds (6515.47 seconds total)