Starting phenix.real_space_refine on Fri Jul 3 19:46:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzm_45071/07_2026/9bzm_45071_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzm_45071/07_2026/9bzm_45071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bzm_45071/07_2026/9bzm_45071_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzm_45071/07_2026/9bzm_45071_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bzm_45071/07_2026/9bzm_45071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzm_45071/07_2026/9bzm_45071.map" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 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: 3.68, per 1000 atoms: 0.23 Number of scatterers: 16038 At special positions: 0 Unit cell: (93.288, 127.764, 130.806, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 758.5 milliseconds 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: 0.47 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: 4.095A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.953A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.664A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.628A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.676A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.646A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.026A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.567A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.359A 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: 6.605A 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: 7.499A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.717A 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: 5.661A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A 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: 4.516A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.906A 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: 8.346A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 1.77 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: 4888 1.34 - 1.46: 3062 1.46 - 1.58: 8255 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21524 2.09 - 4.18: 528 4.18 - 6.27: 64 6.27 - 8.36: 9 8.36 - 10.45: 9 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 110.54 116.59 -6.05 1.36e+00 5.41e-01 1.98e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.13 -4.42 1.15e+00 7.56e-01 1.48e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.22 -3.94 1.09e+00 8.42e-01 1.30e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.88 -4.38 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 111.71 115.68 -3.97 1.15e+00 7.56e-01 1.19e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.06: 9088 25.06 - 50.11: 657 50.11 - 75.17: 125 75.17 - 100.22: 26 100.22 - 125.28: 2 Dihedral angle restraints: 9898 sinusoidal: 4140 harmonic: 5758 Sorted by residual: dihedral pdb=" O4' GDP A 802 " pdb=" C1' GDP A 802 " pdb=" N9 GDP A 802 " pdb=" C8 GDP A 802 " ideal model delta sinusoidal sigma weight residual 27.02 -98.26 125.28 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O4' GDP B 804 " pdb=" C1' GDP B 804 " pdb=" N9 GDP B 804 " pdb=" C8 GDP B 804 " ideal model delta sinusoidal sigma weight residual 27.02 -95.56 122.59 1 2.00e+01 2.50e-03 3.69e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.34 12.34 0 2.50e+00 1.60e-01 2.44e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2134 0.093 - 0.186: 192 0.186 - 0.278: 29 0.278 - 0.371: 3 0.371 - 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 5.38e+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 4.54e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+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 4.12e-02 2.72e+00 pdb=" N PRO D 75 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.017 2.00e-02 2.50e+03 1.11e-02 2.15e+00 pdb=" CG PHE D 92 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 9.83e-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: 131 2.51 - 3.11: 11557 3.11 - 3.70: 27051 3.70 - 4.30: 41544 4.30 - 4.90: 65430 Nonbonded interactions: 145713 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 3.060 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145708 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: 1.180 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.790 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 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 0.139 16386 Z= 0.334 Angle : 0.788 10.446 22134 Z= 0.472 Chirality : 0.058 0.464 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.681 125.280 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.28 % Allowed : 15.38 % Favored : 83.33 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (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 ARG 0.004 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.33 (16386) covalent geometry : angle 0.78750 / 0.47 (22134) hydrogen bonds : bond 0.15420 / 9.51 ( 871) hydrogen bonds : angle 6.51745 / 4.65 ( 2571) *********************** 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 998 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 976 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8814 (mm) cc_final: 0.8406 (mm) REVERT: A 69 LEU cc_start: 0.8277 (mt) cc_final: 0.8074 (mt) REVERT: A 147 GLN cc_start: 0.8267 (mt0) cc_final: 0.7403 (mt0) REVERT: A 171 PHE cc_start: 0.8520 (m-80) cc_final: 0.8261 (m-10) REVERT: A 172 LEU cc_start: 0.9471 (mp) cc_final: 0.9233 (mp) REVERT: A 179 LEU cc_start: 0.8863 (tp) cc_final: 0.8584 (tp) REVERT: A 181 ASP cc_start: 0.8375 (m-30) cc_final: 0.7893 (m-30) REVERT: A 188 ILE cc_start: 0.9195 (mt) cc_final: 0.8963 (mt) REVERT: A 192 LEU cc_start: 0.9448 (mt) cc_final: 0.9076 (mt) REVERT: A 204 SER cc_start: 0.9104 (m) cc_final: 0.8828 (p) REVERT: A 211 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6462 (mm-30) REVERT: A 224 VAL cc_start: 0.8632 (t) cc_final: 0.8365 (p) REVERT: A 258 ILE cc_start: 0.9037 (tp) cc_final: 0.8639 (tp) REVERT: A 278 LEU cc_start: 0.8477 (tp) cc_final: 0.8205 (tp) REVERT: A 294 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6503 (mt-10) REVERT: A 322 MET cc_start: 0.8113 (mmp) cc_final: 0.7471 (mmm) REVERT: A 345 LYS cc_start: 0.8603 (tttt) cc_final: 0.8209 (tttt) REVERT: A 349 LEU cc_start: 0.7856 (mt) cc_final: 0.7546 (mt) REVERT: A 362 ASP cc_start: 0.6167 (m-30) cc_final: 0.5640 (m-30) REVERT: A 407 ILE cc_start: 0.9091 (mt) cc_final: 0.8445 (mt) REVERT: A 417 LEU cc_start: 0.8546 (tt) cc_final: 0.8164 (tt) REVERT: A 420 MET cc_start: 0.8019 (mmm) cc_final: 0.7726 (mmm) REVERT: A 430 LYS cc_start: 0.8978 (mttt) cc_final: 0.8731 (mtpp) REVERT: A 436 LEU cc_start: 0.9196 (mt) cc_final: 0.8960 (mt) REVERT: A 442 THR cc_start: 0.8962 (p) cc_final: 0.8748 (m) REVERT: A 474 GLN cc_start: 0.8573 (mt0) cc_final: 0.8185 (mt0) REVERT: A 494 MET cc_start: 0.8146 (mtp) cc_final: 0.7795 (mtm) REVERT: A 500 ILE cc_start: 0.9349 (mt) cc_final: 0.9130 (mt) REVERT: A 556 GLU cc_start: 0.6880 (tp30) cc_final: 0.6413 (tp30) REVERT: A 558 TRP cc_start: 0.8988 (m100) cc_final: 0.8763 (m100) REVERT: A 573 SER cc_start: 0.9425 (p) cc_final: 0.8953 (p) REVERT: A 587 VAL cc_start: 0.9000 (t) cc_final: 0.8694 (t) REVERT: A 594 VAL cc_start: 0.9180 (m) cc_final: 0.8951 (m) REVERT: A 597 ILE cc_start: 0.9037 (pt) cc_final: 0.8808 (pt) REVERT: A 612 TYR cc_start: 0.7431 (m-80) cc_final: 0.6551 (m-10) REVERT: A 618 LEU cc_start: 0.9165 (tp) cc_final: 0.8895 (tp) REVERT: A 634 MET cc_start: 0.8112 (mmp) cc_final: 0.7737 (mmm) REVERT: A 644 ILE cc_start: 0.8686 (mt) cc_final: 0.7855 (mt) REVERT: A 653 SER cc_start: 0.8990 (OUTLIER) cc_final: 0.8739 (p) REVERT: A 655 THR cc_start: 0.9153 (m) cc_final: 0.8904 (t) REVERT: A 657 PHE cc_start: 0.7945 (m-80) cc_final: 0.7495 (m-80) REVERT: A 667 LEU cc_start: 0.8211 (tt) cc_final: 0.7968 (tt) REVERT: B 11 GLN cc_start: 0.7854 (mt0) cc_final: 0.6858 (mt0) REVERT: B 12 LEU cc_start: 0.9071 (mt) cc_final: 0.8785 (mt) REVERT: B 25 GLN cc_start: 0.7229 (mt0) cc_final: 0.6496 (mt0) REVERT: B 51 LEU cc_start: 0.8138 (tp) cc_final: 0.7822 (tp) REVERT: B 89 PHE cc_start: 0.7544 (t80) cc_final: 0.6837 (t80) REVERT: B 122 ILE cc_start: 0.9370 (mt) cc_final: 0.8918 (mt) REVERT: B 149 TYR cc_start: 0.8400 (t80) cc_final: 0.8038 (t80) REVERT: B 171 PHE cc_start: 0.8786 (m-80) cc_final: 0.8518 (m-80) REVERT: B 181 ASP cc_start: 0.8563 (m-30) cc_final: 0.8332 (m-30) REVERT: B 186 ILE cc_start: 0.9054 (mt) cc_final: 0.8797 (mt) REVERT: B 192 LEU cc_start: 0.9264 (mt) cc_final: 0.8633 (mt) REVERT: B 202 ASN cc_start: 0.8817 (t0) cc_final: 0.8042 (p0) REVERT: B 211 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6006 (mm-30) REVERT: B 232 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.7372 (t0) REVERT: B 256 ARG cc_start: 0.7723 (ttp80) cc_final: 0.7515 (tmt-80) REVERT: B 258 ILE cc_start: 0.8586 (tp) cc_final: 0.8379 (tp) REVERT: B 278 LEU cc_start: 0.8728 (tp) cc_final: 0.8236 (tp) REVERT: B 322 MET cc_start: 0.8012 (mmm) cc_final: 0.6335 (mmt) REVERT: B 332 VAL cc_start: 0.8875 (t) cc_final: 0.8647 (t) REVERT: B 345 LYS cc_start: 0.8630 (tttt) cc_final: 0.8108 (tttt) REVERT: B 362 ASP cc_start: 0.6716 (m-30) cc_final: 0.5833 (m-30) REVERT: B 364 VAL cc_start: 0.8922 (t) cc_final: 0.8520 (t) REVERT: B 381 LEU cc_start: 0.9084 (tp) cc_final: 0.8824 (tp) REVERT: B 384 GLU cc_start: 0.8761 (pm20) cc_final: 0.8504 (pm20) REVERT: B 403 ILE cc_start: 0.9387 (mm) cc_final: 0.8916 (mp) REVERT: B 446 ARG cc_start: 0.7142 (mmm160) cc_final: 0.6901 (mtp85) REVERT: B 453 ARG cc_start: 0.8968 (ttt90) cc_final: 0.8081 (ttp80) REVERT: B 505 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6725 (mt-10) REVERT: B 550 MET cc_start: 0.7401 (mtm) cc_final: 0.5931 (mtp) REVERT: B 558 TRP cc_start: 0.8293 (m100) cc_final: 0.7919 (m100) REVERT: B 570 MET cc_start: 0.7401 (mtm) cc_final: 0.6951 (mtm) REVERT: B 587 VAL cc_start: 0.8816 (t) cc_final: 0.8554 (t) REVERT: B 656 LEU cc_start: 0.8446 (mt) cc_final: 0.8217 (mt) REVERT: C 42 LEU cc_start: 0.6344 (mt) cc_final: 0.5901 (mt) REVERT: C 90 LEU cc_start: 0.5256 (mt) cc_final: 0.4769 (mt) REVERT: C 153 LEU cc_start: 0.5389 (tp) cc_final: 0.5067 (tt) REVERT: D 96 MET cc_start: 0.2343 (mmm) cc_final: 0.2075 (mmt) REVERT: D 178 PHE cc_start: 0.5464 (m-80) cc_final: 0.4361 (m-80) REVERT: D 286 VAL cc_start: 0.7829 (t) cc_final: 0.7046 (p) REVERT: D 321 TYR cc_start: 0.6487 (m-80) cc_final: 0.5325 (m-10) outliers start: 22 outliers final: 7 residues processed: 988 average time/residue: 0.1471 time to fit residues: 209.6186 Evaluate side-chains 682 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 673 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 19 GLN A 43 GLN A 150 GLN A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN A 645 GLN B 11 GLN B 61 ASN B 218 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN B 387 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 645 GLN B 676 HIS ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 71 ASN D 127 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.137702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.094107 restraints weight = 37679.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.097419 restraints weight = 20009.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.099790 restraints weight = 12957.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.101377 restraints weight = 9249.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.102403 restraints weight = 7221.990| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16386 Z= 0.202 Angle : 0.636 7.340 22134 Z= 0.344 Chirality : 0.044 0.313 2360 Planarity : 0.004 0.032 2818 Dihedral : 9.856 132.721 2290 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.23 % Allowed : 2.62 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.18), residues: 1932 helix: 1.24 (0.15), residues: 1130 sheet: 0.35 (0.44), residues: 126 loop : 0.45 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 207 TYR 0.053 0.002 TYR D 130 PHE 0.029 0.002 PHE D 320 TRP 0.010 0.002 TRP C 44 HIS 0.009 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (16386) covalent geometry : angle 0.63607 / 0.34 (22134) hydrogen bonds : bond 0.04847 / 3.06 ( 871) hydrogen bonds : angle 5.10996 / 3.62 ( 2571) *********************** 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 765 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 761 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.9361 (mmtt) cc_final: 0.8845 (mmmt) REVERT: A 31 GLU cc_start: 0.9406 (tp30) cc_final: 0.8999 (tp30) REVERT: A 41 ILE cc_start: 0.9560 (mm) cc_final: 0.9360 (mm) REVERT: A 54 LYS cc_start: 0.9622 (ttmm) cc_final: 0.9203 (ttmm) REVERT: A 87 LYS cc_start: 0.9502 (tptt) cc_final: 0.9131 (mmmm) REVERT: A 101 TYR cc_start: 0.9335 (m-10) cc_final: 0.8964 (m-10) REVERT: A 118 TYR cc_start: 0.9157 (t80) cc_final: 0.8677 (t80) REVERT: A 120 ASP cc_start: 0.9113 (m-30) cc_final: 0.8779 (m-30) REVERT: A 122 ILE cc_start: 0.9686 (mt) cc_final: 0.9466 (mt) REVERT: A 139 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9199 (mm-30) REVERT: A 142 ASN cc_start: 0.9431 (m-40) cc_final: 0.9146 (m110) REVERT: A 147 GLN cc_start: 0.8951 (mt0) cc_final: 0.8665 (mt0) REVERT: A 150 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.9070 (tm-30) REVERT: A 202 ASN cc_start: 0.9580 (t0) cc_final: 0.9274 (t0) REVERT: A 204 SER cc_start: 0.9426 (m) cc_final: 0.9114 (p) REVERT: A 223 VAL cc_start: 0.9546 (m) cc_final: 0.9294 (p) REVERT: A 251 LEU cc_start: 0.9588 (tp) cc_final: 0.9318 (tp) REVERT: A 286 ASP cc_start: 0.8602 (m-30) cc_final: 0.8143 (m-30) REVERT: A 291 LEU cc_start: 0.9333 (mt) cc_final: 0.9013 (mt) REVERT: A 293 ARG cc_start: 0.9198 (ttp80) cc_final: 0.8797 (ttp80) REVERT: A 337 ILE cc_start: 0.9484 (tp) cc_final: 0.9172 (tp) REVERT: A 344 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8582 (mt-10) REVERT: A 348 MET cc_start: 0.8972 (ptp) cc_final: 0.8680 (ptp) REVERT: A 349 LEU cc_start: 0.9584 (mt) cc_final: 0.9300 (mt) REVERT: A 362 ASP cc_start: 0.8069 (m-30) cc_final: 0.7370 (m-30) REVERT: A 405 LEU cc_start: 0.9115 (mt) cc_final: 0.8898 (mt) REVERT: A 407 ILE cc_start: 0.9192 (mt) cc_final: 0.8816 (mt) REVERT: A 421 GLU cc_start: 0.8222 (pp20) cc_final: 0.8009 (pp20) REVERT: A 441 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8361 (mt-10) REVERT: A 443 THR cc_start: 0.9300 (m) cc_final: 0.9066 (t) REVERT: A 458 MET cc_start: 0.9177 (mmp) cc_final: 0.8617 (mmp) REVERT: A 466 MET cc_start: 0.9186 (ptt) cc_final: 0.8885 (ptt) REVERT: A 505 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8899 (mt-10) REVERT: A 550 MET cc_start: 0.7676 (mtt) cc_final: 0.6995 (mtt) REVERT: A 570 MET cc_start: 0.9128 (mtp) cc_final: 0.8882 (mtp) REVERT: A 573 SER cc_start: 0.9478 (p) cc_final: 0.9060 (p) REVERT: A 584 ILE cc_start: 0.9610 (pt) cc_final: 0.9176 (pt) REVERT: A 588 GLN cc_start: 0.9323 (mm-40) cc_final: 0.9054 (tp40) REVERT: A 599 GLU cc_start: 0.8340 (mp0) cc_final: 0.7850 (mp0) REVERT: A 615 MET cc_start: 0.9026 (mmp) cc_final: 0.8777 (mmp) REVERT: A 630 TYR cc_start: 0.7957 (m-80) cc_final: 0.7210 (m-10) REVERT: A 632 MET cc_start: 0.8877 (mtm) cc_final: 0.8591 (mtp) REVERT: A 639 ASP cc_start: 0.9213 (m-30) cc_final: 0.8927 (m-30) REVERT: A 645 GLN cc_start: 0.9075 (tp-100) cc_final: 0.8129 (tp-100) REVERT: A 648 ILE cc_start: 0.9554 (mm) cc_final: 0.9177 (mm) REVERT: A 650 GLN cc_start: 0.8599 (mt0) cc_final: 0.7859 (mt0) REVERT: A 654 PHE cc_start: 0.9502 (t80) cc_final: 0.9201 (t80) REVERT: A 655 THR cc_start: 0.9286 (m) cc_final: 0.8735 (t) REVERT: A 664 THR cc_start: 0.9170 (p) cc_final: 0.8675 (p) REVERT: A 667 LEU cc_start: 0.9378 (tt) cc_final: 0.9108 (tt) REVERT: A 668 ASN cc_start: 0.9274 (m110) cc_final: 0.8946 (m110) REVERT: A 680 LYS cc_start: 0.8877 (mttt) cc_final: 0.8373 (mttp) REVERT: B 51 LEU cc_start: 0.9490 (tp) cc_final: 0.9245 (tp) REVERT: B 58 LEU cc_start: 0.9680 (mt) cc_final: 0.9451 (mt) REVERT: B 65 GLU cc_start: 0.8626 (mt-10) cc_final: 0.7971 (mp0) REVERT: B 87 LYS cc_start: 0.9288 (tptp) cc_final: 0.8753 (tptp) REVERT: B 147 GLN cc_start: 0.9130 (mt0) cc_final: 0.8689 (mt0) REVERT: B 149 TYR cc_start: 0.9177 (t80) cc_final: 0.8762 (t80) REVERT: B 162 LYS cc_start: 0.9357 (tppt) cc_final: 0.8640 (mmmm) REVERT: B 227 MET cc_start: 0.9467 (mtp) cc_final: 0.9258 (mtp) REVERT: B 256 ARG cc_start: 0.9072 (tmt170) cc_final: 0.8798 (tpt90) REVERT: B 257 ASP cc_start: 0.9060 (m-30) cc_final: 0.8733 (m-30) REVERT: B 259 ASN cc_start: 0.8836 (p0) cc_final: 0.8582 (p0) REVERT: B 278 LEU cc_start: 0.9275 (tp) cc_final: 0.9016 (tp) REVERT: B 279 SER cc_start: 0.8541 (m) cc_final: 0.7629 (p) REVERT: B 286 ASP cc_start: 0.8373 (m-30) cc_final: 0.8170 (m-30) REVERT: B 290 GLU cc_start: 0.9279 (tp30) cc_final: 0.9036 (tp30) REVERT: B 316 GLU cc_start: 0.9138 (tt0) cc_final: 0.8908 (tt0) REVERT: B 333 LYS cc_start: 0.9193 (tptp) cc_final: 0.8694 (tttm) REVERT: B 355 TYR cc_start: 0.9012 (m-80) cc_final: 0.8700 (m-80) REVERT: B 381 LEU cc_start: 0.9210 (tp) cc_final: 0.8921 (tp) REVERT: B 413 SER cc_start: 0.9537 (m) cc_final: 0.9021 (t) REVERT: B 415 ASN cc_start: 0.9694 (t0) cc_final: 0.9412 (t0) REVERT: B 458 MET cc_start: 0.9513 (mmm) cc_final: 0.9142 (mmp) REVERT: B 460 SER cc_start: 0.8903 (t) cc_final: 0.8672 (t) REVERT: B 471 TYR cc_start: 0.9302 (t80) cc_final: 0.8971 (t80) REVERT: B 487 PHE cc_start: 0.9740 (t80) cc_final: 0.9446 (t80) REVERT: B 493 MET cc_start: 0.9500 (tmm) cc_final: 0.9182 (tmm) REVERT: B 505 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8410 (mt-10) REVERT: B 570 MET cc_start: 0.9082 (mtp) cc_final: 0.8688 (mtp) REVERT: B 599 GLU cc_start: 0.8719 (pt0) cc_final: 0.8496 (pt0) REVERT: B 601 ILE cc_start: 0.9446 (mm) cc_final: 0.9166 (mm) REVERT: B 612 TYR cc_start: 0.8503 (m-10) cc_final: 0.8236 (m-10) REVERT: B 631 ASP cc_start: 0.9023 (t0) cc_final: 0.8501 (t0) REVERT: B 667 LEU cc_start: 0.9433 (tp) cc_final: 0.9186 (tp) REVERT: B 677 ARG cc_start: 0.9485 (mmm-85) cc_final: 0.9132 (mmm-85) REVERT: C 42 LEU cc_start: 0.9032 (mt) cc_final: 0.8819 (mt) REVERT: C 117 THR cc_start: 0.9093 (p) cc_final: 0.8802 (p) REVERT: C 119 ASN cc_start: 0.9082 (t0) cc_final: 0.8818 (t0) REVERT: C 179 TYR cc_start: 0.8594 (t80) cc_final: 0.8346 (t80) REVERT: C 200 ILE cc_start: 0.6102 (mm) cc_final: 0.5890 (mp) REVERT: D 37 LEU cc_start: 0.5152 (tp) cc_final: 0.2801 (tp) REVERT: D 96 MET cc_start: 0.5053 (mmm) cc_final: 0.4634 (mmm) REVERT: D 100 VAL cc_start: 0.6899 (t) cc_final: 0.6157 (t) REVERT: D 101 HIS cc_start: 0.6642 (m170) cc_final: 0.5346 (m170) REVERT: D 252 LEU cc_start: 0.8779 (mt) cc_final: 0.8484 (mt) outliers start: 4 outliers final: 1 residues processed: 762 average time/residue: 0.1306 time to fit residues: 148.4685 Evaluate side-chains 621 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 619 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 159 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN A 25 GLN A 150 GLN A 191 GLN A 338 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 455 ASN B 19 GLN B 218 ASN B 232 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN D 25 ASN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.137675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.094392 restraints weight = 38826.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.097767 restraints weight = 21139.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.100018 restraints weight = 13595.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.101519 restraints weight = 9808.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102487 restraints weight = 7726.185| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16386 Z= 0.201 Angle : 0.613 10.354 22134 Z= 0.331 Chirality : 0.042 0.230 2360 Planarity : 0.004 0.043 2818 Dihedral : 9.214 134.068 2290 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.29 % Allowed : 2.04 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.19), residues: 1932 helix: 1.27 (0.15), residues: 1133 sheet: -0.24 (0.40), residues: 150 loop : 0.38 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 274 TYR 0.052 0.002 TYR D 130 PHE 0.031 0.002 PHE C 168 TRP 0.016 0.002 TRP A 9 HIS 0.007 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 (16386) covalent geometry : angle 0.61339 / 0.33 (22134) hydrogen bonds : bond 0.04241 / 2.72 ( 871) hydrogen bonds : angle 4.96819 / 3.56 ( 2571) *********************** 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 706 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 701 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9565 (tp) cc_final: 0.9328 (pt) REVERT: A 54 LYS cc_start: 0.9719 (ttmm) cc_final: 0.9277 (ttmm) REVERT: A 64 TYR cc_start: 0.8904 (m-10) cc_final: 0.8520 (m-80) REVERT: A 87 LYS cc_start: 0.9502 (tptt) cc_final: 0.9164 (mmmm) REVERT: A 107 LYS cc_start: 0.9129 (mtpp) cc_final: 0.8851 (mtpp) REVERT: A 118 TYR cc_start: 0.9204 (t80) cc_final: 0.8889 (t80) REVERT: A 120 ASP cc_start: 0.9189 (m-30) cc_final: 0.8901 (m-30) REVERT: A 124 ILE cc_start: 0.9763 (mm) cc_final: 0.9548 (mm) REVERT: A 139 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9142 (mm-30) REVERT: A 142 ASN cc_start: 0.9420 (m-40) cc_final: 0.9130 (m110) REVERT: A 150 GLN cc_start: 0.9255 (tp40) cc_final: 0.8971 (tp40) REVERT: A 156 PHE cc_start: 0.9410 (t80) cc_final: 0.9169 (t80) REVERT: A 168 VAL cc_start: 0.9234 (t) cc_final: 0.8959 (m) REVERT: A 181 ASP cc_start: 0.8974 (m-30) cc_final: 0.8658 (m-30) REVERT: A 223 VAL cc_start: 0.9564 (m) cc_final: 0.9100 (p) REVERT: A 227 MET cc_start: 0.9362 (mtp) cc_final: 0.8953 (mtp) REVERT: A 251 LEU cc_start: 0.9681 (tp) cc_final: 0.9396 (tp) REVERT: A 257 ASP cc_start: 0.9351 (m-30) cc_final: 0.8580 (m-30) REVERT: A 263 ASP cc_start: 0.9061 (m-30) cc_final: 0.8840 (m-30) REVERT: A 286 ASP cc_start: 0.8652 (m-30) cc_final: 0.8187 (m-30) REVERT: A 291 LEU cc_start: 0.9378 (mt) cc_final: 0.9147 (mt) REVERT: A 316 GLU cc_start: 0.8930 (pt0) cc_final: 0.8627 (pp20) REVERT: A 317 MET cc_start: 0.9053 (ptm) cc_final: 0.8845 (ptm) REVERT: A 321 GLU cc_start: 0.8470 (pp20) cc_final: 0.8180 (pp20) REVERT: A 322 MET cc_start: 0.8717 (mmp) cc_final: 0.8369 (mmm) REVERT: A 337 ILE cc_start: 0.9452 (tp) cc_final: 0.9246 (tp) REVERT: A 344 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8620 (mt-10) REVERT: A 348 MET cc_start: 0.9019 (ptp) cc_final: 0.8711 (ptp) REVERT: A 349 LEU cc_start: 0.9595 (mt) cc_final: 0.9303 (mt) REVERT: A 362 ASP cc_start: 0.8099 (m-30) cc_final: 0.7372 (m-30) REVERT: A 387 GLN cc_start: 0.9148 (mt0) cc_final: 0.8907 (mt0) REVERT: A 407 ILE cc_start: 0.9381 (mt) cc_final: 0.9066 (mt) REVERT: A 418 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8528 (m110) REVERT: A 458 MET cc_start: 0.9402 (mmp) cc_final: 0.8949 (mmm) REVERT: A 466 MET cc_start: 0.9231 (ptt) cc_final: 0.8984 (ptt) REVERT: A 485 ARG cc_start: 0.9201 (mtm-85) cc_final: 0.8826 (mtm-85) REVERT: A 490 THR cc_start: 0.9674 (m) cc_final: 0.9345 (p) REVERT: A 505 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8786 (mt-10) REVERT: A 570 MET cc_start: 0.9290 (mtp) cc_final: 0.8992 (mtp) REVERT: A 573 SER cc_start: 0.9398 (p) cc_final: 0.8304 (p) REVERT: A 639 ASP cc_start: 0.9104 (m-30) cc_final: 0.8759 (m-30) REVERT: A 650 GLN cc_start: 0.8553 (mt0) cc_final: 0.8019 (mt0) REVERT: A 668 ASN cc_start: 0.9442 (m110) cc_final: 0.8979 (m110) REVERT: A 686 ARG cc_start: 0.8620 (mmt90) cc_final: 0.8210 (mmt-90) REVERT: B 58 LEU cc_start: 0.9661 (mt) cc_final: 0.9399 (mt) REVERT: B 65 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8440 (mp0) REVERT: B 87 LYS cc_start: 0.9355 (tptp) cc_final: 0.8993 (tptp) REVERT: B 106 LEU cc_start: 0.9519 (tp) cc_final: 0.9294 (tp) REVERT: B 116 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8455 (mp0) REVERT: B 117 ARG cc_start: 0.9047 (ttm110) cc_final: 0.8759 (ttm110) REVERT: B 120 ASP cc_start: 0.8839 (m-30) cc_final: 0.8614 (m-30) REVERT: B 147 GLN cc_start: 0.9209 (mt0) cc_final: 0.8827 (mt0) REVERT: B 149 TYR cc_start: 0.9215 (t80) cc_final: 0.8831 (t80) REVERT: B 172 LEU cc_start: 0.9390 (mp) cc_final: 0.9044 (mp) REVERT: B 174 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8235 (mm-30) REVERT: B 191 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8591 (mm-40) REVERT: B 202 ASN cc_start: 0.9584 (t0) cc_final: 0.9251 (t0) REVERT: B 214 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8846 (mmtt) REVERT: B 221 LYS cc_start: 0.9172 (mmtp) cc_final: 0.8889 (mmtp) REVERT: B 232 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8517 (t0) REVERT: B 257 ASP cc_start: 0.8938 (m-30) cc_final: 0.8521 (m-30) REVERT: B 258 ILE cc_start: 0.9577 (tp) cc_final: 0.9376 (tp) REVERT: B 264 THR cc_start: 0.9480 (p) cc_final: 0.9274 (p) REVERT: B 278 LEU cc_start: 0.9238 (tp) cc_final: 0.8959 (tp) REVERT: B 279 SER cc_start: 0.8474 (m) cc_final: 0.7906 (p) REVERT: B 286 ASP cc_start: 0.8591 (m-30) cc_final: 0.8299 (m-30) REVERT: B 288 PHE cc_start: 0.9495 (t80) cc_final: 0.9247 (t80) REVERT: B 290 GLU cc_start: 0.9253 (tp30) cc_final: 0.8969 (tp30) REVERT: B 316 GLU cc_start: 0.9080 (tt0) cc_final: 0.8810 (tt0) REVERT: B 322 MET cc_start: 0.9113 (tpt) cc_final: 0.8871 (tpp) REVERT: B 333 LYS cc_start: 0.9309 (tptp) cc_final: 0.8923 (tttm) REVERT: B 335 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7578 (mt-10) REVERT: B 378 PHE cc_start: 0.9385 (p90) cc_final: 0.9062 (p90) REVERT: B 381 LEU cc_start: 0.9362 (tp) cc_final: 0.9148 (tp) REVERT: B 407 ILE cc_start: 0.9397 (mt) cc_final: 0.8948 (mt) REVERT: B 415 ASN cc_start: 0.9704 (t0) cc_final: 0.9256 (t0) REVERT: B 459 LYS cc_start: 0.9261 (mttp) cc_final: 0.8733 (mtpt) REVERT: B 479 TYR cc_start: 0.9076 (t80) cc_final: 0.8836 (t80) REVERT: B 493 MET cc_start: 0.9484 (tmm) cc_final: 0.9189 (tmm) REVERT: B 505 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8455 (mt-10) REVERT: B 550 MET cc_start: 0.7934 (mtp) cc_final: 0.7672 (mtm) REVERT: B 588 GLN cc_start: 0.9471 (mm-40) cc_final: 0.9169 (mm-40) REVERT: B 599 GLU cc_start: 0.8783 (pt0) cc_final: 0.8480 (pt0) REVERT: B 604 ARG cc_start: 0.9403 (tpp80) cc_final: 0.8991 (ttm-80) REVERT: B 614 PRO cc_start: 0.9424 (Cg_exo) cc_final: 0.9223 (Cg_endo) REVERT: B 631 ASP cc_start: 0.9068 (t0) cc_final: 0.8578 (t0) REVERT: B 658 LEU cc_start: 0.9579 (mt) cc_final: 0.9361 (mt) REVERT: C 179 TYR cc_start: 0.8599 (t80) cc_final: 0.8249 (t80) REVERT: D 137 MET cc_start: 0.5216 (mmm) cc_final: 0.4813 (mpp) REVERT: D 158 VAL cc_start: 0.8830 (t) cc_final: 0.7697 (t) REVERT: D 162 TYR cc_start: 0.8597 (m-10) cc_final: 0.8374 (m-80) REVERT: D 178 PHE cc_start: 0.9075 (m-80) cc_final: 0.8498 (m-80) REVERT: D 233 ASN cc_start: 0.8835 (m110) cc_final: 0.8397 (m110) REVERT: D 321 TYR cc_start: 0.8525 (m-80) cc_final: 0.7553 (m-80) outliers start: 5 outliers final: 0 residues processed: 702 average time/residue: 0.1256 time to fit residues: 132.1688 Evaluate side-chains 620 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 618 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 4.9990 chunk 157 optimal weight: 30.0000 chunk 168 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 127 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN A 147 GLN A 150 GLN A 338 ASN A 361 GLN A 365 ASN A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 218 ASN B 232 ASN B 304 HIS ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 646 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 HIS ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.135081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.092527 restraints weight = 39734.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.095888 restraints weight = 21228.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.098063 restraints weight = 13433.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.099501 restraints weight = 9713.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.100360 restraints weight = 7648.141| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16386 Z= 0.250 Angle : 0.643 9.542 22134 Z= 0.340 Chirality : 0.042 0.203 2360 Planarity : 0.004 0.058 2818 Dihedral : 9.050 135.723 2290 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.12 % Allowed : 2.39 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.19), residues: 1932 helix: 1.09 (0.15), residues: 1136 sheet: -0.16 (0.41), residues: 150 loop : 0.31 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 274 TYR 0.047 0.002 TYR D 130 PHE 0.040 0.002 PHE D 172 TRP 0.011 0.002 TRP A 623 HIS 0.007 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.25 (16386) covalent geometry : angle 0.64310 / 0.34 (22134) hydrogen bonds : bond 0.04167 / 2.66 ( 871) hydrogen bonds : angle 4.94887 / 3.53 ( 2571) *********************** 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 674 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 672 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9589 (mm) cc_final: 0.9316 (mm) REVERT: A 51 LEU cc_start: 0.9587 (tp) cc_final: 0.9385 (pt) REVERT: A 64 TYR cc_start: 0.8979 (m-10) cc_final: 0.8669 (m-10) REVERT: A 87 LYS cc_start: 0.9528 (tptt) cc_final: 0.9216 (mmmm) REVERT: A 107 LYS cc_start: 0.9204 (mtpp) cc_final: 0.8725 (mtpp) REVERT: A 120 ASP cc_start: 0.9315 (m-30) cc_final: 0.8975 (m-30) REVERT: A 139 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9141 (mm-30) REVERT: A 142 ASN cc_start: 0.9421 (m-40) cc_final: 0.9146 (m110) REVERT: A 147 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8017 (mm-40) REVERT: A 168 VAL cc_start: 0.9127 (t) cc_final: 0.8921 (m) REVERT: A 181 ASP cc_start: 0.8995 (m-30) cc_final: 0.8691 (m-30) REVERT: A 223 VAL cc_start: 0.9614 (m) cc_final: 0.9160 (p) REVERT: A 227 MET cc_start: 0.9373 (mtp) cc_final: 0.8900 (mtp) REVERT: A 228 LYS cc_start: 0.9610 (mmmm) cc_final: 0.9326 (tppt) REVERT: A 251 LEU cc_start: 0.9656 (tp) cc_final: 0.9386 (tp) REVERT: A 257 ASP cc_start: 0.9378 (m-30) cc_final: 0.8854 (m-30) REVERT: A 286 ASP cc_start: 0.8774 (m-30) cc_final: 0.8329 (m-30) REVERT: A 322 MET cc_start: 0.8658 (mmp) cc_final: 0.8251 (mmm) REVERT: A 333 LYS cc_start: 0.9159 (tttt) cc_final: 0.8857 (tptp) REVERT: A 344 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8618 (mt-10) REVERT: A 348 MET cc_start: 0.8946 (ptp) cc_final: 0.8673 (ptp) REVERT: A 349 LEU cc_start: 0.9615 (mt) cc_final: 0.9330 (mt) REVERT: A 361 GLN cc_start: 0.9061 (tp40) cc_final: 0.7973 (tp-100) REVERT: A 362 ASP cc_start: 0.8220 (m-30) cc_final: 0.7327 (m-30) REVERT: A 365 ASN cc_start: 0.9261 (m110) cc_final: 0.7848 (m-40) REVERT: A 370 ASN cc_start: 0.9489 (m-40) cc_final: 0.9170 (m110) REVERT: A 375 LYS cc_start: 0.9312 (mtpt) cc_final: 0.8988 (mtmm) REVERT: A 381 LEU cc_start: 0.9515 (tp) cc_final: 0.9313 (tp) REVERT: A 387 GLN cc_start: 0.9199 (mt0) cc_final: 0.8999 (mt0) REVERT: A 407 ILE cc_start: 0.9432 (mt) cc_final: 0.9150 (mt) REVERT: A 458 MET cc_start: 0.9277 (mmp) cc_final: 0.8974 (mmm) REVERT: A 466 MET cc_start: 0.9263 (ptt) cc_final: 0.9039 (ptt) REVERT: A 485 ARG cc_start: 0.9252 (mtm-85) cc_final: 0.9029 (mtm110) REVERT: A 490 THR cc_start: 0.9673 (m) cc_final: 0.9370 (p) REVERT: A 505 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8754 (mt-10) REVERT: A 570 MET cc_start: 0.9312 (mtp) cc_final: 0.8986 (mtp) REVERT: A 573 SER cc_start: 0.9345 (p) cc_final: 0.8814 (p) REVERT: A 598 MET cc_start: 0.8892 (mtm) cc_final: 0.8636 (ttm) REVERT: A 632 MET cc_start: 0.8827 (mtp) cc_final: 0.8626 (mtp) REVERT: A 639 ASP cc_start: 0.9184 (m-30) cc_final: 0.8835 (m-30) REVERT: A 643 THR cc_start: 0.9576 (p) cc_final: 0.9147 (t) REVERT: A 667 LEU cc_start: 0.9525 (tt) cc_final: 0.9249 (tt) REVERT: A 668 ASN cc_start: 0.9434 (m110) cc_final: 0.9007 (m110) REVERT: A 686 ARG cc_start: 0.8743 (mmt90) cc_final: 0.8256 (mmt-90) REVERT: B 58 LEU cc_start: 0.9688 (mt) cc_final: 0.9440 (mt) REVERT: B 65 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8453 (mp0) REVERT: B 82 LYS cc_start: 0.9504 (mmmm) cc_final: 0.9114 (mmtt) REVERT: B 87 LYS cc_start: 0.9408 (tptp) cc_final: 0.9031 (tptp) REVERT: B 95 MET cc_start: 0.9588 (tpt) cc_final: 0.9366 (tpp) REVERT: B 117 ARG cc_start: 0.9072 (ttm110) cc_final: 0.8756 (ttm110) REVERT: B 120 ASP cc_start: 0.8962 (m-30) cc_final: 0.8685 (m-30) REVERT: B 147 GLN cc_start: 0.9231 (mt0) cc_final: 0.9007 (mt0) REVERT: B 149 TYR cc_start: 0.9326 (t80) cc_final: 0.8871 (t80) REVERT: B 157 LEU cc_start: 0.9518 (tp) cc_final: 0.9258 (tp) REVERT: B 172 LEU cc_start: 0.9404 (mp) cc_final: 0.9104 (mp) REVERT: B 174 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8230 (mm-30) REVERT: B 191 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8462 (mm-40) REVERT: B 202 ASN cc_start: 0.9552 (t0) cc_final: 0.9244 (t0) REVERT: B 221 LYS cc_start: 0.9218 (mmtp) cc_final: 0.8970 (mmtp) REVERT: B 232 ASN cc_start: 0.9088 (t160) cc_final: 0.8633 (t0) REVERT: B 257 ASP cc_start: 0.8954 (m-30) cc_final: 0.8620 (m-30) REVERT: B 258 ILE cc_start: 0.9623 (tp) cc_final: 0.9406 (tp) REVERT: B 264 THR cc_start: 0.9502 (p) cc_final: 0.9278 (p) REVERT: B 278 LEU cc_start: 0.9289 (tp) cc_final: 0.9014 (tp) REVERT: B 279 SER cc_start: 0.8495 (m) cc_final: 0.7920 (p) REVERT: B 286 ASP cc_start: 0.8698 (m-30) cc_final: 0.8474 (m-30) REVERT: B 288 PHE cc_start: 0.9549 (t80) cc_final: 0.9329 (t80) REVERT: B 290 GLU cc_start: 0.9272 (tp30) cc_final: 0.8968 (tp30) REVERT: B 333 LYS cc_start: 0.9345 (tptp) cc_final: 0.8891 (tttm) REVERT: B 398 ASP cc_start: 0.8833 (t0) cc_final: 0.8611 (t0) REVERT: B 413 SER cc_start: 0.9512 (m) cc_final: 0.9010 (t) REVERT: B 415 ASN cc_start: 0.9608 (t0) cc_final: 0.9202 (t0) REVERT: B 459 LYS cc_start: 0.9275 (mttp) cc_final: 0.8708 (mtmm) REVERT: B 493 MET cc_start: 0.9452 (tmm) cc_final: 0.9154 (tmm) REVERT: B 505 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8395 (mt-10) REVERT: B 550 MET cc_start: 0.8156 (mtp) cc_final: 0.7373 (mtt) REVERT: B 599 GLU cc_start: 0.8789 (pt0) cc_final: 0.8537 (pt0) REVERT: B 601 ILE cc_start: 0.9590 (mm) cc_final: 0.9365 (mm) REVERT: B 612 TYR cc_start: 0.8250 (m-10) cc_final: 0.7839 (m-10) REVERT: B 667 LEU cc_start: 0.9396 (tp) cc_final: 0.8883 (tp) REVERT: C 16 ASP cc_start: 0.6383 (p0) cc_final: 0.5853 (p0) REVERT: C 179 TYR cc_start: 0.8678 (t80) cc_final: 0.8456 (t80) REVERT: C 278 GLU cc_start: 0.7669 (pm20) cc_final: 0.7444 (pm20) REVERT: D 56 MET cc_start: 0.6930 (mmp) cc_final: 0.6645 (mmm) REVERT: D 59 LEU cc_start: 0.7744 (mt) cc_final: 0.7327 (pp) REVERT: D 137 MET cc_start: 0.5454 (mmm) cc_final: 0.5130 (mpp) REVERT: D 158 VAL cc_start: 0.8928 (t) cc_final: 0.8602 (t) REVERT: D 176 LEU cc_start: 0.9500 (mt) cc_final: 0.9211 (pp) REVERT: D 178 PHE cc_start: 0.9194 (m-80) cc_final: 0.8499 (m-80) REVERT: D 233 ASN cc_start: 0.8890 (m110) cc_final: 0.8412 (m-40) REVERT: D 252 LEU cc_start: 0.8930 (mt) cc_final: 0.8667 (mt) REVERT: D 321 TYR cc_start: 0.8821 (m-80) cc_final: 0.8035 (m-80) outliers start: 2 outliers final: 0 residues processed: 672 average time/residue: 0.1225 time to fit residues: 124.7198 Evaluate side-chains 601 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 601 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 129 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 122 optimal weight: 0.0050 chunk 115 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 157 optimal weight: 30.0000 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN A 150 GLN A 242 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 232 ASN B 387 GLN B 588 GLN B 645 GLN B 646 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 80 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.134181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.092334 restraints weight = 38962.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.095763 restraints weight = 20339.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.097961 restraints weight = 12710.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099397 restraints weight = 9001.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100354 restraints weight = 6996.622| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16386 Z= 0.129 Angle : 0.576 6.843 22134 Z= 0.308 Chirality : 0.042 0.368 2360 Planarity : 0.003 0.044 2818 Dihedral : 8.708 134.689 2290 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.23 % Allowed : 1.86 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 1932 helix: 1.20 (0.16), residues: 1121 sheet: -0.01 (0.42), residues: 148 loop : 0.20 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 604 TYR 0.032 0.001 TYR D 130 PHE 0.027 0.002 PHE D 154 TRP 0.009 0.001 TRP A 9 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (16386) covalent geometry : angle 0.57568 / 0.31 (22134) hydrogen bonds : bond 0.03884 / 2.49 ( 871) hydrogen bonds : angle 4.84678 / 3.46 ( 2571) *********************** 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 703 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 699 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9576 (mm) cc_final: 0.9264 (mm) REVERT: A 54 LYS cc_start: 0.9705 (ttmm) cc_final: 0.9364 (ttmm) REVERT: A 65 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8549 (mm-30) REVERT: A 87 LYS cc_start: 0.9526 (tptt) cc_final: 0.9241 (mmmm) REVERT: A 106 LEU cc_start: 0.9511 (tp) cc_final: 0.9177 (tp) REVERT: A 107 LYS cc_start: 0.9237 (mtpp) cc_final: 0.8766 (mtpp) REVERT: A 120 ASP cc_start: 0.9265 (m-30) cc_final: 0.8913 (m-30) REVERT: A 139 GLU cc_start: 0.9419 (mm-30) cc_final: 0.9125 (mm-30) REVERT: A 142 ASN cc_start: 0.9417 (m-40) cc_final: 0.9128 (m110) REVERT: A 168 VAL cc_start: 0.9105 (t) cc_final: 0.8862 (m) REVERT: A 171 PHE cc_start: 0.9372 (m-80) cc_final: 0.9155 (m-10) REVERT: A 214 LYS cc_start: 0.9158 (mmmt) cc_final: 0.8956 (mmmt) REVERT: A 223 VAL cc_start: 0.9589 (m) cc_final: 0.9163 (p) REVERT: A 227 MET cc_start: 0.9347 (mtp) cc_final: 0.8848 (mtp) REVERT: A 251 LEU cc_start: 0.9623 (tp) cc_final: 0.9333 (tp) REVERT: A 286 ASP cc_start: 0.8698 (m-30) cc_final: 0.8396 (m-30) REVERT: A 321 GLU cc_start: 0.8622 (pp20) cc_final: 0.8371 (pp20) REVERT: A 322 MET cc_start: 0.8617 (mmp) cc_final: 0.8045 (mmm) REVERT: A 333 LYS cc_start: 0.9112 (tttt) cc_final: 0.8819 (tptp) REVERT: A 345 LYS cc_start: 0.9441 (tttt) cc_final: 0.9220 (tttt) REVERT: A 348 MET cc_start: 0.8950 (ptp) cc_final: 0.8703 (ptp) REVERT: A 349 LEU cc_start: 0.9561 (mt) cc_final: 0.9274 (mt) REVERT: A 361 GLN cc_start: 0.9073 (tp40) cc_final: 0.8092 (tp40) REVERT: A 362 ASP cc_start: 0.8100 (m-30) cc_final: 0.7325 (m-30) REVERT: A 365 ASN cc_start: 0.9215 (m110) cc_final: 0.8357 (m-40) REVERT: A 370 ASN cc_start: 0.9524 (m-40) cc_final: 0.9256 (m110) REVERT: A 405 LEU cc_start: 0.9371 (mt) cc_final: 0.9163 (mt) REVERT: A 407 ILE cc_start: 0.9423 (mt) cc_final: 0.9146 (mt) REVERT: A 441 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8335 (mt-10) REVERT: A 458 MET cc_start: 0.9232 (mmp) cc_final: 0.8765 (mmp) REVERT: A 468 LEU cc_start: 0.9564 (tp) cc_final: 0.9277 (tp) REVERT: A 479 TYR cc_start: 0.9270 (t80) cc_final: 0.8915 (t80) REVERT: A 490 THR cc_start: 0.9672 (m) cc_final: 0.9400 (p) REVERT: A 505 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8748 (mt-10) REVERT: A 570 MET cc_start: 0.9347 (mtp) cc_final: 0.8981 (mtp) REVERT: A 573 SER cc_start: 0.9304 (p) cc_final: 0.8631 (p) REVERT: A 585 SER cc_start: 0.9420 (p) cc_final: 0.8690 (t) REVERT: A 598 MET cc_start: 0.8872 (mtm) cc_final: 0.8604 (ttm) REVERT: A 615 MET cc_start: 0.9000 (mmp) cc_final: 0.8778 (mmp) REVERT: A 639 ASP cc_start: 0.9162 (m-30) cc_final: 0.8746 (m-30) REVERT: A 643 THR cc_start: 0.9599 (p) cc_final: 0.9272 (t) REVERT: A 645 GLN cc_start: 0.9267 (tp-100) cc_final: 0.8558 (tp40) REVERT: A 664 THR cc_start: 0.9269 (p) cc_final: 0.8399 (p) REVERT: A 667 LEU cc_start: 0.9521 (tt) cc_final: 0.9236 (tt) REVERT: A 668 ASN cc_start: 0.9369 (m110) cc_final: 0.8986 (m110) REVERT: A 686 ARG cc_start: 0.8620 (mmt90) cc_final: 0.8182 (mmt180) REVERT: B 58 LEU cc_start: 0.9620 (mt) cc_final: 0.9410 (mt) REVERT: B 65 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8407 (mp0) REVERT: B 87 LYS cc_start: 0.9383 (tptp) cc_final: 0.9017 (tptp) REVERT: B 104 TYR cc_start: 0.9252 (m-80) cc_final: 0.8589 (m-80) REVERT: B 147 GLN cc_start: 0.9212 (mt0) cc_final: 0.8712 (mt0) REVERT: B 149 TYR cc_start: 0.9335 (t80) cc_final: 0.8769 (t80) REVERT: B 172 LEU cc_start: 0.9433 (mp) cc_final: 0.9045 (mp) REVERT: B 174 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8099 (mm-30) REVERT: B 191 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8540 (mm-40) REVERT: B 202 ASN cc_start: 0.9541 (t0) cc_final: 0.9191 (t0) REVERT: B 221 LYS cc_start: 0.9225 (mmtp) cc_final: 0.8928 (mmtp) REVERT: B 232 ASN cc_start: 0.9084 (t160) cc_final: 0.8507 (t0) REVERT: B 235 ARG cc_start: 0.9260 (tpp80) cc_final: 0.9033 (ttm-80) REVERT: B 257 ASP cc_start: 0.8918 (m-30) cc_final: 0.8529 (m-30) REVERT: B 278 LEU cc_start: 0.9211 (tp) cc_final: 0.8964 (tp) REVERT: B 279 SER cc_start: 0.8147 (m) cc_final: 0.7558 (p) REVERT: B 286 ASP cc_start: 0.8682 (m-30) cc_final: 0.8459 (m-30) REVERT: B 290 GLU cc_start: 0.9226 (tp30) cc_final: 0.8789 (tp30) REVERT: B 333 LYS cc_start: 0.9366 (tptp) cc_final: 0.9033 (tttp) REVERT: B 348 MET cc_start: 0.9189 (ptp) cc_final: 0.8860 (ptp) REVERT: B 350 ARG cc_start: 0.7629 (mmm160) cc_final: 0.6884 (mmm160) REVERT: B 378 PHE cc_start: 0.9362 (p90) cc_final: 0.8883 (p90) REVERT: B 386 LEU cc_start: 0.9258 (mt) cc_final: 0.8977 (mt) REVERT: B 398 ASP cc_start: 0.8776 (t0) cc_final: 0.8525 (t0) REVERT: B 407 ILE cc_start: 0.9452 (mt) cc_final: 0.8997 (mt) REVERT: B 415 ASN cc_start: 0.9614 (t0) cc_final: 0.9206 (t0) REVERT: B 425 ILE cc_start: 0.9605 (mt) cc_final: 0.9387 (mt) REVERT: B 447 ASN cc_start: 0.8890 (m-40) cc_final: 0.8243 (m-40) REVERT: B 459 LYS cc_start: 0.9261 (mttp) cc_final: 0.8702 (mtmm) REVERT: B 467 ASN cc_start: 0.9338 (m-40) cc_final: 0.9055 (m-40) REVERT: B 493 MET cc_start: 0.9435 (tmm) cc_final: 0.9186 (tmm) REVERT: B 494 MET cc_start: 0.9517 (mmm) cc_final: 0.9104 (mmt) REVERT: B 505 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8349 (mt-10) REVERT: B 550 MET cc_start: 0.7993 (mtp) cc_final: 0.7762 (mtm) REVERT: B 588 GLN cc_start: 0.9523 (mm-40) cc_final: 0.9062 (mm-40) REVERT: B 599 GLU cc_start: 0.8784 (pt0) cc_final: 0.8500 (pt0) REVERT: B 601 ILE cc_start: 0.9562 (mm) cc_final: 0.9327 (mm) REVERT: B 604 ARG cc_start: 0.9333 (tpp80) cc_final: 0.8843 (ttm-80) REVERT: B 628 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8336 (mm-30) REVERT: B 632 MET cc_start: 0.8754 (mtp) cc_final: 0.7928 (mtp) REVERT: B 646 GLN cc_start: 0.9504 (pt0) cc_final: 0.8821 (pm20) REVERT: B 650 GLN cc_start: 0.8112 (mt0) cc_final: 0.7863 (mt0) REVERT: B 667 LEU cc_start: 0.9413 (tp) cc_final: 0.9150 (tp) REVERT: C 16 ASP cc_start: 0.6436 (p0) cc_final: 0.5839 (p0) REVERT: C 179 TYR cc_start: 0.8791 (t80) cc_final: 0.8487 (t80) REVERT: C 278 GLU cc_start: 0.8029 (pm20) cc_final: 0.7825 (pm20) REVERT: D 46 TYR cc_start: 0.8213 (m-80) cc_final: 0.7789 (m-10) REVERT: D 56 MET cc_start: 0.6969 (mmp) cc_final: 0.6430 (mmm) REVERT: D 59 LEU cc_start: 0.7871 (mt) cc_final: 0.7280 (pp) REVERT: D 112 LEU cc_start: 0.5875 (mm) cc_final: 0.5618 (mm) REVERT: D 137 MET cc_start: 0.5617 (mmm) cc_final: 0.5389 (mpp) REVERT: D 154 PHE cc_start: 0.4614 (m-10) cc_final: 0.4272 (m-80) REVERT: D 158 VAL cc_start: 0.8120 (t) cc_final: 0.6992 (m) REVERT: D 162 TYR cc_start: 0.8211 (m-10) cc_final: 0.8007 (m-80) REVERT: D 178 PHE cc_start: 0.9062 (m-80) cc_final: 0.8531 (m-80) REVERT: D 233 ASN cc_start: 0.8800 (m110) cc_final: 0.8296 (m-40) REVERT: D 252 LEU cc_start: 0.8867 (mt) cc_final: 0.8497 (mp) outliers start: 4 outliers final: 1 residues processed: 699 average time/residue: 0.1232 time to fit residues: 129.9842 Evaluate side-chains 626 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 625 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN A 242 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN B 19 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN B 387 GLN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.090792 restraints weight = 40057.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.094194 restraints weight = 20913.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.096372 restraints weight = 12991.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.097826 restraints weight = 9235.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.098770 restraints weight = 7219.859| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 16386 Z= 0.205 Angle : 0.620 10.178 22134 Z= 0.330 Chirality : 0.043 0.363 2360 Planarity : 0.004 0.039 2818 Dihedral : 8.730 136.421 2290 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.06 % Allowed : 1.81 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1932 helix: 1.13 (0.15), residues: 1129 sheet: -0.24 (0.42), residues: 152 loop : 0.04 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 274 TYR 0.032 0.002 TYR B 612 PHE 0.030 0.002 PHE C 178 TRP 0.019 0.002 TRP C 44 HIS 0.006 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (16386) covalent geometry : angle 0.62025 / 0.33 (22134) hydrogen bonds : bond 0.03965 / 2.52 ( 871) hydrogen bonds : angle 4.90598 / 3.51 ( 2571) *********************** 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 669 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 668 time to evaluate : 0.691 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9611 (mm) cc_final: 0.9274 (mm) REVERT: A 54 LYS cc_start: 0.9730 (ttmm) cc_final: 0.9392 (ttmm) REVERT: A 107 LYS cc_start: 0.9274 (mtpp) cc_final: 0.8794 (mtpp) REVERT: A 120 ASP cc_start: 0.9152 (m-30) cc_final: 0.8877 (m-30) REVERT: A 139 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9111 (mm-30) REVERT: A 142 ASN cc_start: 0.9370 (m-40) cc_final: 0.9083 (m110) REVERT: A 147 GLN cc_start: 0.8676 (mm-40) cc_final: 0.7785 (mm-40) REVERT: A 150 GLN cc_start: 0.9390 (tp-100) cc_final: 0.9133 (tp40) REVERT: A 223 VAL cc_start: 0.9630 (m) cc_final: 0.9174 (p) REVERT: A 227 MET cc_start: 0.9375 (mtp) cc_final: 0.8909 (mtp) REVERT: A 228 LYS cc_start: 0.9564 (mmmm) cc_final: 0.9143 (mmmt) REVERT: A 251 LEU cc_start: 0.9680 (tp) cc_final: 0.9366 (tp) REVERT: A 286 ASP cc_start: 0.8709 (m-30) cc_final: 0.8375 (m-30) REVERT: A 321 GLU cc_start: 0.8675 (pp20) cc_final: 0.8242 (pp20) REVERT: A 322 MET cc_start: 0.8644 (mmp) cc_final: 0.8061 (mmm) REVERT: A 348 MET cc_start: 0.9054 (ptp) cc_final: 0.8807 (ptp) REVERT: A 349 LEU cc_start: 0.9606 (mt) cc_final: 0.9305 (mt) REVERT: A 361 GLN cc_start: 0.9197 (tp40) cc_final: 0.8271 (tp40) REVERT: A 362 ASP cc_start: 0.8185 (m-30) cc_final: 0.7390 (m-30) REVERT: A 365 ASN cc_start: 0.9271 (m110) cc_final: 0.8386 (m-40) REVERT: A 405 LEU cc_start: 0.9310 (mt) cc_final: 0.9058 (mt) REVERT: A 407 ILE cc_start: 0.9439 (mt) cc_final: 0.9162 (mt) REVERT: A 421 GLU cc_start: 0.8515 (pp20) cc_final: 0.8256 (pp20) REVERT: A 441 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8620 (mt-10) REVERT: A 479 TYR cc_start: 0.9448 (t80) cc_final: 0.9143 (t80) REVERT: A 505 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8835 (mt-10) REVERT: A 506 ILE cc_start: 0.9732 (mt) cc_final: 0.9458 (mm) REVERT: A 570 MET cc_start: 0.9183 (mtp) cc_final: 0.8868 (mtp) REVERT: A 573 SER cc_start: 0.9244 (p) cc_final: 0.8713 (p) REVERT: A 632 MET cc_start: 0.8814 (mtp) cc_final: 0.8506 (mtp) REVERT: A 636 LYS cc_start: 0.9632 (mmmm) cc_final: 0.8891 (mmmm) REVERT: A 639 ASP cc_start: 0.9123 (m-30) cc_final: 0.8793 (m-30) REVERT: A 643 THR cc_start: 0.9557 (p) cc_final: 0.9324 (t) REVERT: A 646 GLN cc_start: 0.9133 (pt0) cc_final: 0.8910 (pt0) REVERT: A 664 THR cc_start: 0.9356 (p) cc_final: 0.8552 (p) REVERT: A 667 LEU cc_start: 0.9542 (tt) cc_final: 0.9247 (tt) REVERT: A 668 ASN cc_start: 0.9378 (m110) cc_final: 0.8964 (m110) REVERT: A 686 ARG cc_start: 0.8623 (mmt90) cc_final: 0.8305 (mmt180) REVERT: B 58 LEU cc_start: 0.9687 (mt) cc_final: 0.9470 (mt) REVERT: B 65 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8418 (mp0) REVERT: B 82 LYS cc_start: 0.9313 (mtmt) cc_final: 0.8789 (ptpp) REVERT: B 87 LYS cc_start: 0.9398 (tptp) cc_final: 0.9070 (tptp) REVERT: B 95 MET cc_start: 0.9598 (tpt) cc_final: 0.9355 (tpp) REVERT: B 116 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8780 (mt-10) REVERT: B 117 ARG cc_start: 0.8893 (mtt180) cc_final: 0.8578 (ttm110) REVERT: B 120 ASP cc_start: 0.8906 (m-30) cc_final: 0.8651 (m-30) REVERT: B 147 GLN cc_start: 0.9256 (mt0) cc_final: 0.8955 (mt0) REVERT: B 149 TYR cc_start: 0.9404 (t80) cc_final: 0.8770 (t80) REVERT: B 172 LEU cc_start: 0.9401 (mp) cc_final: 0.8971 (mp) REVERT: B 191 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8532 (mm-40) REVERT: B 202 ASN cc_start: 0.9479 (t0) cc_final: 0.9258 (t0) REVERT: B 232 ASN cc_start: 0.9031 (t0) cc_final: 0.8494 (t0) REVERT: B 257 ASP cc_start: 0.8888 (m-30) cc_final: 0.8592 (m-30) REVERT: B 278 LEU cc_start: 0.9278 (tp) cc_final: 0.8998 (tp) REVERT: B 279 SER cc_start: 0.8259 (m) cc_final: 0.7814 (p) REVERT: B 286 ASP cc_start: 0.8652 (m-30) cc_final: 0.8451 (m-30) REVERT: B 290 GLU cc_start: 0.9264 (tp30) cc_final: 0.8916 (tp30) REVERT: B 333 LYS cc_start: 0.9392 (tptp) cc_final: 0.9075 (tttp) REVERT: B 348 MET cc_start: 0.9088 (ptp) cc_final: 0.8865 (ptp) REVERT: B 398 ASP cc_start: 0.8779 (t0) cc_final: 0.8510 (t0) REVERT: B 407 ILE cc_start: 0.9519 (mt) cc_final: 0.9044 (mt) REVERT: B 415 ASN cc_start: 0.9593 (t0) cc_final: 0.9222 (t0) REVERT: B 447 ASN cc_start: 0.8966 (m-40) cc_final: 0.8291 (m-40) REVERT: B 458 MET cc_start: 0.9263 (mmp) cc_final: 0.8844 (mmp) REVERT: B 459 LYS cc_start: 0.9307 (mttp) cc_final: 0.8793 (mtmm) REVERT: B 485 ARG cc_start: 0.9264 (mtm180) cc_final: 0.8857 (mtm-85) REVERT: B 493 MET cc_start: 0.9407 (tmm) cc_final: 0.9104 (tmm) REVERT: B 501 GLN cc_start: 0.9204 (tt0) cc_final: 0.8843 (tt0) REVERT: B 505 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8240 (mt-10) REVERT: B 550 MET cc_start: 0.7960 (mtp) cc_final: 0.7730 (mtt) REVERT: B 588 GLN cc_start: 0.9480 (mm-40) cc_final: 0.9257 (mm-40) REVERT: B 595 MET cc_start: 0.9274 (mmm) cc_final: 0.9064 (mmm) REVERT: B 599 GLU cc_start: 0.8773 (pt0) cc_final: 0.8546 (pt0) REVERT: B 604 ARG cc_start: 0.9344 (tpp80) cc_final: 0.8973 (ttm-80) REVERT: B 628 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8414 (mm-30) REVERT: B 640 MET cc_start: 0.9188 (tpp) cc_final: 0.8986 (tpp) REVERT: B 646 GLN cc_start: 0.9452 (pt0) cc_final: 0.9213 (pt0) REVERT: B 650 GLN cc_start: 0.8120 (mt0) cc_final: 0.7795 (mt0) REVERT: B 667 LEU cc_start: 0.9397 (tp) cc_final: 0.9035 (tp) REVERT: C 16 ASP cc_start: 0.6114 (p0) cc_final: 0.5585 (p0) REVERT: C 42 LEU cc_start: 0.8787 (pt) cc_final: 0.8519 (pt) REVERT: C 179 TYR cc_start: 0.8815 (t80) cc_final: 0.8498 (t80) REVERT: C 278 GLU cc_start: 0.7867 (pm20) cc_final: 0.7638 (pm20) REVERT: D 162 TYR cc_start: 0.8293 (m-10) cc_final: 0.8012 (m-80) REVERT: D 176 LEU cc_start: 0.9531 (mt) cc_final: 0.9247 (pp) REVERT: D 178 PHE cc_start: 0.9076 (m-80) cc_final: 0.8561 (m-80) REVERT: D 233 ASN cc_start: 0.8775 (m110) cc_final: 0.8283 (m-40) REVERT: D 269 MET cc_start: 0.6399 (tmm) cc_final: 0.6133 (tmm) outliers start: 1 outliers final: 0 residues processed: 668 average time/residue: 0.1237 time to fit residues: 123.8913 Evaluate side-chains 594 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 594 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN A 44 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN B 645 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.132234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.091419 restraints weight = 40182.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.094650 restraints weight = 21505.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.096814 restraints weight = 13510.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.098254 restraints weight = 9618.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099174 restraints weight = 7492.919| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.6807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 16386 Z= 0.236 Angle : 0.651 10.338 22134 Z= 0.346 Chirality : 0.044 0.217 2360 Planarity : 0.004 0.041 2818 Dihedral : 8.823 137.962 2290 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1932 helix: 0.95 (0.15), residues: 1140 sheet: -0.35 (0.41), residues: 144 loop : -0.08 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 274 TYR 0.036 0.002 TYR A 683 PHE 0.023 0.002 PHE D 109 TRP 0.012 0.002 TRP A 623 HIS 0.007 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.24 (16386) covalent geometry : angle 0.65140 / 0.35 (22134) hydrogen bonds : bond 0.04073 / 2.63 ( 871) hydrogen bonds : angle 5.03243 / 3.61 ( 2571) *********************** 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 663 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 663 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.9735 (mp) cc_final: 0.9141 (mt) REVERT: A 54 LYS cc_start: 0.9741 (ttmm) cc_final: 0.9384 (ttmm) REVERT: A 65 GLU cc_start: 0.8827 (mm-30) cc_final: 0.7989 (mp0) REVERT: A 107 LYS cc_start: 0.9279 (mtpp) cc_final: 0.8817 (mtpp) REVERT: A 120 ASP cc_start: 0.9199 (m-30) cc_final: 0.8903 (m-30) REVERT: A 139 GLU cc_start: 0.9388 (mm-30) cc_final: 0.9093 (mm-30) REVERT: A 142 ASN cc_start: 0.9381 (m-40) cc_final: 0.9091 (m110) REVERT: A 150 GLN cc_start: 0.9446 (tp-100) cc_final: 0.9123 (tp40) REVERT: A 214 LYS cc_start: 0.9462 (mmmt) cc_final: 0.9185 (mmmt) REVERT: A 223 VAL cc_start: 0.9595 (m) cc_final: 0.9181 (p) REVERT: A 227 MET cc_start: 0.9368 (mtp) cc_final: 0.8921 (mtp) REVERT: A 251 LEU cc_start: 0.9671 (tp) cc_final: 0.9364 (tp) REVERT: A 254 PHE cc_start: 0.8897 (m-10) cc_final: 0.8695 (m-10) REVERT: A 286 ASP cc_start: 0.8683 (m-30) cc_final: 0.8374 (m-30) REVERT: A 301 PHE cc_start: 0.9361 (m-80) cc_final: 0.9055 (m-10) REVERT: A 321 GLU cc_start: 0.8621 (pp20) cc_final: 0.8214 (pp20) REVERT: A 322 MET cc_start: 0.8730 (mmp) cc_final: 0.8065 (mmm) REVERT: A 333 LYS cc_start: 0.9201 (tttt) cc_final: 0.8992 (tptm) REVERT: A 349 LEU cc_start: 0.9596 (mt) cc_final: 0.9280 (mt) REVERT: A 361 GLN cc_start: 0.9293 (tp40) cc_final: 0.8428 (tp40) REVERT: A 362 ASP cc_start: 0.8350 (m-30) cc_final: 0.7512 (m-30) REVERT: A 365 ASN cc_start: 0.9318 (m110) cc_final: 0.8500 (m-40) REVERT: A 387 GLN cc_start: 0.9162 (mt0) cc_final: 0.8888 (mt0) REVERT: A 407 ILE cc_start: 0.9412 (mt) cc_final: 0.9143 (mt) REVERT: A 421 GLU cc_start: 0.8454 (pp20) cc_final: 0.8173 (pp20) REVERT: A 441 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8671 (mt-10) REVERT: A 458 MET cc_start: 0.9354 (mmm) cc_final: 0.8618 (mmm) REVERT: A 479 TYR cc_start: 0.9457 (t80) cc_final: 0.9249 (t80) REVERT: A 505 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8851 (mt-10) REVERT: A 570 MET cc_start: 0.9192 (mtp) cc_final: 0.8818 (mtp) REVERT: A 599 GLU cc_start: 0.8271 (mp0) cc_final: 0.7987 (mp0) REVERT: A 615 MET cc_start: 0.9011 (mmp) cc_final: 0.8768 (mmp) REVERT: A 632 MET cc_start: 0.8829 (mtp) cc_final: 0.8552 (mtp) REVERT: A 636 LYS cc_start: 0.9618 (mmmm) cc_final: 0.8979 (mmmm) REVERT: A 639 ASP cc_start: 0.9166 (m-30) cc_final: 0.8874 (m-30) REVERT: A 643 THR cc_start: 0.9592 (p) cc_final: 0.9300 (t) REVERT: A 646 GLN cc_start: 0.9163 (pt0) cc_final: 0.8901 (pt0) REVERT: A 650 GLN cc_start: 0.8655 (mt0) cc_final: 0.8385 (mt0) REVERT: A 667 LEU cc_start: 0.9584 (tt) cc_final: 0.9329 (tt) REVERT: A 668 ASN cc_start: 0.9445 (m110) cc_final: 0.9129 (m110) REVERT: B 58 LEU cc_start: 0.9703 (mt) cc_final: 0.9450 (mt) REVERT: B 87 LYS cc_start: 0.9432 (tptp) cc_final: 0.9106 (tptp) REVERT: B 95 MET cc_start: 0.9571 (tpt) cc_final: 0.9322 (tpp) REVERT: B 116 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8915 (mp0) REVERT: B 117 ARG cc_start: 0.8942 (mtt180) cc_final: 0.8610 (ttm110) REVERT: B 120 ASP cc_start: 0.8975 (m-30) cc_final: 0.8717 (m-30) REVERT: B 147 GLN cc_start: 0.9274 (mt0) cc_final: 0.8886 (mt0) REVERT: B 149 TYR cc_start: 0.9440 (t80) cc_final: 0.8821 (t80) REVERT: B 172 LEU cc_start: 0.9433 (mp) cc_final: 0.8966 (mp) REVERT: B 191 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8638 (mm-40) REVERT: B 227 MET cc_start: 0.9417 (mtp) cc_final: 0.9122 (mtp) REVERT: B 232 ASN cc_start: 0.9057 (t0) cc_final: 0.8541 (t0) REVERT: B 238 ASP cc_start: 0.8452 (p0) cc_final: 0.7984 (p0) REVERT: B 257 ASP cc_start: 0.8821 (m-30) cc_final: 0.8558 (m-30) REVERT: B 278 LEU cc_start: 0.9300 (tp) cc_final: 0.9076 (tp) REVERT: B 279 SER cc_start: 0.8320 (m) cc_final: 0.7874 (p) REVERT: B 290 GLU cc_start: 0.9242 (tp30) cc_final: 0.8767 (tp30) REVERT: B 291 LEU cc_start: 0.9763 (mm) cc_final: 0.9491 (mm) REVERT: B 333 LYS cc_start: 0.9346 (tptp) cc_final: 0.9068 (tttp) REVERT: B 384 GLU cc_start: 0.8708 (pm20) cc_final: 0.7992 (pm20) REVERT: B 398 ASP cc_start: 0.8866 (t0) cc_final: 0.8642 (t0) REVERT: B 407 ILE cc_start: 0.9517 (mt) cc_final: 0.9041 (mt) REVERT: B 413 SER cc_start: 0.9551 (m) cc_final: 0.9079 (t) REVERT: B 414 LEU cc_start: 0.9694 (mt) cc_final: 0.9489 (mt) REVERT: B 415 ASN cc_start: 0.9579 (t0) cc_final: 0.9208 (t0) REVERT: B 458 MET cc_start: 0.9268 (mmp) cc_final: 0.8868 (mmp) REVERT: B 459 LYS cc_start: 0.9337 (mttp) cc_final: 0.8900 (mtmm) REVERT: B 485 ARG cc_start: 0.9307 (mtm180) cc_final: 0.9002 (mtm-85) REVERT: B 493 MET cc_start: 0.9395 (tmm) cc_final: 0.9116 (tmm) REVERT: B 501 GLN cc_start: 0.9261 (tt0) cc_final: 0.8865 (tt0) REVERT: B 505 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8376 (mt-10) REVERT: B 588 GLN cc_start: 0.9430 (mm-40) cc_final: 0.9155 (mm-40) REVERT: B 599 GLU cc_start: 0.8790 (pt0) cc_final: 0.8455 (pt0) REVERT: B 601 ILE cc_start: 0.9416 (mm) cc_final: 0.9214 (mm) REVERT: B 604 ARG cc_start: 0.9219 (tpp80) cc_final: 0.9019 (ttm-80) REVERT: B 628 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8302 (mm-30) REVERT: B 646 GLN cc_start: 0.9478 (pt0) cc_final: 0.9255 (pt0) REVERT: C 16 ASP cc_start: 0.6128 (p0) cc_final: 0.5618 (p0) REVERT: C 179 TYR cc_start: 0.8892 (t80) cc_final: 0.8597 (t80) REVERT: C 214 ASN cc_start: 0.8542 (p0) cc_final: 0.7846 (p0) REVERT: D 59 LEU cc_start: 0.7615 (mt) cc_final: 0.7258 (pp) REVERT: D 105 TYR cc_start: 0.7899 (m-80) cc_final: 0.7629 (m-80) REVERT: D 172 PHE cc_start: 0.8350 (m-80) cc_final: 0.8142 (m-80) REVERT: D 176 LEU cc_start: 0.9536 (mt) cc_final: 0.9270 (pp) REVERT: D 178 PHE cc_start: 0.9039 (m-80) cc_final: 0.8460 (m-80) REVERT: D 208 LEU cc_start: 0.8966 (mt) cc_final: 0.8709 (mt) REVERT: D 233 ASN cc_start: 0.8594 (m110) cc_final: 0.8016 (m110) REVERT: D 321 TYR cc_start: 0.9243 (m-80) cc_final: 0.8712 (m-80) outliers start: 0 outliers final: 0 residues processed: 663 average time/residue: 0.1207 time to fit residues: 121.4942 Evaluate side-chains 593 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 593 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 158 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN B 645 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.129802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.089147 restraints weight = 40318.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.092415 restraints weight = 21340.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.094536 restraints weight = 13443.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.095917 restraints weight = 9636.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.096884 restraints weight = 7547.777| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.7089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 16386 Z= 0.241 Angle : 0.676 10.371 22134 Z= 0.357 Chirality : 0.045 0.239 2360 Planarity : 0.004 0.044 2818 Dihedral : 8.775 138.505 2290 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.06 % Allowed : 0.99 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.19), residues: 1932 helix: 0.89 (0.15), residues: 1140 sheet: -0.50 (0.41), residues: 148 loop : -0.19 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 196 TYR 0.025 0.002 TYR B 612 PHE 0.027 0.002 PHE A 360 TRP 0.012 0.002 TRP A 623 HIS 0.006 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.24 (16386) covalent geometry : angle 0.67602 / 0.36 (22134) hydrogen bonds : bond 0.04160 / 2.67 ( 871) hydrogen bonds : angle 5.04973 / 3.62 ( 2571) *********************** 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 664 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 663 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.9711 (ttmm) cc_final: 0.9361 (ttmm) REVERT: A 65 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8230 (mp0) REVERT: A 106 LEU cc_start: 0.9618 (tp) cc_final: 0.9272 (tp) REVERT: A 107 LYS cc_start: 0.9294 (mtpp) cc_final: 0.8837 (mtpp) REVERT: A 116 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8675 (mt-10) REVERT: A 120 ASP cc_start: 0.9204 (m-30) cc_final: 0.8886 (m-30) REVERT: A 139 GLU cc_start: 0.9370 (mm-30) cc_final: 0.9090 (mm-30) REVERT: A 142 ASN cc_start: 0.9382 (m-40) cc_final: 0.9089 (m110) REVERT: A 150 GLN cc_start: 0.9494 (tp-100) cc_final: 0.9287 (tp40) REVERT: A 214 LYS cc_start: 0.9519 (mmmt) cc_final: 0.9295 (mmmm) REVERT: A 223 VAL cc_start: 0.9601 (m) cc_final: 0.9179 (p) REVERT: A 227 MET cc_start: 0.9347 (mtp) cc_final: 0.8902 (mtp) REVERT: A 235 ARG cc_start: 0.8601 (ttm110) cc_final: 0.8188 (ttm110) REVERT: A 251 LEU cc_start: 0.9678 (tp) cc_final: 0.9395 (tp) REVERT: A 271 GLU cc_start: 0.9213 (mp0) cc_final: 0.8814 (mp0) REVERT: A 286 ASP cc_start: 0.8672 (m-30) cc_final: 0.8330 (m-30) REVERT: A 322 MET cc_start: 0.8751 (mmp) cc_final: 0.8357 (mmm) REVERT: A 349 LEU cc_start: 0.9603 (mt) cc_final: 0.9259 (mt) REVERT: A 361 GLN cc_start: 0.9283 (tp40) cc_final: 0.8425 (tp40) REVERT: A 362 ASP cc_start: 0.8340 (m-30) cc_final: 0.7478 (m-30) REVERT: A 365 ASN cc_start: 0.9354 (m110) cc_final: 0.8539 (m-40) REVERT: A 387 GLN cc_start: 0.9179 (mt0) cc_final: 0.8895 (mt0) REVERT: A 405 LEU cc_start: 0.9215 (mt) cc_final: 0.8987 (mt) REVERT: A 407 ILE cc_start: 0.9403 (mt) cc_final: 0.9131 (mt) REVERT: A 421 GLU cc_start: 0.8436 (pp20) cc_final: 0.8181 (pp20) REVERT: A 437 THR cc_start: 0.9686 (m) cc_final: 0.9468 (m) REVERT: A 441 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8620 (mt-10) REVERT: A 458 MET cc_start: 0.9335 (mmm) cc_final: 0.8664 (mmm) REVERT: A 505 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8676 (mt-10) REVERT: A 570 MET cc_start: 0.9174 (mtp) cc_final: 0.8752 (mtp) REVERT: A 615 MET cc_start: 0.8999 (mmp) cc_final: 0.8770 (mmp) REVERT: A 632 MET cc_start: 0.8807 (mtp) cc_final: 0.8467 (mtp) REVERT: A 636 LYS cc_start: 0.9593 (mmmm) cc_final: 0.8901 (mmmm) REVERT: A 639 ASP cc_start: 0.9165 (m-30) cc_final: 0.8779 (m-30) REVERT: A 643 THR cc_start: 0.9610 (p) cc_final: 0.9318 (t) REVERT: A 650 GLN cc_start: 0.8646 (mt0) cc_final: 0.8387 (mt0) REVERT: A 667 LEU cc_start: 0.9587 (tt) cc_final: 0.9336 (tt) REVERT: A 668 ASN cc_start: 0.9477 (m110) cc_final: 0.9143 (m110) REVERT: B 67 GLU cc_start: 0.9269 (mp0) cc_final: 0.9051 (pm20) REVERT: B 87 LYS cc_start: 0.9459 (tptp) cc_final: 0.9142 (tptp) REVERT: B 95 MET cc_start: 0.9578 (tpt) cc_final: 0.9292 (tpp) REVERT: B 117 ARG cc_start: 0.8973 (mtt180) cc_final: 0.8685 (ttm110) REVERT: B 120 ASP cc_start: 0.8977 (m-30) cc_final: 0.8721 (m-30) REVERT: B 147 GLN cc_start: 0.9328 (mt0) cc_final: 0.8879 (mt0) REVERT: B 149 TYR cc_start: 0.9461 (t80) cc_final: 0.8876 (t80) REVERT: B 172 LEU cc_start: 0.9439 (mp) cc_final: 0.8976 (mp) REVERT: B 174 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7936 (mm-30) REVERT: B 191 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8663 (mm-40) REVERT: B 227 MET cc_start: 0.9389 (mtp) cc_final: 0.9080 (mtp) REVERT: B 232 ASN cc_start: 0.9099 (t0) cc_final: 0.8538 (t0) REVERT: B 238 ASP cc_start: 0.8548 (p0) cc_final: 0.8123 (p0) REVERT: B 257 ASP cc_start: 0.8754 (m-30) cc_final: 0.8516 (m-30) REVERT: B 278 LEU cc_start: 0.9315 (tp) cc_final: 0.9092 (tp) REVERT: B 279 SER cc_start: 0.8335 (m) cc_final: 0.7851 (p) REVERT: B 290 GLU cc_start: 0.9248 (tp30) cc_final: 0.8769 (tp30) REVERT: B 333 LYS cc_start: 0.9325 (tptp) cc_final: 0.8992 (tttm) REVERT: B 348 MET cc_start: 0.9109 (ptp) cc_final: 0.8864 (ptp) REVERT: B 384 GLU cc_start: 0.8757 (pm20) cc_final: 0.7860 (pm20) REVERT: B 398 ASP cc_start: 0.8887 (t0) cc_final: 0.8679 (t0) REVERT: B 407 ILE cc_start: 0.9521 (mt) cc_final: 0.9005 (mt) REVERT: B 413 SER cc_start: 0.9563 (m) cc_final: 0.9126 (t) REVERT: B 414 LEU cc_start: 0.9711 (mt) cc_final: 0.9469 (mt) REVERT: B 415 ASN cc_start: 0.9586 (t0) cc_final: 0.9271 (t0) REVERT: B 458 MET cc_start: 0.9264 (mmp) cc_final: 0.8861 (mmp) REVERT: B 459 LYS cc_start: 0.9335 (mttp) cc_final: 0.8821 (mtmm) REVERT: B 493 MET cc_start: 0.9367 (tmm) cc_final: 0.9117 (tmm) REVERT: B 494 MET cc_start: 0.9497 (mmm) cc_final: 0.9149 (mmt) REVERT: B 501 GLN cc_start: 0.9241 (tt0) cc_final: 0.8938 (tt0) REVERT: B 505 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8097 (mt-10) REVERT: B 588 GLN cc_start: 0.9456 (mm-40) cc_final: 0.9193 (mm-40) REVERT: B 628 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8492 (mm-30) REVERT: B 646 GLN cc_start: 0.9490 (pt0) cc_final: 0.9280 (pt0) REVERT: C 16 ASP cc_start: 0.5964 (p0) cc_final: 0.5518 (p0) REVERT: C 42 LEU cc_start: 0.8712 (pt) cc_final: 0.8494 (pt) REVERT: C 179 TYR cc_start: 0.8951 (t80) cc_final: 0.8657 (t80) REVERT: C 278 GLU cc_start: 0.7443 (pm20) cc_final: 0.7215 (pm20) REVERT: D 56 MET cc_start: 0.5910 (mmm) cc_final: 0.5534 (ttt) REVERT: D 59 LEU cc_start: 0.7679 (mt) cc_final: 0.7321 (pp) REVERT: D 105 TYR cc_start: 0.7908 (m-80) cc_final: 0.7604 (m-80) REVERT: D 158 VAL cc_start: 0.8572 (t) cc_final: 0.7428 (m) REVERT: D 178 PHE cc_start: 0.9073 (m-80) cc_final: 0.8523 (m-80) REVERT: D 233 ASN cc_start: 0.8676 (m110) cc_final: 0.8253 (m110) REVERT: D 269 MET cc_start: 0.7167 (tmm) cc_final: 0.6824 (ppp) REVERT: D 285 ILE cc_start: 0.7709 (mm) cc_final: 0.7503 (mm) REVERT: D 321 TYR cc_start: 0.9257 (m-80) cc_final: 0.8772 (m-80) outliers start: 1 outliers final: 0 residues processed: 663 average time/residue: 0.1198 time to fit residues: 119.5992 Evaluate side-chains 588 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 588 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 149 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 114 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN B 645 GLN ** C 98 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 = 0.3697 r_free = 0.3697 target = 0.135912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.094396 restraints weight = 39566.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.097770 restraints weight = 20823.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.099966 restraints weight = 13097.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.101440 restraints weight = 9335.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.102376 restraints weight = 7268.582| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.7261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16386 Z= 0.136 Angle : 0.639 7.448 22134 Z= 0.339 Chirality : 0.043 0.204 2360 Planarity : 0.004 0.039 2818 Dihedral : 8.399 137.832 2290 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.06 % Allowed : 0.70 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 1932 helix: 0.97 (0.15), residues: 1128 sheet: -0.50 (0.42), residues: 148 loop : -0.11 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 196 TYR 0.054 0.002 TYR D 162 PHE 0.031 0.002 PHE D 172 TRP 0.058 0.002 TRP D 124 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (16386) covalent geometry : angle 0.63886 / 0.34 (22134) hydrogen bonds : bond 0.03982 / 2.56 ( 871) hydrogen bonds : angle 5.03470 / 3.62 ( 2571) *********************** 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 667 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 666 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.9279 (tt0) cc_final: 0.9069 (tt0) REVERT: A 31 GLU cc_start: 0.9247 (tp30) cc_final: 0.8749 (tp30) REVERT: A 54 LYS cc_start: 0.9725 (ttmm) cc_final: 0.9400 (ttmm) REVERT: A 65 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8087 (mp0) REVERT: A 99 LYS cc_start: 0.9408 (mmmt) cc_final: 0.9199 (mmmm) REVERT: A 107 LYS cc_start: 0.9285 (mtpp) cc_final: 0.8837 (mtpp) REVERT: A 116 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8698 (mt-10) REVERT: A 120 ASP cc_start: 0.9033 (m-30) cc_final: 0.8764 (m-30) REVERT: A 139 GLU cc_start: 0.9410 (mm-30) cc_final: 0.9074 (mm-30) REVERT: A 142 ASN cc_start: 0.9359 (m-40) cc_final: 0.9044 (m110) REVERT: A 150 GLN cc_start: 0.9478 (tp-100) cc_final: 0.9156 (tp40) REVERT: A 214 LYS cc_start: 0.9444 (mmmt) cc_final: 0.9190 (mmmm) REVERT: A 223 VAL cc_start: 0.9551 (m) cc_final: 0.9137 (p) REVERT: A 227 MET cc_start: 0.9364 (mtp) cc_final: 0.8912 (mtp) REVERT: A 235 ARG cc_start: 0.8634 (ttm110) cc_final: 0.8124 (ttm110) REVERT: A 251 LEU cc_start: 0.9620 (tp) cc_final: 0.9335 (tp) REVERT: A 279 SER cc_start: 0.8970 (m) cc_final: 0.8340 (t) REVERT: A 286 ASP cc_start: 0.8646 (m-30) cc_final: 0.8354 (m-30) REVERT: A 301 PHE cc_start: 0.9363 (m-80) cc_final: 0.9159 (m-10) REVERT: A 322 MET cc_start: 0.8768 (mmp) cc_final: 0.8333 (mmm) REVERT: A 333 LYS cc_start: 0.9543 (ttmt) cc_final: 0.9214 (ttmm) REVERT: A 349 LEU cc_start: 0.9560 (mt) cc_final: 0.9277 (mt) REVERT: A 361 GLN cc_start: 0.9262 (tp40) cc_final: 0.8900 (tp40) REVERT: A 362 ASP cc_start: 0.8364 (m-30) cc_final: 0.7613 (m-30) REVERT: A 365 ASN cc_start: 0.9239 (m110) cc_final: 0.8933 (m110) REVERT: A 387 GLN cc_start: 0.9123 (mt0) cc_final: 0.8835 (mt0) REVERT: A 407 ILE cc_start: 0.9429 (mt) cc_final: 0.9178 (mt) REVERT: A 417 LEU cc_start: 0.9626 (tt) cc_final: 0.9316 (tt) REVERT: A 421 GLU cc_start: 0.8355 (pp20) cc_final: 0.8062 (pp20) REVERT: A 431 LEU cc_start: 0.9225 (mm) cc_final: 0.9008 (mm) REVERT: A 437 THR cc_start: 0.9639 (m) cc_final: 0.9387 (m) REVERT: A 441 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8571 (mt-10) REVERT: A 458 MET cc_start: 0.9200 (mmm) cc_final: 0.8587 (mmm) REVERT: A 505 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8856 (mt-10) REVERT: A 570 MET cc_start: 0.9184 (mtp) cc_final: 0.8779 (mtp) REVERT: A 599 GLU cc_start: 0.8480 (mp0) cc_final: 0.7917 (mp0) REVERT: A 615 MET cc_start: 0.8992 (mmp) cc_final: 0.8747 (mmp) REVERT: A 632 MET cc_start: 0.8817 (mtp) cc_final: 0.8543 (mtp) REVERT: A 636 LYS cc_start: 0.9551 (mmmm) cc_final: 0.8918 (mmmm) REVERT: A 639 ASP cc_start: 0.9158 (m-30) cc_final: 0.8716 (m-30) REVERT: A 643 THR cc_start: 0.9493 (p) cc_final: 0.9259 (t) REVERT: A 645 GLN cc_start: 0.9388 (tp40) cc_final: 0.9034 (tp-100) REVERT: A 650 GLN cc_start: 0.8639 (mt0) cc_final: 0.8206 (mt0) REVERT: A 667 LEU cc_start: 0.9560 (tt) cc_final: 0.9248 (tt) REVERT: A 668 ASN cc_start: 0.9393 (m110) cc_final: 0.9157 (m110) REVERT: B 67 GLU cc_start: 0.9277 (mp0) cc_final: 0.9077 (pm20) REVERT: B 79 GLU cc_start: 0.8992 (mp0) cc_final: 0.8552 (mp0) REVERT: B 82 LYS cc_start: 0.9436 (mtmt) cc_final: 0.9077 (ptpp) REVERT: B 87 LYS cc_start: 0.9379 (tptp) cc_final: 0.9054 (tptp) REVERT: B 117 ARG cc_start: 0.8903 (mtt180) cc_final: 0.8582 (ttm110) REVERT: B 120 ASP cc_start: 0.8888 (m-30) cc_final: 0.8680 (m-30) REVERT: B 147 GLN cc_start: 0.9270 (mt0) cc_final: 0.8868 (mt0) REVERT: B 149 TYR cc_start: 0.9482 (t80) cc_final: 0.8686 (t80) REVERT: B 172 LEU cc_start: 0.9443 (mp) cc_final: 0.8948 (mp) REVERT: B 174 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7878 (mm-30) REVERT: B 227 MET cc_start: 0.9402 (mtp) cc_final: 0.9058 (mtp) REVERT: B 232 ASN cc_start: 0.9041 (t0) cc_final: 0.8489 (t0) REVERT: B 235 ARG cc_start: 0.9261 (tpp80) cc_final: 0.9022 (ttm-80) REVERT: B 238 ASP cc_start: 0.8547 (p0) cc_final: 0.8045 (p0) REVERT: B 274 ARG cc_start: 0.7775 (mmt180) cc_final: 0.7528 (mpt180) REVERT: B 278 LEU cc_start: 0.9285 (tp) cc_final: 0.9061 (tp) REVERT: B 279 SER cc_start: 0.8082 (m) cc_final: 0.7698 (p) REVERT: B 286 ASP cc_start: 0.8742 (m-30) cc_final: 0.8532 (m-30) REVERT: B 290 GLU cc_start: 0.9274 (tp30) cc_final: 0.8720 (tp30) REVERT: B 333 LYS cc_start: 0.9372 (tptp) cc_final: 0.9157 (tttp) REVERT: B 348 MET cc_start: 0.9090 (ptp) cc_final: 0.8842 (ptp) REVERT: B 384 GLU cc_start: 0.8333 (pm20) cc_final: 0.7563 (pm20) REVERT: B 398 ASP cc_start: 0.8830 (t0) cc_final: 0.8581 (t0) REVERT: B 407 ILE cc_start: 0.9517 (mt) cc_final: 0.9042 (mt) REVERT: B 415 ASN cc_start: 0.9575 (t0) cc_final: 0.9269 (t0) REVERT: B 458 MET cc_start: 0.9292 (mmp) cc_final: 0.8836 (mmp) REVERT: B 459 LYS cc_start: 0.9340 (mttp) cc_final: 0.8927 (mtmm) REVERT: B 472 LEU cc_start: 0.9673 (mm) cc_final: 0.9468 (mm) REVERT: B 493 MET cc_start: 0.9381 (tmm) cc_final: 0.9106 (tmm) REVERT: B 494 MET cc_start: 0.9478 (mmm) cc_final: 0.9208 (mmt) REVERT: B 505 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8596 (mt-10) REVERT: B 588 GLN cc_start: 0.9417 (mm-40) cc_final: 0.8925 (mm-40) REVERT: B 595 MET cc_start: 0.9072 (mmm) cc_final: 0.8857 (mmm) REVERT: B 628 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8324 (mm-30) REVERT: B 645 GLN cc_start: 0.9352 (tp40) cc_final: 0.9071 (tp-100) REVERT: B 646 GLN cc_start: 0.9470 (pt0) cc_final: 0.9259 (pt0) REVERT: B 650 GLN cc_start: 0.7960 (mt0) cc_final: 0.7098 (mm-40) REVERT: C 153 LEU cc_start: 0.5095 (tt) cc_final: 0.4883 (mm) REVERT: C 179 TYR cc_start: 0.8880 (t80) cc_final: 0.8607 (t80) REVERT: D 38 ASN cc_start: 0.8759 (m110) cc_final: 0.8173 (t0) REVERT: D 56 MET cc_start: 0.5974 (mmm) cc_final: 0.5539 (ttt) REVERT: D 59 LEU cc_start: 0.7761 (mt) cc_final: 0.7461 (pp) REVERT: D 66 ASP cc_start: 0.7174 (t0) cc_final: 0.6374 (t70) REVERT: D 105 TYR cc_start: 0.7832 (m-80) cc_final: 0.7613 (m-80) REVERT: D 162 TYR cc_start: 0.8844 (m-80) cc_final: 0.8442 (m-80) REVERT: D 176 LEU cc_start: 0.9533 (mt) cc_final: 0.9308 (pp) REVERT: D 178 PHE cc_start: 0.9037 (m-80) cc_final: 0.8482 (m-80) REVERT: D 208 LEU cc_start: 0.8809 (mt) cc_final: 0.8399 (mt) REVERT: D 233 ASN cc_start: 0.8295 (m110) cc_final: 0.7978 (m110) REVERT: D 285 ILE cc_start: 0.7805 (mm) cc_final: 0.7599 (mm) REVERT: D 321 TYR cc_start: 0.9296 (m-80) cc_final: 0.9061 (m-80) outliers start: 1 outliers final: 0 residues processed: 666 average time/residue: 0.1197 time to fit residues: 119.7056 Evaluate side-chains 596 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 596 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 189 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 16 optimal weight: 0.0070 chunk 54 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 232 ASN B 387 GLN ** C 98 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 = 0.3723 r_free = 0.3723 target = 0.139478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.097916 restraints weight = 39510.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.101453 restraints weight = 20666.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.103655 restraints weight = 12962.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.105122 restraints weight = 9230.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.106138 restraints weight = 7218.038| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.7453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16386 Z= 0.134 Angle : 0.658 9.106 22134 Z= 0.348 Chirality : 0.044 0.214 2360 Planarity : 0.004 0.038 2818 Dihedral : 8.056 138.441 2290 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.12 % Allowed : 0.17 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.19), residues: 1932 helix: 0.87 (0.15), residues: 1156 sheet: -0.47 (0.42), residues: 148 loop : -0.20 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 196 TYR 0.042 0.002 TYR D 162 PHE 0.023 0.002 PHE C 168 TRP 0.050 0.002 TRP D 124 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (16386) covalent geometry : angle 0.65848 / 0.35 (22134) hydrogen bonds : bond 0.03992 / 2.54 ( 871) hydrogen bonds : angle 5.07492 / 3.64 ( 2571) ********************** 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 659 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 657 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.9255 (tt0) cc_final: 0.9013 (tt0) REVERT: A 31 GLU cc_start: 0.9238 (tp30) cc_final: 0.8788 (tp30) REVERT: A 54 LYS cc_start: 0.9693 (ttmm) cc_final: 0.9376 (ttmm) REVERT: A 99 LYS cc_start: 0.9374 (mmmt) cc_final: 0.9148 (mmmm) REVERT: A 107 LYS cc_start: 0.9259 (mtpp) cc_final: 0.8796 (mtpp) REVERT: A 116 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8666 (mt-10) REVERT: A 120 ASP cc_start: 0.8889 (m-30) cc_final: 0.8654 (m-30) REVERT: A 139 GLU cc_start: 0.9376 (mm-30) cc_final: 0.9077 (mm-30) REVERT: A 142 ASN cc_start: 0.9375 (m-40) cc_final: 0.9047 (m110) REVERT: A 150 GLN cc_start: 0.9481 (tp-100) cc_final: 0.9251 (tp40) REVERT: A 214 LYS cc_start: 0.9431 (mmmt) cc_final: 0.9158 (mmmm) REVERT: A 223 VAL cc_start: 0.9529 (m) cc_final: 0.9142 (p) REVERT: A 227 MET cc_start: 0.9340 (mtp) cc_final: 0.8886 (mtp) REVERT: A 235 ARG cc_start: 0.8703 (ttm110) cc_final: 0.8445 (ttm110) REVERT: A 251 LEU cc_start: 0.9591 (tp) cc_final: 0.9365 (tp) REVERT: A 286 ASP cc_start: 0.8584 (m-30) cc_final: 0.8314 (m-30) REVERT: A 321 GLU cc_start: 0.8750 (pp20) cc_final: 0.8337 (pp20) REVERT: A 322 MET cc_start: 0.8714 (mmp) cc_final: 0.8087 (mmm) REVERT: A 333 LYS cc_start: 0.9554 (ttmt) cc_final: 0.9270 (ttmm) REVERT: A 345 LYS cc_start: 0.9464 (tttt) cc_final: 0.9165 (tttt) REVERT: A 349 LEU cc_start: 0.9557 (mt) cc_final: 0.9246 (mt) REVERT: A 361 GLN cc_start: 0.9260 (tp40) cc_final: 0.8605 (tp40) REVERT: A 362 ASP cc_start: 0.8351 (m-30) cc_final: 0.7529 (m-30) REVERT: A 365 ASN cc_start: 0.9150 (m110) cc_final: 0.8591 (m-40) REVERT: A 370 ASN cc_start: 0.9581 (m-40) cc_final: 0.9310 (m-40) REVERT: A 387 GLN cc_start: 0.9126 (mt0) cc_final: 0.8821 (mt0) REVERT: A 407 ILE cc_start: 0.9452 (mt) cc_final: 0.9161 (mt) REVERT: A 410 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8430 (t160) REVERT: A 421 GLU cc_start: 0.8314 (pp20) cc_final: 0.8026 (pp20) REVERT: A 437 THR cc_start: 0.9621 (m) cc_final: 0.9308 (p) REVERT: A 458 MET cc_start: 0.9109 (mmm) cc_final: 0.8501 (mmm) REVERT: A 474 GLN cc_start: 0.9290 (mt0) cc_final: 0.9082 (mt0) REVERT: A 505 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8847 (mt-10) REVERT: A 570 MET cc_start: 0.9118 (mtp) cc_final: 0.8758 (mtp) REVERT: A 599 GLU cc_start: 0.8520 (mp0) cc_final: 0.8067 (mp0) REVERT: A 636 LYS cc_start: 0.9565 (mmmm) cc_final: 0.9082 (mmmm) REVERT: A 639 ASP cc_start: 0.9047 (m-30) cc_final: 0.8674 (m-30) REVERT: A 640 MET cc_start: 0.9212 (tpp) cc_final: 0.8977 (tpp) REVERT: A 645 GLN cc_start: 0.9346 (tp40) cc_final: 0.8961 (tp-100) REVERT: A 650 GLN cc_start: 0.8642 (mt0) cc_final: 0.8282 (mt0) REVERT: A 664 THR cc_start: 0.9129 (p) cc_final: 0.8326 (p) REVERT: A 667 LEU cc_start: 0.9568 (tt) cc_final: 0.9267 (tt) REVERT: A 668 ASN cc_start: 0.9374 (m110) cc_final: 0.9144 (m110) REVERT: B 71 LEU cc_start: 0.9713 (mm) cc_final: 0.9509 (mp) REVERT: B 82 LYS cc_start: 0.9393 (mtmt) cc_final: 0.9040 (ptpp) REVERT: B 87 LYS cc_start: 0.9390 (tptp) cc_final: 0.9090 (tptp) REVERT: B 116 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8711 (mt-10) REVERT: B 117 ARG cc_start: 0.8897 (mtt180) cc_final: 0.8584 (ttm110) REVERT: B 147 GLN cc_start: 0.9297 (mt0) cc_final: 0.8885 (mt0) REVERT: B 149 TYR cc_start: 0.9451 (t80) cc_final: 0.8558 (t80) REVERT: B 157 LEU cc_start: 0.9409 (tp) cc_final: 0.9206 (tp) REVERT: B 172 LEU cc_start: 0.9418 (mp) cc_final: 0.9136 (mp) REVERT: B 174 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7919 (mm-30) REVERT: B 227 MET cc_start: 0.9395 (mtp) cc_final: 0.9048 (mtp) REVERT: B 232 ASN cc_start: 0.9050 (t0) cc_final: 0.8522 (t0) REVERT: B 235 ARG cc_start: 0.9258 (tpp80) cc_final: 0.8993 (ttm-80) REVERT: B 257 ASP cc_start: 0.8866 (m-30) cc_final: 0.8655 (m-30) REVERT: B 274 ARG cc_start: 0.7907 (mmt180) cc_final: 0.7667 (mpt180) REVERT: B 278 LEU cc_start: 0.9298 (tp) cc_final: 0.9089 (tp) REVERT: B 333 LYS cc_start: 0.9368 (tptp) cc_final: 0.9082 (tttp) REVERT: B 348 MET cc_start: 0.9072 (ptp) cc_final: 0.8815 (ptp) REVERT: B 378 PHE cc_start: 0.9301 (p90) cc_final: 0.8951 (p90) REVERT: B 384 GLU cc_start: 0.8281 (pm20) cc_final: 0.7541 (pm20) REVERT: B 387 GLN cc_start: 0.9184 (mt0) cc_final: 0.8902 (mt0) REVERT: B 398 ASP cc_start: 0.8755 (t0) cc_final: 0.8550 (t0) REVERT: B 415 ASN cc_start: 0.9575 (t0) cc_final: 0.9244 (t0) REVERT: B 458 MET cc_start: 0.9193 (mmp) cc_final: 0.8784 (mmp) REVERT: B 459 LYS cc_start: 0.9337 (mttp) cc_final: 0.8876 (mtmm) REVERT: B 493 MET cc_start: 0.9349 (tmm) cc_final: 0.9082 (tmm) REVERT: B 494 MET cc_start: 0.9509 (mmm) cc_final: 0.9233 (mmt) REVERT: B 501 GLN cc_start: 0.9266 (tt0) cc_final: 0.8849 (tt0) REVERT: B 505 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8396 (mt-10) REVERT: B 570 MET cc_start: 0.8805 (mtp) cc_final: 0.8112 (mtp) REVERT: B 588 GLN cc_start: 0.9397 (mm-40) cc_final: 0.8877 (mm-40) REVERT: B 595 MET cc_start: 0.9026 (mmm) cc_final: 0.8823 (mmm) REVERT: B 628 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8311 (mm-30) REVERT: B 646 GLN cc_start: 0.9376 (pt0) cc_final: 0.9146 (pt0) REVERT: B 650 GLN cc_start: 0.8234 (mt0) cc_final: 0.7417 (mm-40) REVERT: B 677 ARG cc_start: 0.9314 (mmm-85) cc_final: 0.8688 (mtp85) REVERT: C 42 LEU cc_start: 0.8654 (pt) cc_final: 0.8440 (pt) REVERT: C 179 TYR cc_start: 0.8893 (t80) cc_final: 0.8660 (t80) REVERT: C 214 ASN cc_start: 0.8214 (p0) cc_final: 0.8013 (p0) REVERT: D 38 ASN cc_start: 0.8769 (m110) cc_final: 0.8173 (t0) REVERT: D 56 MET cc_start: 0.5951 (mmm) cc_final: 0.5467 (ttt) REVERT: D 59 LEU cc_start: 0.7842 (mt) cc_final: 0.7550 (pp) REVERT: D 66 ASP cc_start: 0.7411 (t0) cc_final: 0.6641 (t0) REVERT: D 158 VAL cc_start: 0.8299 (m) cc_final: 0.7897 (t) REVERT: D 162 TYR cc_start: 0.8748 (m-80) cc_final: 0.8319 (m-80) REVERT: D 176 LEU cc_start: 0.9552 (mt) cc_final: 0.9243 (pp) REVERT: D 178 PHE cc_start: 0.9019 (m-80) cc_final: 0.8420 (m-80) REVERT: D 233 ASN cc_start: 0.8402 (m110) cc_final: 0.7955 (m110) REVERT: D 269 MET cc_start: 0.7576 (ptm) cc_final: 0.7248 (ppp) REVERT: D 278 GLU cc_start: 0.8768 (tp30) cc_final: 0.8431 (pp20) REVERT: D 285 ILE cc_start: 0.7746 (mm) cc_final: 0.7541 (mm) outliers start: 2 outliers final: 0 residues processed: 658 average time/residue: 0.1193 time to fit residues: 117.8607 Evaluate side-chains 603 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 602 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 0.0870 chunk 25 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 125 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN D 238 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.136381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.095328 restraints weight = 39881.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.098688 restraints weight = 20888.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.100822 restraints weight = 13080.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.102216 restraints weight = 9363.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.103169 restraints weight = 7335.946| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.7586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16386 Z= 0.184 Angle : 0.672 9.643 22134 Z= 0.358 Chirality : 0.044 0.224 2360 Planarity : 0.004 0.039 2818 Dihedral : 8.154 140.064 2290 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.06 % Allowed : 0.29 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.19), residues: 1932 helix: 0.79 (0.15), residues: 1169 sheet: -0.53 (0.41), residues: 150 loop : -0.30 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 196 TYR 0.041 0.002 TYR D 162 PHE 0.024 0.002 PHE D 172 TRP 0.046 0.002 TRP D 124 HIS 0.004 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (16386) covalent geometry : angle 0.67196 / 0.36 (22134) hydrogen bonds : bond 0.04073 / 2.61 ( 871) hydrogen bonds : angle 5.05987 / 3.64 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3466.64 seconds wall clock time: 60 minutes 49.53 seconds (3649.53 seconds total)