Starting phenix.real_space_refine on Thu Sep 18 10:03:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzm_45071/09_2025/9bzm_45071_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzm_45071/09_2025/9bzm_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_45071/09_2025/9bzm_45071_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzm_45071/09_2025/9bzm_45071_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bzm_45071/09_2025/9bzm_45071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzm_45071/09_2025/9bzm_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.60, per 1000 atoms: 0.22 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: 1.42 Conformation dependent library (CDL) restraints added in 711.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.56 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: 2.67 Time building geometry restraints manager: 1.86 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=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.039 1.20e-02 6.94e+03 1.03e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 9.00e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.570 -0.033 1.17e-02 7.31e+03 7.75e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 6.95e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21574 2.09 - 4.18: 517 4.18 - 6.27: 37 6.27 - 8.36: 2 8.36 - 10.45: 4 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.59 -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 - 35.81: 9468 35.81 - 71.63: 339 71.63 - 107.44: 37 107.44 - 143.25: 3 143.25 - 179.06: 3 Dihedral angle restraints: 9850 sinusoidal: 4092 harmonic: 5758 Sorted by residual: dihedral pdb=" C2 TTP A 803 " pdb=" C1' TTP A 803 " pdb=" N1 TTP A 803 " pdb=" O4' TTP A 803 " ideal model delta sinusoidal sigma weight residual -58.32 120.75 -179.06 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 151.18 150.50 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' TTP A 803 " pdb=" O5' TTP A 803 " pdb=" PA TTP A 803 " pdb=" O3A TTP A 803 " ideal model delta sinusoidal sigma weight residual 179.97 31.90 148.07 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2139 0.093 - 0.186: 187 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 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.850 Find NCS groups from input model: 0.290 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: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16386 Z= 0.315 Angle : 0.740 10.446 22134 Z= 0.463 Chirality : 0.058 0.464 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.953 179.065 6154 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 aren 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 covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74013 (22134) hydrogen bonds : bond 0.15420 ( 871) hydrogen bonds : angle 6.51745 ( 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 : 0.601 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: 0.8405 (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: 0.7402 (mt0) REVERT: A 171 PHE cc_start: 0.8520 (m-80) cc_final: 0.8260 (m-10) REVERT: A 172 LEU cc_start: 0.9471 (mp) cc_final: 0.9232 (mp) REVERT: A 179 LEU cc_start: 0.8863 (tp) cc_final: 0.8584 (tp) REVERT: A 181 ASP cc_start: 0.8374 (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: 0.8827 (p) REVERT: A 211 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6462 (mm-30) REVERT: A 224 VAL cc_start: 0.8631 (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: 0.8204 (tp) REVERT: A 294 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6504 (mt-10) REVERT: A 322 MET cc_start: 0.8112 (mmp) cc_final: 0.7470 (mmm) REVERT: A 345 LYS cc_start: 0.8603 (tttt) cc_final: 0.8208 (tttt) REVERT: A 349 LEU cc_start: 0.7857 (mt) cc_final: 0.7544 (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: 0.8446 (mt) REVERT: A 417 LEU cc_start: 0.8546 (tt) cc_final: 0.8165 (tt) REVERT: A 420 MET cc_start: 0.8019 (mmm) cc_final: 0.7724 (mmm) REVERT: A 430 LYS cc_start: 0.8978 (mttt) cc_final: 0.8732 (mtpp) REVERT: A 436 LEU cc_start: 0.9196 (mt) cc_final: 0.8961 (mt) REVERT: A 442 THR cc_start: 0.8962 (p) cc_final: 0.8749 (m) REVERT: A 474 GLN cc_start: 0.8573 (mt0) cc_final: 0.8186 (mt0) REVERT: A 494 MET cc_start: 0.8146 (mtp) cc_final: 0.7793 (mtm) REVERT: A 500 ILE cc_start: 0.9349 (mt) cc_final: 0.9129 (mt) REVERT: A 556 GLU cc_start: 0.6880 (tp30) cc_final: 0.6411 (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: 0.8999 (t) cc_final: 0.8695 (t) REVERT: A 594 VAL cc_start: 0.9180 (m) cc_final: 0.8950 (m) REVERT: A 597 ILE cc_start: 0.9037 (pt) cc_final: 0.8811 (pt) REVERT: A 612 TYR cc_start: 0.7431 (m-80) cc_final: 0.6557 (m-10) REVERT: A 618 LEU cc_start: 0.9165 (tp) cc_final: 0.8895 (tp) REVERT: A 634 MET cc_start: 0.8111 (mmp) cc_final: 0.7738 (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: 0.8740 (p) REVERT: A 655 THR cc_start: 0.9153 (m) cc_final: 0.8901 (t) REVERT: A 657 PHE cc_start: 0.7945 (m-80) cc_final: 0.7492 (m-80) REVERT: A 667 LEU cc_start: 0.8211 (tt) cc_final: 0.7969 (tt) REVERT: B 11 GLN cc_start: 0.7854 (mt0) cc_final: 0.6857 (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: 0.7823 (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: 0.8919 (mt) REVERT: B 149 TYR cc_start: 0.8400 (t80) cc_final: 0.8037 (t80) REVERT: B 171 PHE cc_start: 0.8787 (m-80) cc_final: 0.8518 (m-80) REVERT: B 181 ASP cc_start: 0.8563 (m-30) cc_final: 0.8331 (m-30) REVERT: B 186 ILE cc_start: 0.9054 (mt) cc_final: 0.8798 (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: 0.6002 (mm-30) REVERT: B 232 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.7374 (t0) REVERT: B 256 ARG cc_start: 0.7723 (ttp80) cc_final: 0.7514 (tmt-80) REVERT: B 258 ILE cc_start: 0.8587 (tp) cc_final: 0.8378 (tp) REVERT: B 278 LEU cc_start: 0.8728 (tp) cc_final: 0.8237 (tp) REVERT: B 322 MET cc_start: 0.8012 (mmm) cc_final: 0.6336 (mmt) REVERT: B 332 VAL cc_start: 0.8875 (t) cc_final: 0.8648 (t) REVERT: B 345 LYS cc_start: 0.8630 (tttt) cc_final: 0.8111 (tttt) REVERT: B 362 ASP cc_start: 0.6716 (m-30) cc_final: 0.5834 (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: 0.6902 (mtp85) REVERT: B 453 ARG cc_start: 0.8968 (ttt90) cc_final: 0.8080 (ttp80) REVERT: B 505 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6725 (mt-10) REVERT: B 550 MET cc_start: 0.7400 (mtm) cc_final: 0.5930 (mtp) REVERT: B 558 TRP cc_start: 0.8293 (m100) cc_final: 0.7920 (m100) REVERT: B 570 MET cc_start: 0.7401 (mtm) cc_final: 0.6952 (mtm) REVERT: B 587 VAL cc_start: 0.8816 (t) cc_final: 0.8555 (t) REVERT: B 656 LEU cc_start: 0.8446 (mt) cc_final: 0.8218 (mt) REVERT: C 42 LEU cc_start: 0.6344 (mt) cc_final: 0.5897 (mt) REVERT: C 90 LEU cc_start: 0.5256 (mt) cc_final: 0.4763 (mt) REVERT: C 153 LEU cc_start: 0.5389 (tp) cc_final: 0.5079 (tt) REVERT: D 96 MET cc_start: 0.2343 (mmm) cc_final: 0.2078 (mmt) REVERT: D 178 PHE cc_start: 0.5464 (m-80) cc_final: 0.4360 (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: 0.1351 time to fit residues: 191.5329 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 : 0.450 ------------------------------------------------------------------------------- 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: 7.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 43 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 645 GLN B 11 GLN B 19 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 418 ASN 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 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.139261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.095467 restraints weight = 37615.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.098905 restraints weight = 20190.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.101274 restraints weight = 12943.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.102802 restraints weight = 9297.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.103851 restraints weight = 7301.150| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 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 = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16386 Z= 0.198 Angle : 0.649 8.031 22134 Z= 0.349 Chirality : 0.044 0.309 2360 Planarity : 0.004 0.032 2818 Dihedral : 11.481 179.656 2242 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.17 % Allowed : 2.56 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.18), residues: 1932 helix: 1.19 (0.15), residues: 1128 sheet: 0.35 (0.44), residues: 126 loop : 0.43 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 207 TYR 0.054 0.002 TYR D 130 PHE 0.030 0.002 PHE D 320 TRP 0.011 0.002 TRP C 30 HIS 0.008 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00423 (16386) covalent geometry : angle 0.64940 (22134) hydrogen bonds : bond 0.04697 ( 871) hydrogen bonds : angle 5.11890 ( 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 757 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 754 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.9364 (mmtt) cc_final: 0.8854 (mmmt) REVERT: A 31 GLU cc_start: 0.9391 (tp30) cc_final: 0.8971 (tp30) REVERT: A 51 LEU cc_start: 0.9515 (tp) cc_final: 0.9285 (pt) REVERT: A 54 LYS cc_start: 0.9616 (ttmm) cc_final: 0.9205 (ttmm) REVERT: A 87 LYS cc_start: 0.9501 (tptt) cc_final: 0.9139 (mmmm) REVERT: A 101 TYR cc_start: 0.9341 (m-10) cc_final: 0.8979 (m-10) REVERT: A 118 TYR cc_start: 0.9160 (t80) cc_final: 0.8670 (t80) REVERT: A 120 ASP cc_start: 0.9117 (m-30) cc_final: 0.8786 (m-30) REVERT: A 122 ILE cc_start: 0.9689 (mt) cc_final: 0.9477 (mt) REVERT: A 139 GLU cc_start: 0.9443 (mm-30) cc_final: 0.9193 (mm-30) REVERT: A 142 ASN cc_start: 0.9426 (m-40) cc_final: 0.9154 (m110) REVERT: A 147 GLN cc_start: 0.8969 (mt0) cc_final: 0.8678 (mt0) REVERT: A 168 VAL cc_start: 0.9382 (t) cc_final: 0.8970 (m) REVERT: A 171 PHE cc_start: 0.9482 (m-80) cc_final: 0.9219 (m-10) REVERT: A 181 ASP cc_start: 0.9001 (m-30) cc_final: 0.8595 (m-30) REVERT: A 184 ARG cc_start: 0.9116 (tpp-160) cc_final: 0.8890 (tpp-160) REVERT: A 202 ASN cc_start: 0.9586 (t0) cc_final: 0.9261 (t0) REVERT: A 204 SER cc_start: 0.9426 (m) cc_final: 0.9114 (p) REVERT: A 223 VAL cc_start: 0.9563 (m) cc_final: 0.9312 (p) REVERT: A 251 LEU cc_start: 0.9599 (tp) cc_final: 0.9323 (tp) REVERT: A 286 ASP cc_start: 0.8602 (m-30) cc_final: 0.8146 (m-30) REVERT: A 291 LEU cc_start: 0.9355 (mt) cc_final: 0.9053 (mt) REVERT: A 293 ARG cc_start: 0.9188 (ttp80) cc_final: 0.8780 (ttp80) REVERT: A 337 ILE cc_start: 0.9483 (tp) cc_final: 0.9172 (tp) REVERT: A 344 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8580 (mt-10) REVERT: A 348 MET cc_start: 0.8960 (ptp) cc_final: 0.8665 (ptp) REVERT: A 349 LEU cc_start: 0.9583 (mt) cc_final: 0.9298 (mt) REVERT: A 362 ASP cc_start: 0.8027 (m-30) cc_final: 0.7392 (m-30) REVERT: A 387 GLN cc_start: 0.9052 (mt0) cc_final: 0.8736 (mt0) REVERT: A 405 LEU cc_start: 0.9131 (mt) cc_final: 0.8925 (mt) REVERT: A 407 ILE cc_start: 0.9205 (mt) cc_final: 0.8833 (mt) REVERT: A 421 GLU cc_start: 0.8209 (pp20) cc_final: 0.8003 (pp20) REVERT: A 441 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8298 (mt-10) REVERT: A 443 THR cc_start: 0.9325 (m) cc_final: 0.9076 (t) REVERT: A 458 MET cc_start: 0.9177 (mmp) cc_final: 0.8630 (mmp) REVERT: A 505 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8908 (mt-10) REVERT: A 550 MET cc_start: 0.7786 (mtt) cc_final: 0.7332 (mtt) REVERT: A 570 MET cc_start: 0.9159 (mtp) cc_final: 0.8912 (mtp) REVERT: A 573 SER cc_start: 0.9488 (p) cc_final: 0.9064 (p) REVERT: A 584 ILE cc_start: 0.9607 (pt) cc_final: 0.9100 (pt) REVERT: A 588 GLN cc_start: 0.9349 (mm-40) cc_final: 0.9142 (tp40) REVERT: A 599 GLU cc_start: 0.8321 (mp0) cc_final: 0.7815 (mp0) REVERT: A 615 MET cc_start: 0.9014 (mmp) cc_final: 0.8780 (mmp) REVERT: A 630 TYR cc_start: 0.7936 (m-80) cc_final: 0.7188 (m-10) REVERT: A 632 MET cc_start: 0.8898 (mtm) cc_final: 0.8622 (mtp) REVERT: A 639 ASP cc_start: 0.9192 (m-30) cc_final: 0.8917 (m-30) REVERT: A 650 GLN cc_start: 0.8626 (mt0) cc_final: 0.8303 (tt0) REVERT: A 654 PHE cc_start: 0.9493 (t80) cc_final: 0.9198 (t80) REVERT: A 655 THR cc_start: 0.9283 (m) cc_final: 0.8766 (t) REVERT: A 664 THR cc_start: 0.9174 (p) cc_final: 0.8614 (p) REVERT: A 667 LEU cc_start: 0.9381 (tt) cc_final: 0.9113 (tt) REVERT: A 668 ASN cc_start: 0.9286 (m110) cc_final: 0.9023 (m110) REVERT: B 51 LEU cc_start: 0.9481 (tp) cc_final: 0.9253 (tp) REVERT: B 58 LEU cc_start: 0.9676 (mt) cc_final: 0.9445 (mt) REVERT: B 65 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8294 (mp0) REVERT: B 87 LYS cc_start: 0.9292 (tptp) cc_final: 0.8779 (tptp) REVERT: B 95 MET cc_start: 0.9565 (tpt) cc_final: 0.9308 (tpp) REVERT: B 147 GLN cc_start: 0.9137 (mt0) cc_final: 0.8721 (mt0) REVERT: B 149 TYR cc_start: 0.9159 (t80) cc_final: 0.8790 (t80) REVERT: B 181 ASP cc_start: 0.9179 (m-30) cc_final: 0.8888 (m-30) REVERT: B 227 MET cc_start: 0.9480 (mtp) cc_final: 0.9278 (mtp) REVERT: B 256 ARG cc_start: 0.9065 (tmt170) cc_final: 0.8806 (tpt90) REVERT: B 257 ASP cc_start: 0.9052 (m-30) cc_final: 0.8726 (m-30) REVERT: B 278 LEU cc_start: 0.9287 (tp) cc_final: 0.9017 (tp) REVERT: B 279 SER cc_start: 0.8539 (m) cc_final: 0.7638 (p) REVERT: B 290 GLU cc_start: 0.9268 (tp30) cc_final: 0.9028 (tp30) REVERT: B 316 GLU cc_start: 0.9120 (tt0) cc_final: 0.8891 (tt0) REVERT: B 333 LYS cc_start: 0.9215 (tptp) cc_final: 0.8739 (tttm) REVERT: B 355 TYR cc_start: 0.9033 (m-80) cc_final: 0.8712 (m-80) REVERT: B 381 LEU cc_start: 0.9238 (tp) cc_final: 0.8938 (tp) REVERT: B 393 SER cc_start: 0.9182 (t) cc_final: 0.8970 (p) REVERT: B 413 SER cc_start: 0.9539 (m) cc_final: 0.9040 (t) REVERT: B 415 ASN cc_start: 0.9696 (t0) cc_final: 0.9409 (t0) REVERT: B 458 MET cc_start: 0.9517 (mmm) cc_final: 0.9165 (mmp) REVERT: B 459 LYS cc_start: 0.9285 (mttm) cc_final: 0.8439 (mtpt) REVERT: B 460 SER cc_start: 0.8935 (t) cc_final: 0.8705 (t) REVERT: B 471 TYR cc_start: 0.9278 (t80) cc_final: 0.8951 (t80) REVERT: B 487 PHE cc_start: 0.9738 (t80) cc_final: 0.9437 (t80) REVERT: B 493 MET cc_start: 0.9491 (tmm) cc_final: 0.9184 (tmm) REVERT: B 505 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8415 (mt-10) REVERT: B 570 MET cc_start: 0.9110 (mtp) cc_final: 0.8733 (mtp) REVERT: B 588 GLN cc_start: 0.9430 (mm-40) cc_final: 0.9224 (mm-40) REVERT: B 599 GLU cc_start: 0.8720 (pt0) cc_final: 0.8440 (pt0) REVERT: B 601 ILE cc_start: 0.9437 (mm) cc_final: 0.9106 (mm) REVERT: B 612 TYR cc_start: 0.8496 (m-10) cc_final: 0.8215 (m-10) REVERT: B 631 ASP cc_start: 0.9022 (t0) cc_final: 0.8499 (t0) REVERT: B 667 LEU cc_start: 0.9429 (tp) cc_final: 0.9191 (tp) REVERT: B 677 ARG cc_start: 0.9484 (mmm-85) cc_final: 0.9157 (mmm-85) REVERT: C 42 LEU cc_start: 0.9022 (mt) cc_final: 0.8806 (mt) REVERT: C 117 THR cc_start: 0.9097 (p) cc_final: 0.8804 (p) REVERT: C 119 ASN cc_start: 0.9092 (t0) cc_final: 0.8823 (t0) REVERT: C 179 TYR cc_start: 0.8584 (t80) cc_final: 0.8331 (t80) REVERT: D 37 LEU cc_start: 0.5172 (tp) cc_final: 0.2876 (tp) REVERT: D 178 PHE cc_start: 0.8802 (m-80) cc_final: 0.8473 (m-80) REVERT: D 252 LEU cc_start: 0.8775 (mt) cc_final: 0.8479 (mt) outliers start: 3 outliers final: 0 residues processed: 755 average time/residue: 0.1206 time to fit residues: 135.3719 Evaluate side-chains 616 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 616 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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: 10.0000 chunk 131 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 158 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 19 GLN A 191 GLN A 338 ASN A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 232 ASN B 361 GLN B 387 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN D 69 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.142383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.098099 restraints weight = 38492.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.101486 restraints weight = 20548.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.103876 restraints weight = 13404.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105574 restraints weight = 9535.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106640 restraints weight = 7432.516| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16386 Z= 0.149 Angle : 0.593 10.106 22134 Z= 0.315 Chirality : 0.042 0.235 2360 Planarity : 0.003 0.030 2818 Dihedral : 11.089 177.831 2242 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.29 % Allowed : 2.10 % Favored : 97.61 % 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 aren not related in a simple way. whole: 1.21 (0.19), residues: 1932 helix: 1.23 (0.15), residues: 1133 sheet: 0.29 (0.43), residues: 134 loop : 0.36 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 274 TYR 0.040 0.002 TYR D 130 PHE 0.026 0.002 PHE D 320 TRP 0.016 0.001 TRP A 9 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00327 (16386) covalent geometry : angle 0.59253 (22134) hydrogen bonds : bond 0.04136 ( 871) hydrogen bonds : angle 4.92530 ( 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 724 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 719 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.9529 (mm) cc_final: 0.9169 (tp) REVERT: A 40 TYR cc_start: 0.9315 (t80) cc_final: 0.9043 (t80) REVERT: A 64 TYR cc_start: 0.8902 (m-10) cc_final: 0.8516 (m-80) REVERT: A 87 LYS cc_start: 0.9506 (tptt) cc_final: 0.9193 (mmmm) REVERT: A 107 LYS cc_start: 0.9055 (mtpp) cc_final: 0.8755 (mtpp) REVERT: A 118 TYR cc_start: 0.9149 (t80) cc_final: 0.8704 (t80) REVERT: A 120 ASP cc_start: 0.9100 (m-30) cc_final: 0.8866 (m-30) REVERT: A 124 ILE cc_start: 0.9759 (mm) cc_final: 0.9539 (mm) REVERT: A 139 GLU cc_start: 0.9420 (mm-30) cc_final: 0.9123 (mm-30) REVERT: A 142 ASN cc_start: 0.9413 (m-40) cc_final: 0.9126 (m110) REVERT: A 147 GLN cc_start: 0.8982 (mt0) cc_final: 0.8685 (mt0) REVERT: A 150 GLN cc_start: 0.9263 (tm-30) cc_final: 0.8829 (tm-30) REVERT: A 168 VAL cc_start: 0.9279 (t) cc_final: 0.8950 (m) REVERT: A 171 PHE cc_start: 0.9488 (m-80) cc_final: 0.9193 (m-10) REVERT: A 181 ASP cc_start: 0.8897 (m-30) cc_final: 0.8572 (m-30) REVERT: A 223 VAL cc_start: 0.9520 (m) cc_final: 0.9071 (p) REVERT: A 227 MET cc_start: 0.9389 (mtp) cc_final: 0.8975 (mtp) REVERT: A 251 LEU cc_start: 0.9656 (tp) cc_final: 0.9356 (tp) REVERT: A 257 ASP cc_start: 0.9318 (m-30) cc_final: 0.8314 (m-30) REVERT: A 286 ASP cc_start: 0.8658 (m-30) cc_final: 0.8206 (m-30) REVERT: A 291 LEU cc_start: 0.9343 (mt) cc_final: 0.9027 (mt) REVERT: A 316 GLU cc_start: 0.8850 (pt0) cc_final: 0.8578 (pp20) REVERT: A 317 MET cc_start: 0.9100 (ptm) cc_final: 0.8820 (ptm) REVERT: A 321 GLU cc_start: 0.8468 (pp20) cc_final: 0.8132 (tm-30) REVERT: A 322 MET cc_start: 0.8706 (mmp) cc_final: 0.7811 (mmm) REVERT: A 337 ILE cc_start: 0.9441 (tp) cc_final: 0.9226 (tp) REVERT: A 344 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8702 (mt-10) REVERT: A 348 MET cc_start: 0.9054 (ptp) cc_final: 0.8724 (ptp) REVERT: A 349 LEU cc_start: 0.9584 (mt) cc_final: 0.9291 (mt) REVERT: A 362 ASP cc_start: 0.8055 (m-30) cc_final: 0.7394 (m-30) REVERT: A 379 SER cc_start: 0.9070 (t) cc_final: 0.8780 (p) REVERT: A 387 GLN cc_start: 0.8999 (mt0) cc_final: 0.8753 (mt0) REVERT: A 396 ASP cc_start: 0.8643 (p0) cc_final: 0.8400 (p0) REVERT: A 405 LEU cc_start: 0.9254 (mt) cc_final: 0.8992 (mt) REVERT: A 407 ILE cc_start: 0.9259 (mt) cc_final: 0.8887 (mt) REVERT: A 418 ASN cc_start: 0.8977 (OUTLIER) cc_final: 0.8357 (m-40) REVERT: A 421 GLU cc_start: 0.8411 (pp20) cc_final: 0.8132 (pp20) REVERT: A 441 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8684 (mt-10) REVERT: A 443 THR cc_start: 0.9439 (m) cc_final: 0.9230 (t) REVERT: A 458 MET cc_start: 0.9386 (mmp) cc_final: 0.8755 (mmm) REVERT: A 468 LEU cc_start: 0.9644 (tp) cc_final: 0.9418 (tp) REVERT: A 490 THR cc_start: 0.9654 (m) cc_final: 0.9328 (p) REVERT: A 505 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8694 (mt-10) REVERT: A 550 MET cc_start: 0.8228 (mtt) cc_final: 0.7905 (mtt) REVERT: A 588 GLN cc_start: 0.9276 (mm-40) cc_final: 0.9046 (tp40) REVERT: A 601 ILE cc_start: 0.9501 (mm) cc_final: 0.9299 (tp) REVERT: A 630 TYR cc_start: 0.8332 (m-80) cc_final: 0.7614 (m-80) REVERT: A 632 MET cc_start: 0.8849 (mtm) cc_final: 0.8393 (mtp) REVERT: A 639 ASP cc_start: 0.9070 (m-30) cc_final: 0.8675 (m-30) REVERT: A 645 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8874 (tp-100) REVERT: A 650 GLN cc_start: 0.8700 (mt0) cc_final: 0.8047 (mt0) REVERT: A 664 THR cc_start: 0.9258 (p) cc_final: 0.8414 (p) REVERT: A 667 LEU cc_start: 0.9491 (tt) cc_final: 0.9252 (tt) REVERT: A 668 ASN cc_start: 0.9367 (m110) cc_final: 0.9048 (m110) REVERT: A 672 LEU cc_start: 0.9382 (mt) cc_final: 0.9180 (mt) REVERT: B 58 LEU cc_start: 0.9645 (mt) cc_final: 0.9404 (mt) REVERT: B 65 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8218 (mt-10) REVERT: B 67 GLU cc_start: 0.9241 (mp0) cc_final: 0.8904 (pm20) REVERT: B 87 LYS cc_start: 0.9298 (tptp) cc_final: 0.8970 (tptp) REVERT: B 106 LEU cc_start: 0.9481 (tp) cc_final: 0.9238 (tp) REVERT: B 107 LYS cc_start: 0.9160 (mttt) cc_final: 0.8673 (mptt) REVERT: B 117 ARG cc_start: 0.8943 (ttm110) cc_final: 0.8726 (mmm-85) REVERT: B 120 ASP cc_start: 0.8801 (m-30) cc_final: 0.8310 (m-30) REVERT: B 147 GLN cc_start: 0.8885 (mt0) cc_final: 0.8620 (mt0) REVERT: B 149 TYR cc_start: 0.9195 (t80) cc_final: 0.8700 (t80) REVERT: B 172 LEU cc_start: 0.9357 (mp) cc_final: 0.9013 (mp) REVERT: B 181 ASP cc_start: 0.9182 (m-30) cc_final: 0.8932 (m-30) REVERT: B 232 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8392 (t0) REVERT: B 257 ASP cc_start: 0.8996 (m-30) cc_final: 0.8753 (m-30) REVERT: B 264 THR cc_start: 0.9427 (p) cc_final: 0.9202 (p) REVERT: B 278 LEU cc_start: 0.9241 (tp) cc_final: 0.8982 (tp) REVERT: B 279 SER cc_start: 0.8464 (m) cc_final: 0.7617 (p) REVERT: B 290 GLU cc_start: 0.9262 (tp30) cc_final: 0.8920 (tp30) REVERT: B 316 GLU cc_start: 0.9093 (tt0) cc_final: 0.8822 (tt0) REVERT: B 321 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8366 (pp20) REVERT: B 333 LYS cc_start: 0.9283 (tptp) cc_final: 0.8834 (tttp) REVERT: B 350 ARG cc_start: 0.7849 (mmm160) cc_final: 0.7455 (mmm160) REVERT: B 355 TYR cc_start: 0.9046 (m-80) cc_final: 0.8507 (m-80) REVERT: B 378 PHE cc_start: 0.9375 (p90) cc_final: 0.9174 (p90) REVERT: B 393 SER cc_start: 0.9093 (t) cc_final: 0.8863 (p) REVERT: B 407 ILE cc_start: 0.9371 (mt) cc_final: 0.8999 (mt) REVERT: B 415 ASN cc_start: 0.9580 (t0) cc_final: 0.9200 (t0) REVERT: B 458 MET cc_start: 0.9529 (mmm) cc_final: 0.9117 (mmp) REVERT: B 459 LYS cc_start: 0.9197 (mttm) cc_final: 0.8373 (mtmt) REVERT: B 472 LEU cc_start: 0.9689 (mm) cc_final: 0.9437 (mm) REVERT: B 474 GLN cc_start: 0.8602 (mm110) cc_final: 0.8189 (mm-40) REVERT: B 479 TYR cc_start: 0.8946 (t80) cc_final: 0.8659 (t80) REVERT: B 493 MET cc_start: 0.9487 (tmm) cc_final: 0.9282 (tmm) REVERT: B 505 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8402 (mt-10) REVERT: B 550 MET cc_start: 0.7885 (mtp) cc_final: 0.7607 (mtm) REVERT: B 558 TRP cc_start: 0.9496 (m100) cc_final: 0.8508 (m100) REVERT: B 599 GLU cc_start: 0.8762 (pt0) cc_final: 0.8485 (pt0) REVERT: B 604 ARG cc_start: 0.9407 (tpp80) cc_final: 0.9052 (ttm-80) REVERT: B 612 TYR cc_start: 0.8140 (m-80) cc_final: 0.7503 (m-10) REVERT: B 631 ASP cc_start: 0.9073 (t0) cc_final: 0.8596 (t0) REVERT: B 677 ARG cc_start: 0.9462 (mmm-85) cc_final: 0.9192 (mmm-85) REVERT: C 179 TYR cc_start: 0.8481 (t80) cc_final: 0.8130 (t80) REVERT: D 59 LEU cc_start: 0.7593 (mt) cc_final: 0.7248 (pp) REVERT: D 150 GLU cc_start: 0.8523 (pm20) cc_final: 0.8257 (tp30) REVERT: D 178 PHE cc_start: 0.8929 (m-80) cc_final: 0.8407 (m-80) REVERT: D 233 ASN cc_start: 0.8794 (m110) cc_final: 0.8442 (m110) REVERT: D 252 LEU cc_start: 0.8836 (mt) cc_final: 0.8494 (mp) REVERT: D 278 GLU cc_start: 0.8524 (pp20) cc_final: 0.8244 (pp20) REVERT: D 321 TYR cc_start: 0.8307 (m-80) cc_final: 0.7414 (m-10) outliers start: 5 outliers final: 0 residues processed: 720 average time/residue: 0.1238 time to fit residues: 133.4164 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 : 0.476 ------------------------------------------------------------------------------- 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: 1.9990 chunk 157 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 182 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN A 25 GLN A 338 ASN A 361 GLN A 365 ASN A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 232 ASN B 320 ASN B 387 GLN B 474 GLN B 645 GLN B 646 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.137256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.093986 restraints weight = 39363.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.097394 restraints weight = 20785.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.099645 restraints weight = 13230.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.101086 restraints weight = 9496.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.102011 restraints weight = 7470.228| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.204 Angle : 0.614 8.971 22134 Z= 0.324 Chirality : 0.042 0.339 2360 Planarity : 0.004 0.059 2818 Dihedral : 11.080 175.229 2242 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.17 % Allowed : 2.33 % 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 aren not related in a simple way. whole: 1.12 (0.19), residues: 1932 helix: 1.18 (0.15), residues: 1135 sheet: 0.92 (0.48), residues: 104 loop : 0.16 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 235 TYR 0.039 0.002 TYR D 130 PHE 0.036 0.002 PHE D 172 TRP 0.011 0.002 TRP A 9 HIS 0.007 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00433 (16386) covalent geometry : angle 0.61424 (22134) hydrogen bonds : bond 0.04061 ( 871) hydrogen bonds : angle 4.92639 ( 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 698 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 695 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9531 (mm) cc_final: 0.9273 (mm) REVERT: A 51 LEU cc_start: 0.9540 (tp) cc_final: 0.9312 (pt) REVERT: A 54 LYS cc_start: 0.9723 (ttmm) cc_final: 0.9326 (ttmm) REVERT: A 64 TYR cc_start: 0.8895 (m-10) cc_final: 0.8508 (m-80) REVERT: A 65 GLU cc_start: 0.8643 (mm-30) cc_final: 0.7751 (mp0) REVERT: A 87 LYS cc_start: 0.9519 (tptt) cc_final: 0.9208 (mmmm) REVERT: A 107 LYS cc_start: 0.9141 (mtpp) cc_final: 0.8627 (mtpp) REVERT: A 118 TYR cc_start: 0.9233 (t80) cc_final: 0.8915 (t80) REVERT: A 120 ASP cc_start: 0.9201 (m-30) cc_final: 0.8882 (m-30) REVERT: A 139 GLU cc_start: 0.9364 (mm-30) cc_final: 0.9105 (mm-30) REVERT: A 142 ASN cc_start: 0.9418 (m-40) cc_final: 0.9133 (m110) REVERT: A 168 VAL cc_start: 0.9174 (t) cc_final: 0.8890 (m) REVERT: A 175 VAL cc_start: 0.9527 (t) cc_final: 0.9309 (t) REVERT: A 223 VAL cc_start: 0.9609 (m) cc_final: 0.9215 (p) REVERT: A 227 MET cc_start: 0.9323 (mtp) cc_final: 0.8902 (mtp) REVERT: A 251 LEU cc_start: 0.9687 (tp) cc_final: 0.9369 (tp) REVERT: A 263 ASP cc_start: 0.9063 (m-30) cc_final: 0.8709 (m-30) REVERT: A 266 LYS cc_start: 0.8841 (ptmm) cc_final: 0.8535 (tmmt) REVERT: A 286 ASP cc_start: 0.8653 (m-30) cc_final: 0.8261 (m-30) REVERT: A 321 GLU cc_start: 0.8605 (pp20) cc_final: 0.8334 (pp20) REVERT: A 322 MET cc_start: 0.8763 (mmp) cc_final: 0.8072 (mmm) REVERT: A 341 LYS cc_start: 0.9373 (pttp) cc_final: 0.9165 (pttp) REVERT: A 344 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8598 (mt-10) REVERT: A 348 MET cc_start: 0.9041 (ptp) cc_final: 0.8753 (ptp) REVERT: A 349 LEU cc_start: 0.9626 (mt) cc_final: 0.9341 (mt) REVERT: A 361 GLN cc_start: 0.9001 (tp40) cc_final: 0.7924 (tp40) REVERT: A 362 ASP cc_start: 0.8104 (m-30) cc_final: 0.7302 (m-30) REVERT: A 365 ASN cc_start: 0.9139 (m110) cc_final: 0.8130 (m-40) REVERT: A 375 LYS cc_start: 0.9219 (mtpt) cc_final: 0.8920 (mtmm) REVERT: A 387 GLN cc_start: 0.9152 (mt0) cc_final: 0.8892 (mt0) REVERT: A 405 LEU cc_start: 0.9274 (mt) cc_final: 0.9074 (mt) REVERT: A 407 ILE cc_start: 0.9399 (mt) cc_final: 0.9072 (mt) REVERT: A 421 GLU cc_start: 0.8639 (pp20) cc_final: 0.8390 (pp20) REVERT: A 458 MET cc_start: 0.9316 (mmp) cc_final: 0.9004 (mmm) REVERT: A 466 MET cc_start: 0.9280 (ptt) cc_final: 0.8980 (ptt) REVERT: A 490 THR cc_start: 0.9681 (m) cc_final: 0.9344 (p) REVERT: A 505 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8614 (mt-10) REVERT: A 552 ILE cc_start: 0.9562 (mp) cc_final: 0.9342 (mp) REVERT: A 570 MET cc_start: 0.9191 (mtp) cc_final: 0.8705 (mtp) REVERT: A 573 SER cc_start: 0.9412 (p) cc_final: 0.8826 (p) REVERT: A 599 GLU cc_start: 0.8590 (mp0) cc_final: 0.8378 (mp0) REVERT: A 632 MET cc_start: 0.8832 (mtm) cc_final: 0.8548 (mtp) REVERT: A 639 ASP cc_start: 0.9165 (m-30) cc_final: 0.8672 (m-30) REVERT: A 643 THR cc_start: 0.9623 (p) cc_final: 0.9134 (t) REVERT: A 645 GLN cc_start: 0.9147 (tp-100) cc_final: 0.8515 (tp-100) REVERT: A 650 GLN cc_start: 0.8722 (mt0) cc_final: 0.7742 (mt0) REVERT: A 664 THR cc_start: 0.9450 (p) cc_final: 0.8748 (p) REVERT: A 668 ASN cc_start: 0.9459 (m110) cc_final: 0.9091 (m110) REVERT: A 680 LYS cc_start: 0.8940 (mttt) cc_final: 0.8442 (mttt) REVERT: A 686 ARG cc_start: 0.8562 (mmt180) cc_final: 0.7927 (mmt-90) REVERT: B 58 LEU cc_start: 0.9685 (mt) cc_final: 0.9446 (mt) REVERT: B 65 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8401 (mp0) REVERT: B 82 LYS cc_start: 0.9491 (mmmm) cc_final: 0.9133 (mmtt) REVERT: B 87 LYS cc_start: 0.9384 (tptp) cc_final: 0.9019 (tptp) REVERT: B 116 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8670 (mt-10) REVERT: B 117 ARG cc_start: 0.9064 (ttm110) cc_final: 0.8752 (ttm110) REVERT: B 120 ASP cc_start: 0.8882 (m-30) cc_final: 0.8620 (m-30) REVERT: B 147 GLN cc_start: 0.9166 (mt0) cc_final: 0.8790 (mt0) REVERT: B 149 TYR cc_start: 0.9248 (t80) cc_final: 0.8747 (t80) REVERT: B 157 LEU cc_start: 0.9524 (tp) cc_final: 0.9293 (tp) REVERT: B 172 LEU cc_start: 0.9426 (mp) cc_final: 0.9019 (mp) REVERT: B 181 ASP cc_start: 0.9269 (m-30) cc_final: 0.9047 (m-30) REVERT: B 191 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8505 (mm-40) REVERT: B 232 ASN cc_start: 0.9087 (t0) cc_final: 0.8547 (t0) REVERT: B 257 ASP cc_start: 0.8976 (m-30) cc_final: 0.8633 (m-30) REVERT: B 258 ILE cc_start: 0.9627 (tp) cc_final: 0.9425 (tp) REVERT: B 264 THR cc_start: 0.9500 (p) cc_final: 0.9237 (p) REVERT: B 278 LEU cc_start: 0.9281 (tp) cc_final: 0.9032 (tp) REVERT: B 279 SER cc_start: 0.8347 (m) cc_final: 0.7769 (p) REVERT: B 286 ASP cc_start: 0.8704 (m-30) cc_final: 0.8316 (m-30) REVERT: B 290 GLU cc_start: 0.9231 (tp30) cc_final: 0.8928 (tp30) REVERT: B 316 GLU cc_start: 0.9096 (tt0) cc_final: 0.8880 (tt0) REVERT: B 319 MET cc_start: 0.9156 (tpp) cc_final: 0.8718 (tpp) REVERT: B 333 LYS cc_start: 0.9283 (tptp) cc_final: 0.8886 (tttp) REVERT: B 335 GLU cc_start: 0.7792 (mp0) cc_final: 0.7538 (mp0) REVERT: B 348 MET cc_start: 0.9389 (ptp) cc_final: 0.9077 (ptp) REVERT: B 350 ARG cc_start: 0.7769 (mmm160) cc_final: 0.7156 (mmm160) REVERT: B 386 LEU cc_start: 0.9339 (mt) cc_final: 0.9080 (mt) REVERT: B 393 SER cc_start: 0.9260 (t) cc_final: 0.8955 (p) REVERT: B 407 ILE cc_start: 0.9496 (mt) cc_final: 0.9030 (mt) REVERT: B 415 ASN cc_start: 0.9610 (t0) cc_final: 0.9060 (t0) REVERT: B 427 LYS cc_start: 0.9466 (tppt) cc_final: 0.9169 (mmmm) REVERT: B 435 SER cc_start: 0.9725 (p) cc_final: 0.9522 (t) REVERT: B 459 LYS cc_start: 0.9259 (mttm) cc_final: 0.9035 (mttm) REVERT: B 467 ASN cc_start: 0.9280 (m-40) cc_final: 0.9037 (m-40) REVERT: B 493 MET cc_start: 0.9451 (tmm) cc_final: 0.9126 (tmm) REVERT: B 505 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8353 (mt-10) REVERT: B 516 GLN cc_start: 0.9080 (mp10) cc_final: 0.8868 (mp10) REVERT: B 588 GLN cc_start: 0.9469 (mm-40) cc_final: 0.9249 (mm-40) REVERT: B 599 GLU cc_start: 0.8754 (pt0) cc_final: 0.8469 (pt0) REVERT: B 604 ARG cc_start: 0.9313 (tpp80) cc_final: 0.9014 (ttm-80) REVERT: B 650 GLN cc_start: 0.8096 (mt0) cc_final: 0.7808 (mt0) REVERT: B 667 LEU cc_start: 0.9411 (tp) cc_final: 0.8887 (tp) REVERT: C 16 ASP cc_start: 0.6311 (p0) cc_final: 0.5749 (p0) REVERT: C 179 TYR cc_start: 0.8683 (t80) cc_final: 0.8399 (t80) REVERT: D 56 MET cc_start: 0.6936 (mmp) cc_final: 0.6656 (mmm) REVERT: D 137 MET cc_start: 0.5492 (mtp) cc_final: 0.5071 (mpp) REVERT: D 158 VAL cc_start: 0.8920 (t) cc_final: 0.8567 (t) REVERT: D 176 LEU cc_start: 0.9471 (mt) cc_final: 0.9159 (pp) REVERT: D 178 PHE cc_start: 0.9069 (m-80) cc_final: 0.8526 (m-80) REVERT: D 233 ASN cc_start: 0.8852 (m110) cc_final: 0.8388 (m110) REVERT: D 252 LEU cc_start: 0.8910 (mt) cc_final: 0.8537 (mp) outliers start: 3 outliers final: 0 residues processed: 695 average time/residue: 0.1288 time to fit residues: 133.3446 Evaluate side-chains 622 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 622 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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: 0.4980 chunk 46 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 157 optimal weight: 30.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN B 218 ASN B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 646 GLN C 254 HIS ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.138589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.096633 restraints weight = 34378.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.099722 restraints weight = 20306.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.101513 restraints weight = 13919.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.102628 restraints weight = 10651.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.103257 restraints weight = 8932.885| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- 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: 4 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.167 Angle : 0.610 11.504 22134 Z= 0.320 Chirality : 0.043 0.327 2360 Planarity : 0.004 0.086 2818 Dihedral : 11.007 176.195 2242 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.12 % Allowed : 2.33 % Favored : 97.55 % 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 aren not related in a simple way. whole: 1.06 (0.19), residues: 1932 helix: 1.16 (0.15), residues: 1132 sheet: 0.94 (0.49), residues: 104 loop : 0.05 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 274 TYR 0.031 0.002 TYR D 130 PHE 0.024 0.002 PHE B 491 TRP 0.010 0.001 TRP A 9 HIS 0.011 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00359 (16386) covalent geometry : angle 0.60982 (22134) hydrogen bonds : bond 0.03942 ( 871) hydrogen bonds : angle 4.89242 ( 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 692 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 690 time to evaluate : 0.687 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: A 13 ASN cc_start: 0.9349 (t0) cc_final: 0.9149 (t0) REVERT: A 15 GLU cc_start: 0.9147 (tt0) cc_final: 0.8843 (tt0) REVERT: A 41 ILE cc_start: 0.9545 (mm) cc_final: 0.9204 (mm) REVERT: A 51 LEU cc_start: 0.9526 (tp) cc_final: 0.9313 (pt) REVERT: A 54 LYS cc_start: 0.9699 (ttmm) cc_final: 0.9336 (ttmm) REVERT: A 66 GLU cc_start: 0.8720 (tp30) cc_final: 0.8468 (tp30) REVERT: A 87 LYS cc_start: 0.9553 (tptt) cc_final: 0.9271 (mmmm) REVERT: A 95 MET cc_start: 0.9433 (mmm) cc_final: 0.9133 (tpp) REVERT: A 106 LEU cc_start: 0.9498 (tp) cc_final: 0.9297 (tp) REVERT: A 107 LYS cc_start: 0.9183 (mtpp) cc_final: 0.8705 (mtpp) REVERT: A 118 TYR cc_start: 0.9258 (t80) cc_final: 0.8961 (t80) REVERT: A 120 ASP cc_start: 0.9318 (m-30) cc_final: 0.8924 (m-30) REVERT: A 139 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9122 (mm-30) REVERT: A 142 ASN cc_start: 0.9427 (m-40) cc_final: 0.9141 (m110) REVERT: A 150 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8816 (tm-30) REVERT: A 223 VAL cc_start: 0.9602 (m) cc_final: 0.9170 (p) REVERT: A 227 MET cc_start: 0.9333 (mtp) cc_final: 0.8878 (mtp) REVERT: A 251 LEU cc_start: 0.9677 (tp) cc_final: 0.9356 (tp) REVERT: A 263 ASP cc_start: 0.9107 (m-30) cc_final: 0.8783 (m-30) REVERT: A 286 ASP cc_start: 0.8597 (m-30) cc_final: 0.8273 (m-30) REVERT: A 291 LEU cc_start: 0.9439 (mt) cc_final: 0.9215 (mt) REVERT: A 322 MET cc_start: 0.8591 (mmp) cc_final: 0.7963 (mmm) REVERT: A 348 MET cc_start: 0.8934 (ptp) cc_final: 0.8707 (ptp) REVERT: A 349 LEU cc_start: 0.9599 (mt) cc_final: 0.9371 (mt) REVERT: A 361 GLN cc_start: 0.9047 (tp40) cc_final: 0.8010 (tp40) REVERT: A 362 ASP cc_start: 0.8025 (m-30) cc_final: 0.7193 (m-30) REVERT: A 365 ASN cc_start: 0.9231 (m110) cc_final: 0.8325 (m-40) REVERT: A 370 ASN cc_start: 0.9590 (m-40) cc_final: 0.9222 (m-40) REVERT: A 387 GLN cc_start: 0.9150 (mt0) cc_final: 0.8925 (mt0) REVERT: A 407 ILE cc_start: 0.9398 (mt) cc_final: 0.9093 (mt) REVERT: A 458 MET cc_start: 0.9290 (mmp) cc_final: 0.8971 (mmm) REVERT: A 466 MET cc_start: 0.9245 (ptt) cc_final: 0.9026 (ptt) REVERT: A 505 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8772 (mt-10) REVERT: A 570 MET cc_start: 0.9227 (mtp) cc_final: 0.8749 (mtp) REVERT: A 573 SER cc_start: 0.9430 (p) cc_final: 0.8809 (p) REVERT: A 599 GLU cc_start: 0.8063 (mp0) cc_final: 0.7851 (mp0) REVERT: A 602 GLU cc_start: 0.7995 (pt0) cc_final: 0.7724 (pt0) REVERT: A 604 ARG cc_start: 0.9108 (mmp-170) cc_final: 0.8838 (mmm-85) REVERT: A 632 MET cc_start: 0.9095 (mtm) cc_final: 0.8351 (mtp) REVERT: A 634 MET cc_start: 0.9214 (mmm) cc_final: 0.8905 (mmm) REVERT: A 639 ASP cc_start: 0.9153 (m-30) cc_final: 0.8731 (m-30) REVERT: A 643 THR cc_start: 0.9590 (p) cc_final: 0.9204 (t) REVERT: A 650 GLN cc_start: 0.8709 (mt0) cc_final: 0.8016 (mt0) REVERT: A 664 THR cc_start: 0.9291 (p) cc_final: 0.8510 (p) REVERT: A 667 LEU cc_start: 0.9586 (tt) cc_final: 0.9325 (tt) REVERT: A 668 ASN cc_start: 0.9340 (m110) cc_final: 0.8929 (m110) REVERT: A 686 ARG cc_start: 0.8792 (mmt180) cc_final: 0.8460 (mmt180) REVERT: B 58 LEU cc_start: 0.9685 (mt) cc_final: 0.9483 (mt) REVERT: B 79 GLU cc_start: 0.9062 (mm-30) cc_final: 0.7960 (mm-30) REVERT: B 87 LYS cc_start: 0.9389 (tptp) cc_final: 0.9014 (tptp) REVERT: B 116 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8514 (mt-10) REVERT: B 118 TYR cc_start: 0.9445 (t80) cc_final: 0.9211 (t80) REVERT: B 147 GLN cc_start: 0.9210 (mt0) cc_final: 0.8889 (mt0) REVERT: B 149 TYR cc_start: 0.9328 (t80) cc_final: 0.8801 (t80) REVERT: B 157 LEU cc_start: 0.9490 (tp) cc_final: 0.9258 (tp) REVERT: B 172 LEU cc_start: 0.9380 (mp) cc_final: 0.9043 (mp) REVERT: B 191 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8521 (mm-40) REVERT: B 232 ASN cc_start: 0.8998 (t160) cc_final: 0.8586 (t0) REVERT: B 257 ASP cc_start: 0.8894 (m-30) cc_final: 0.8583 (m-30) REVERT: B 278 LEU cc_start: 0.9283 (tp) cc_final: 0.9065 (tp) REVERT: B 279 SER cc_start: 0.8267 (m) cc_final: 0.7620 (p) REVERT: B 286 ASP cc_start: 0.8660 (m-30) cc_final: 0.8313 (m-30) REVERT: B 290 GLU cc_start: 0.9120 (tp30) cc_final: 0.8822 (tp30) REVERT: B 316 GLU cc_start: 0.9063 (tt0) cc_final: 0.8798 (tt0) REVERT: B 333 LYS cc_start: 0.9315 (tptp) cc_final: 0.9023 (tttp) REVERT: B 348 MET cc_start: 0.9264 (ptp) cc_final: 0.8975 (ptp) REVERT: B 350 ARG cc_start: 0.7632 (mmm160) cc_final: 0.7020 (mmm160) REVERT: B 351 SER cc_start: 0.9635 (m) cc_final: 0.9429 (p) REVERT: B 384 GLU cc_start: 0.8581 (pm20) cc_final: 0.7993 (pm20) REVERT: B 398 ASP cc_start: 0.9031 (t0) cc_final: 0.8761 (t0) REVERT: B 415 ASN cc_start: 0.9512 (t0) cc_final: 0.9068 (t0) REVERT: B 427 LYS cc_start: 0.9518 (tppt) cc_final: 0.9241 (mmmm) REVERT: B 435 SER cc_start: 0.9714 (p) cc_final: 0.9502 (t) REVERT: B 493 MET cc_start: 0.9436 (tmm) cc_final: 0.9139 (tmm) REVERT: B 505 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8332 (mt-10) REVERT: B 516 GLN cc_start: 0.9132 (mp10) cc_final: 0.8843 (mp10) REVERT: B 599 GLU cc_start: 0.8741 (pt0) cc_final: 0.8504 (pt0) REVERT: B 628 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8326 (mm-30) REVERT: B 632 MET cc_start: 0.8702 (mtp) cc_final: 0.7931 (mtp) REVERT: B 646 GLN cc_start: 0.9542 (pt0) cc_final: 0.8859 (pm20) REVERT: B 667 LEU cc_start: 0.9442 (tp) cc_final: 0.9173 (tp) REVERT: C 16 ASP cc_start: 0.6239 (p0) cc_final: 0.5647 (p0) REVERT: C 179 TYR cc_start: 0.8684 (t80) cc_final: 0.8367 (t80) REVERT: D 137 MET cc_start: 0.5807 (mtp) cc_final: 0.5324 (mpp) REVERT: D 154 PHE cc_start: 0.5074 (m-10) cc_final: 0.4778 (m-80) REVERT: D 158 VAL cc_start: 0.8084 (t) cc_final: 0.7142 (m) REVERT: D 173 TYR cc_start: 0.7359 (t80) cc_final: 0.6543 (t80) REVERT: D 176 LEU cc_start: 0.9545 (mt) cc_final: 0.9223 (pp) REVERT: D 233 ASN cc_start: 0.8767 (m110) cc_final: 0.8255 (m-40) outliers start: 2 outliers final: 0 residues processed: 690 average time/residue: 0.1261 time to fit residues: 130.9888 Evaluate side-chains 585 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 585 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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: 0.8980 chunk 183 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 172 optimal weight: 20.0000 chunk 52 optimal weight: 0.0570 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN A 242 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 232 ASN B 387 GLN B 645 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.139803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.097522 restraints weight = 39199.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.101076 restraints weight = 20583.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.103342 restraints weight = 12812.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.104840 restraints weight = 9114.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.105799 restraints weight = 7095.501| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.6399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 16386 Z= 0.130 Angle : 0.596 7.614 22134 Z= 0.316 Chirality : 0.042 0.328 2360 Planarity : 0.004 0.061 2818 Dihedral : 10.754 173.129 2242 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.06 % Allowed : 1.17 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.19), residues: 1932 helix: 1.13 (0.15), residues: 1133 sheet: 0.68 (0.45), residues: 114 loop : 0.04 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 604 TYR 0.034 0.002 TYR D 174 PHE 0.026 0.002 PHE C 178 TRP 0.019 0.002 TRP C 44 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00286 (16386) covalent geometry : angle 0.59585 (22134) hydrogen bonds : bond 0.03795 ( 871) hydrogen bonds : angle 4.85804 ( 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 703 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 702 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.9163 (tt0) cc_final: 0.8870 (tt0) REVERT: A 41 ILE cc_start: 0.9600 (mm) cc_final: 0.9254 (mm) REVERT: A 54 LYS cc_start: 0.9727 (ttmm) cc_final: 0.9369 (ttmm) REVERT: A 65 GLU cc_start: 0.8706 (mm-30) cc_final: 0.7649 (mp0) REVERT: A 106 LEU cc_start: 0.9513 (tp) cc_final: 0.9006 (tp) REVERT: A 107 LYS cc_start: 0.9190 (mtpp) cc_final: 0.8698 (mtpp) REVERT: A 116 GLU cc_start: 0.8723 (mt-10) cc_final: 0.7913 (tt0) REVERT: A 118 TYR cc_start: 0.9283 (t80) cc_final: 0.8983 (t80) REVERT: A 139 GLU cc_start: 0.9411 (mm-30) cc_final: 0.9105 (mm-30) REVERT: A 142 ASN cc_start: 0.9401 (m-40) cc_final: 0.9085 (m110) REVERT: A 147 GLN cc_start: 0.9005 (mt0) cc_final: 0.8670 (mt0) REVERT: A 150 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8928 (tm-30) REVERT: A 223 VAL cc_start: 0.9567 (m) cc_final: 0.9170 (p) REVERT: A 227 MET cc_start: 0.9347 (mtp) cc_final: 0.8931 (mtp) REVERT: A 251 LEU cc_start: 0.9641 (tp) cc_final: 0.9343 (tp) REVERT: A 263 ASP cc_start: 0.9016 (m-30) cc_final: 0.8693 (m-30) REVERT: A 286 ASP cc_start: 0.8721 (m-30) cc_final: 0.8398 (m-30) REVERT: A 301 PHE cc_start: 0.9272 (m-80) cc_final: 0.9072 (m-10) REVERT: A 319 MET cc_start: 0.9077 (tpp) cc_final: 0.8841 (tpp) REVERT: A 321 GLU cc_start: 0.8555 (pp20) cc_final: 0.8250 (pp20) REVERT: A 322 MET cc_start: 0.8605 (mmp) cc_final: 0.8112 (mmm) REVERT: A 333 LYS cc_start: 0.9060 (tttt) cc_final: 0.8783 (tptp) REVERT: A 348 MET cc_start: 0.9090 (ptp) cc_final: 0.8882 (ptp) REVERT: A 349 LEU cc_start: 0.9629 (mt) cc_final: 0.9340 (mt) REVERT: A 361 GLN cc_start: 0.9248 (tp40) cc_final: 0.8793 (tp40) REVERT: A 362 ASP cc_start: 0.8257 (m-30) cc_final: 0.7477 (m-30) REVERT: A 365 ASN cc_start: 0.9196 (m110) cc_final: 0.8890 (m110) REVERT: A 370 ASN cc_start: 0.9571 (m-40) cc_final: 0.9302 (m-40) REVERT: A 407 ILE cc_start: 0.9464 (mt) cc_final: 0.9166 (mt) REVERT: A 421 GLU cc_start: 0.8477 (pp20) cc_final: 0.8236 (pp20) REVERT: A 437 THR cc_start: 0.9620 (m) cc_final: 0.9396 (m) REVERT: A 441 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8612 (mt-10) REVERT: A 458 MET cc_start: 0.9251 (mmp) cc_final: 0.8899 (mmm) REVERT: A 505 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8705 (mt-10) REVERT: A 506 ILE cc_start: 0.9654 (mm) cc_final: 0.9156 (mm) REVERT: A 570 MET cc_start: 0.9167 (mtp) cc_final: 0.8794 (mtp) REVERT: A 599 GLU cc_start: 0.8088 (mp0) cc_final: 0.7883 (mp0) REVERT: A 602 GLU cc_start: 0.8094 (pt0) cc_final: 0.7883 (pt0) REVERT: A 604 ARG cc_start: 0.9077 (mmp-170) cc_final: 0.8835 (mmm-85) REVERT: A 639 ASP cc_start: 0.9134 (m-30) cc_final: 0.8767 (m-30) REVERT: A 643 THR cc_start: 0.9551 (p) cc_final: 0.9231 (t) REVERT: A 645 GLN cc_start: 0.9280 (tp-100) cc_final: 0.8578 (tp40) REVERT: A 646 GLN cc_start: 0.9170 (pt0) cc_final: 0.8951 (pt0) REVERT: A 650 GLN cc_start: 0.8877 (mt0) cc_final: 0.7671 (mt0) REVERT: A 664 THR cc_start: 0.9341 (p) cc_final: 0.8889 (p) REVERT: A 667 LEU cc_start: 0.9593 (tt) cc_final: 0.9309 (tt) REVERT: A 668 ASN cc_start: 0.9316 (m110) cc_final: 0.8962 (m110) REVERT: A 680 LYS cc_start: 0.8882 (mttt) cc_final: 0.8543 (mttp) REVERT: B 15 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8655 (mt-10) REVERT: B 79 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8687 (mm-30) REVERT: B 87 LYS cc_start: 0.9372 (tptp) cc_final: 0.9014 (tptp) REVERT: B 117 ARG cc_start: 0.8810 (mtt180) cc_final: 0.8542 (ttm110) REVERT: B 120 ASP cc_start: 0.8864 (m-30) cc_final: 0.8620 (m-30) REVERT: B 147 GLN cc_start: 0.9288 (mt0) cc_final: 0.9027 (mt0) REVERT: B 149 TYR cc_start: 0.9300 (t80) cc_final: 0.8595 (t80) REVERT: B 157 LEU cc_start: 0.9467 (tp) cc_final: 0.9160 (tp) REVERT: B 161 ARG cc_start: 0.8714 (ttm170) cc_final: 0.8391 (ttm170) REVERT: B 172 LEU cc_start: 0.9427 (mp) cc_final: 0.9081 (mp) REVERT: B 191 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8218 (mm-40) REVERT: B 232 ASN cc_start: 0.8941 (t160) cc_final: 0.8578 (t0) REVERT: B 257 ASP cc_start: 0.8974 (m-30) cc_final: 0.8759 (m-30) REVERT: B 277 THR cc_start: 0.8695 (p) cc_final: 0.8470 (p) REVERT: B 278 LEU cc_start: 0.9215 (tp) cc_final: 0.8944 (tp) REVERT: B 279 SER cc_start: 0.8088 (m) cc_final: 0.7544 (p) REVERT: B 286 ASP cc_start: 0.8756 (m-30) cc_final: 0.8485 (m-30) REVERT: B 290 GLU cc_start: 0.9251 (tp30) cc_final: 0.8873 (tp30) REVERT: B 319 MET cc_start: 0.9127 (tpp) cc_final: 0.8839 (tpp) REVERT: B 322 MET cc_start: 0.8834 (mmt) cc_final: 0.8464 (mmm) REVERT: B 333 LYS cc_start: 0.9278 (tptp) cc_final: 0.9050 (tttp) REVERT: B 348 MET cc_start: 0.9298 (ptp) cc_final: 0.9034 (ptp) REVERT: B 350 ARG cc_start: 0.7702 (mmm160) cc_final: 0.6963 (mmm160) REVERT: B 378 PHE cc_start: 0.9351 (p90) cc_final: 0.9089 (p90) REVERT: B 384 GLU cc_start: 0.8694 (pm20) cc_final: 0.8006 (pm20) REVERT: B 386 LEU cc_start: 0.9205 (mt) cc_final: 0.8948 (mt) REVERT: B 398 ASP cc_start: 0.8691 (t0) cc_final: 0.8403 (t0) REVERT: B 407 ILE cc_start: 0.9487 (mt) cc_final: 0.9062 (mt) REVERT: B 415 ASN cc_start: 0.9601 (t0) cc_final: 0.9243 (t0) REVERT: B 427 LYS cc_start: 0.9471 (tppt) cc_final: 0.9174 (mmmm) REVERT: B 437 THR cc_start: 0.9636 (m) cc_final: 0.9422 (p) REVERT: B 447 ASN cc_start: 0.8895 (m-40) cc_final: 0.7953 (m-40) REVERT: B 458 MET cc_start: 0.9234 (mmp) cc_final: 0.8872 (mmp) REVERT: B 459 LYS cc_start: 0.9154 (mttp) cc_final: 0.8635 (mtpt) REVERT: B 493 MET cc_start: 0.9472 (tmm) cc_final: 0.9160 (tmm) REVERT: B 505 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8346 (mt-10) REVERT: B 516 GLN cc_start: 0.9188 (mp10) cc_final: 0.8879 (mp10) REVERT: B 599 GLU cc_start: 0.8743 (pt0) cc_final: 0.8480 (pt0) REVERT: B 612 TYR cc_start: 0.8468 (m-80) cc_final: 0.8232 (m-80) REVERT: B 628 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8317 (mm-30) REVERT: C 16 ASP cc_start: 0.6342 (p0) cc_final: 0.5714 (p0) REVERT: C 179 TYR cc_start: 0.8644 (t80) cc_final: 0.8363 (t80) REVERT: D 56 MET cc_start: 0.5525 (mmm) cc_final: 0.5288 (tpt) REVERT: D 112 LEU cc_start: 0.6314 (mm) cc_final: 0.6092 (mm) REVERT: D 137 MET cc_start: 0.5488 (mtp) cc_final: 0.5104 (mpp) REVERT: D 158 VAL cc_start: 0.7977 (t) cc_final: 0.6798 (m) REVERT: D 162 TYR cc_start: 0.8320 (m-10) cc_final: 0.7966 (m-10) REVERT: D 178 PHE cc_start: 0.9129 (m-80) cc_final: 0.8025 (m-80) REVERT: D 231 LEU cc_start: 0.7044 (mt) cc_final: 0.6749 (mt) REVERT: D 233 ASN cc_start: 0.8813 (m110) cc_final: 0.8331 (m-40) REVERT: D 252 LEU cc_start: 0.8801 (mt) cc_final: 0.8488 (mp) outliers start: 1 outliers final: 0 residues processed: 702 average time/residue: 0.1200 time to fit residues: 126.0993 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 : 0.655 ------------------------------------------------------------------------------- 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: 0.9990 chunk 51 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 30.0000 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 646 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** 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 = 0.3732 r_free = 0.3732 target = 0.139268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.097108 restraints weight = 39176.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.100631 restraints weight = 20488.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.102840 restraints weight = 12862.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.104206 restraints weight = 9151.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.105196 restraints weight = 7193.762| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.6660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 16386 Z= 0.153 Angle : 0.605 8.108 22134 Z= 0.317 Chirality : 0.043 0.271 2360 Planarity : 0.003 0.038 2818 Dihedral : 10.661 173.513 2242 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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 aren not related in a simple way. whole: 1.03 (0.19), residues: 1932 helix: 1.16 (0.16), residues: 1131 sheet: 0.70 (0.46), residues: 114 loop : 0.04 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.031 0.002 TYR D 130 PHE 0.026 0.002 PHE A 171 TRP 0.010 0.001 TRP A 558 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00335 (16386) covalent geometry : angle 0.60510 (22134) hydrogen bonds : bond 0.03825 ( 871) hydrogen bonds : angle 4.76971 ( 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 679 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 679 time to evaluate : 0.666 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 15 GLU cc_start: 0.9106 (tt0) cc_final: 0.8891 (tt0) REVERT: A 41 ILE cc_start: 0.9606 (mm) cc_final: 0.9260 (mm) REVERT: A 54 LYS cc_start: 0.9707 (ttmm) cc_final: 0.9370 (tttp) REVERT: A 87 LYS cc_start: 0.9523 (tptt) cc_final: 0.9250 (mmmm) REVERT: A 107 LYS cc_start: 0.9192 (mtpp) cc_final: 0.8659 (mtpp) REVERT: A 118 TYR cc_start: 0.9297 (t80) cc_final: 0.9015 (t80) REVERT: A 139 GLU cc_start: 0.9399 (mm-30) cc_final: 0.9104 (mm-30) REVERT: A 142 ASN cc_start: 0.9398 (m-40) cc_final: 0.9070 (m110) REVERT: A 147 GLN cc_start: 0.9020 (mt0) cc_final: 0.8679 (mt0) REVERT: A 150 GLN cc_start: 0.9269 (tm-30) cc_final: 0.8919 (tm-30) REVERT: A 223 VAL cc_start: 0.9574 (m) cc_final: 0.9149 (p) REVERT: A 227 MET cc_start: 0.9350 (mtp) cc_final: 0.8913 (mtp) REVERT: A 251 LEU cc_start: 0.9673 (tp) cc_final: 0.9360 (tp) REVERT: A 279 SER cc_start: 0.8789 (m) cc_final: 0.8220 (t) REVERT: A 286 ASP cc_start: 0.8707 (m-30) cc_final: 0.8394 (m-30) REVERT: A 321 GLU cc_start: 0.8600 (pp20) cc_final: 0.8270 (pp20) REVERT: A 322 MET cc_start: 0.8648 (mmp) cc_final: 0.8048 (mmm) REVERT: A 349 LEU cc_start: 0.9590 (mt) cc_final: 0.9287 (mt) REVERT: A 361 GLN cc_start: 0.9304 (tp40) cc_final: 0.8417 (tp40) REVERT: A 362 ASP cc_start: 0.8314 (m-30) cc_final: 0.7469 (m-30) REVERT: A 365 ASN cc_start: 0.9303 (m110) cc_final: 0.8497 (m-40) REVERT: A 407 ILE cc_start: 0.9416 (mt) cc_final: 0.9144 (mt) REVERT: A 437 THR cc_start: 0.9645 (m) cc_final: 0.9428 (m) REVERT: A 441 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8660 (mt-10) REVERT: A 458 MET cc_start: 0.9210 (mmp) cc_final: 0.8688 (mmm) REVERT: A 505 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8835 (mt-10) REVERT: A 570 MET cc_start: 0.9178 (mtp) cc_final: 0.8766 (mtp) REVERT: A 599 GLU cc_start: 0.8124 (mp0) cc_final: 0.7875 (mp0) REVERT: A 604 ARG cc_start: 0.9070 (mmp-170) cc_final: 0.8845 (mmm-85) REVERT: A 615 MET cc_start: 0.8970 (mmp) cc_final: 0.8669 (mmp) REVERT: A 632 MET cc_start: 0.8868 (mtp) cc_final: 0.8643 (mtp) REVERT: A 636 LYS cc_start: 0.9578 (mmmm) cc_final: 0.8917 (mmmm) REVERT: A 639 ASP cc_start: 0.9113 (m-30) cc_final: 0.8747 (m-30) REVERT: A 643 THR cc_start: 0.9566 (p) cc_final: 0.9197 (t) REVERT: A 646 GLN cc_start: 0.9180 (pt0) cc_final: 0.8898 (pt0) REVERT: A 650 GLN cc_start: 0.8849 (mt0) cc_final: 0.8039 (mt0) REVERT: A 667 LEU cc_start: 0.9604 (tt) cc_final: 0.9392 (tt) REVERT: A 668 ASN cc_start: 0.9420 (m110) cc_final: 0.9087 (m110) REVERT: B 16 ILE cc_start: 0.9316 (tp) cc_final: 0.9063 (tp) REVERT: B 58 LEU cc_start: 0.9665 (mt) cc_final: 0.9440 (mt) REVERT: B 71 LEU cc_start: 0.9693 (mm) cc_final: 0.9457 (mp) REVERT: B 87 LYS cc_start: 0.9376 (tptp) cc_final: 0.9032 (tptp) REVERT: B 117 ARG cc_start: 0.8811 (mtt180) cc_final: 0.8558 (ttm110) REVERT: B 120 ASP cc_start: 0.8822 (m-30) cc_final: 0.8622 (m-30) REVERT: B 147 GLN cc_start: 0.9234 (mt0) cc_final: 0.8985 (mt0) REVERT: B 149 TYR cc_start: 0.9363 (t80) cc_final: 0.8692 (t80) REVERT: B 157 LEU cc_start: 0.9469 (tp) cc_final: 0.9222 (tp) REVERT: B 172 LEU cc_start: 0.9421 (mp) cc_final: 0.9087 (mp) REVERT: B 174 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7960 (mm-30) REVERT: B 191 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8268 (mm-40) REVERT: B 227 MET cc_start: 0.9406 (mtp) cc_final: 0.9117 (mtp) REVERT: B 228 LYS cc_start: 0.9419 (mmmt) cc_final: 0.9159 (mmtm) REVERT: B 232 ASN cc_start: 0.8932 (t0) cc_final: 0.8523 (t0) REVERT: B 274 ARG cc_start: 0.7891 (mmt-90) cc_final: 0.7421 (mpt180) REVERT: B 278 LEU cc_start: 0.9256 (tp) cc_final: 0.9023 (tp) REVERT: B 279 SER cc_start: 0.8071 (m) cc_final: 0.7597 (p) REVERT: B 286 ASP cc_start: 0.8793 (m-30) cc_final: 0.8447 (m-30) REVERT: B 290 GLU cc_start: 0.9250 (tp30) cc_final: 0.8892 (tp30) REVERT: B 312 GLN cc_start: 0.9110 (pm20) cc_final: 0.8832 (pm20) REVERT: B 321 GLU cc_start: 0.8784 (pp20) cc_final: 0.8315 (pp20) REVERT: B 322 MET cc_start: 0.8881 (mmt) cc_final: 0.8422 (mmt) REVERT: B 333 LYS cc_start: 0.9277 (tptp) cc_final: 0.9058 (tttm) REVERT: B 348 MET cc_start: 0.9168 (ptp) cc_final: 0.8965 (ptp) REVERT: B 350 ARG cc_start: 0.7746 (mmm160) cc_final: 0.6970 (mmm160) REVERT: B 378 PHE cc_start: 0.9410 (p90) cc_final: 0.8974 (p90) REVERT: B 384 GLU cc_start: 0.8749 (pm20) cc_final: 0.8018 (pm20) REVERT: B 398 ASP cc_start: 0.8662 (t0) cc_final: 0.8356 (t0) REVERT: B 407 ILE cc_start: 0.9523 (mt) cc_final: 0.9068 (mt) REVERT: B 415 ASN cc_start: 0.9548 (t0) cc_final: 0.9116 (t0) REVERT: B 426 GLU cc_start: 0.8634 (tm-30) cc_final: 0.7808 (tm-30) REVERT: B 427 LYS cc_start: 0.9428 (tppt) cc_final: 0.9098 (mmmm) REVERT: B 437 THR cc_start: 0.9642 (m) cc_final: 0.9437 (m) REVERT: B 447 ASN cc_start: 0.8921 (m-40) cc_final: 0.8162 (m-40) REVERT: B 458 MET cc_start: 0.9260 (mmp) cc_final: 0.8832 (mmp) REVERT: B 459 LYS cc_start: 0.9218 (mttp) cc_final: 0.8627 (mtmm) REVERT: B 467 ASN cc_start: 0.9247 (m-40) cc_final: 0.8998 (m-40) REVERT: B 493 MET cc_start: 0.9478 (tmm) cc_final: 0.9157 (tmm) REVERT: B 501 GLN cc_start: 0.9378 (tt0) cc_final: 0.8903 (tt0) REVERT: B 505 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8309 (mt-10) REVERT: B 516 GLN cc_start: 0.9199 (mp10) cc_final: 0.8872 (mp10) REVERT: B 570 MET cc_start: 0.8675 (mtp) cc_final: 0.8393 (mtp) REVERT: B 588 GLN cc_start: 0.9471 (mm-40) cc_final: 0.8928 (mm-40) REVERT: B 604 ARG cc_start: 0.9316 (tpp80) cc_final: 0.8909 (ttm-80) REVERT: B 628 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8371 (mm-30) REVERT: B 646 GLN cc_start: 0.9467 (pt0) cc_final: 0.9170 (pt0) REVERT: B 667 LEU cc_start: 0.9503 (tp) cc_final: 0.8948 (tp) REVERT: C 16 ASP cc_start: 0.6506 (p0) cc_final: 0.5928 (p0) REVERT: C 179 TYR cc_start: 0.8657 (t80) cc_final: 0.8402 (t80) REVERT: D 56 MET cc_start: 0.5547 (mmm) cc_final: 0.5254 (tpt) REVERT: D 112 LEU cc_start: 0.6134 (mm) cc_final: 0.5756 (mm) REVERT: D 137 MET cc_start: 0.5673 (mtp) cc_final: 0.5241 (mpp) REVERT: D 162 TYR cc_start: 0.8360 (m-10) cc_final: 0.8043 (m-10) REVERT: D 178 PHE cc_start: 0.9112 (m-80) cc_final: 0.8795 (m-80) REVERT: D 233 ASN cc_start: 0.8812 (m110) cc_final: 0.8339 (m110) REVERT: D 252 LEU cc_start: 0.8901 (mt) cc_final: 0.8592 (mp) outliers start: 0 outliers final: 0 residues processed: 679 average time/residue: 0.1296 time to fit residues: 133.1468 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 : 0.607 ------------------------------------------------------------------------------- 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: 0.6980 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 158 optimal weight: 30.0000 chunk 97 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 ASN A 242 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN B 218 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 HIS B 645 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.132811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.092660 restraints weight = 35803.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.095511 restraints weight = 20821.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.097243 restraints weight = 14142.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.098367 restraints weight = 10813.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.098937 restraints weight = 9027.678| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.6971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 16386 Z= 0.275 Angle : 0.713 11.058 22134 Z= 0.375 Chirality : 0.046 0.233 2360 Planarity : 0.004 0.046 2818 Dihedral : 10.885 174.481 2242 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.19), residues: 1932 helix: 0.89 (0.15), residues: 1143 sheet: 0.04 (0.42), residues: 136 loop : -0.13 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 196 TYR 0.043 0.002 TYR B 612 PHE 0.033 0.002 PHE A 171 TRP 0.015 0.002 TRP A 623 HIS 0.008 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00581 (16386) covalent geometry : angle 0.71268 (22134) hydrogen bonds : bond 0.04144 ( 871) hydrogen bonds : angle 5.06743 ( 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 657 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 657 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8931 (tt0) cc_final: 0.8653 (tt0) REVERT: A 54 LYS cc_start: 0.9717 (ttmm) cc_final: 0.9363 (ttmm) REVERT: A 99 LYS cc_start: 0.9564 (mmmt) cc_final: 0.9187 (mmmm) REVERT: A 106 LEU cc_start: 0.9616 (tp) cc_final: 0.9191 (tp) REVERT: A 107 LYS cc_start: 0.9261 (mtpp) cc_final: 0.8904 (mtpp) REVERT: A 116 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8726 (mt-10) REVERT: A 139 GLU cc_start: 0.9376 (mm-30) cc_final: 0.9104 (mm-30) REVERT: A 142 ASN cc_start: 0.9389 (m-40) cc_final: 0.9107 (m110) REVERT: A 150 GLN cc_start: 0.9329 (tm-30) cc_final: 0.8983 (tm-30) REVERT: A 180 ASN cc_start: 0.9138 (m-40) cc_final: 0.8748 (m-40) REVERT: A 223 VAL cc_start: 0.9572 (m) cc_final: 0.9152 (p) REVERT: A 227 MET cc_start: 0.9376 (mtp) cc_final: 0.8914 (mtp) REVERT: A 235 ARG cc_start: 0.8601 (ttm110) cc_final: 0.8320 (ttm110) REVERT: A 251 LEU cc_start: 0.9725 (tp) cc_final: 0.9441 (tp) REVERT: A 286 ASP cc_start: 0.8403 (m-30) cc_final: 0.8106 (m-30) REVERT: A 321 GLU cc_start: 0.8595 (pp20) cc_final: 0.8238 (pp20) REVERT: A 322 MET cc_start: 0.8602 (mmp) cc_final: 0.8004 (mmm) REVERT: A 349 LEU cc_start: 0.9619 (mt) cc_final: 0.9347 (mt) REVERT: A 362 ASP cc_start: 0.8239 (m-30) cc_final: 0.7398 (m-30) REVERT: A 386 LEU cc_start: 0.9684 (mt) cc_final: 0.9421 (mt) REVERT: A 407 ILE cc_start: 0.9214 (mt) cc_final: 0.8926 (mt) REVERT: A 437 THR cc_start: 0.9668 (m) cc_final: 0.9354 (p) REVERT: A 458 MET cc_start: 0.9206 (mmp) cc_final: 0.8945 (mmm) REVERT: A 505 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8639 (mt-10) REVERT: A 632 MET cc_start: 0.8783 (mtp) cc_final: 0.8549 (mtp) REVERT: A 636 LYS cc_start: 0.9563 (mmmm) cc_final: 0.8832 (mmmm) REVERT: A 639 ASP cc_start: 0.9149 (m-30) cc_final: 0.8744 (m-30) REVERT: A 643 THR cc_start: 0.9613 (p) cc_final: 0.9284 (t) REVERT: A 646 GLN cc_start: 0.9167 (pt0) cc_final: 0.8874 (pt0) REVERT: A 650 GLN cc_start: 0.8718 (mt0) cc_final: 0.7873 (mt0) REVERT: A 667 LEU cc_start: 0.9638 (tt) cc_final: 0.9426 (tt) REVERT: A 668 ASN cc_start: 0.9453 (m110) cc_final: 0.9152 (m110) REVERT: B 25 GLN cc_start: 0.9029 (mt0) cc_final: 0.8590 (mt0) REVERT: B 58 LEU cc_start: 0.9727 (mt) cc_final: 0.9525 (mt) REVERT: B 87 LYS cc_start: 0.9416 (tptp) cc_final: 0.9082 (tptp) REVERT: B 95 MET cc_start: 0.9451 (tpt) cc_final: 0.9169 (tpp) REVERT: B 117 ARG cc_start: 0.8928 (mtt180) cc_final: 0.8634 (ttm110) REVERT: B 120 ASP cc_start: 0.8938 (m-30) cc_final: 0.8664 (m-30) REVERT: B 147 GLN cc_start: 0.9272 (mt0) cc_final: 0.8975 (mt0) REVERT: B 149 TYR cc_start: 0.9400 (t80) cc_final: 0.8825 (t80) REVERT: B 166 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8891 (mm-30) REVERT: B 172 LEU cc_start: 0.9382 (mp) cc_final: 0.8934 (mp) REVERT: B 174 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8006 (mm-30) REVERT: B 193 SER cc_start: 0.9289 (m) cc_final: 0.9025 (p) REVERT: B 227 MET cc_start: 0.9412 (mtp) cc_final: 0.9089 (mtp) REVERT: B 232 ASN cc_start: 0.9051 (t0) cc_final: 0.8555 (t0) REVERT: B 235 ARG cc_start: 0.9141 (ttm-80) cc_final: 0.8759 (tpp80) REVERT: B 238 ASP cc_start: 0.8421 (p0) cc_final: 0.8027 (p0) REVERT: B 274 ARG cc_start: 0.8101 (mmt-90) cc_final: 0.7711 (mmt180) REVERT: B 277 THR cc_start: 0.8820 (p) cc_final: 0.8550 (p) REVERT: B 278 LEU cc_start: 0.9333 (tp) cc_final: 0.9111 (tp) REVERT: B 279 SER cc_start: 0.8267 (m) cc_final: 0.7846 (p) REVERT: B 286 ASP cc_start: 0.8682 (m-30) cc_final: 0.8412 (m-30) REVERT: B 312 GLN cc_start: 0.9135 (pm20) cc_final: 0.8395 (pm20) REVERT: B 333 LYS cc_start: 0.9309 (tptp) cc_final: 0.8991 (tttp) REVERT: B 350 ARG cc_start: 0.7757 (mmm160) cc_final: 0.7104 (mmm160) REVERT: B 386 LEU cc_start: 0.9387 (mt) cc_final: 0.9174 (mt) REVERT: B 398 ASP cc_start: 0.9077 (t0) cc_final: 0.8766 (t0) REVERT: B 407 ILE cc_start: 0.9518 (mt) cc_final: 0.9020 (mt) REVERT: B 413 SER cc_start: 0.9511 (m) cc_final: 0.9032 (t) REVERT: B 415 ASN cc_start: 0.9522 (t0) cc_final: 0.9179 (t0) REVERT: B 426 GLU cc_start: 0.8576 (tm-30) cc_final: 0.7876 (tm-30) REVERT: B 427 LYS cc_start: 0.9342 (tppt) cc_final: 0.8999 (mmmm) REVERT: B 437 THR cc_start: 0.9626 (m) cc_final: 0.9405 (m) REVERT: B 447 ASN cc_start: 0.8772 (m-40) cc_final: 0.8464 (m-40) REVERT: B 459 LYS cc_start: 0.9328 (mttp) cc_final: 0.8759 (mtmm) REVERT: B 493 MET cc_start: 0.9357 (tmm) cc_final: 0.9059 (tmm) REVERT: B 501 GLN cc_start: 0.9243 (tt0) cc_final: 0.8984 (tt0) REVERT: B 505 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8135 (mt-10) REVERT: B 516 GLN cc_start: 0.9238 (mp10) cc_final: 0.8935 (mp10) REVERT: B 588 GLN cc_start: 0.9491 (mm-40) cc_final: 0.9100 (mm-40) REVERT: B 598 MET cc_start: 0.9160 (mtm) cc_final: 0.8903 (mtm) REVERT: B 599 GLU cc_start: 0.8726 (pt0) cc_final: 0.8479 (pt0) REVERT: B 628 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8199 (mm-30) REVERT: B 646 GLN cc_start: 0.9551 (pt0) cc_final: 0.9309 (pt0) REVERT: B 667 LEU cc_start: 0.9550 (tp) cc_final: 0.8961 (tp) REVERT: B 671 ASP cc_start: 0.9024 (m-30) cc_final: 0.8814 (m-30) REVERT: C 16 ASP cc_start: 0.6597 (p0) cc_final: 0.6084 (p0) REVERT: C 179 TYR cc_start: 0.8876 (t80) cc_final: 0.8565 (t80) REVERT: C 214 ASN cc_start: 0.8404 (p0) cc_final: 0.7767 (p0) REVERT: C 315 LEU cc_start: 0.8974 (mt) cc_final: 0.8770 (tt) REVERT: D 137 MET cc_start: 0.5977 (mtp) cc_final: 0.5457 (mpp) REVERT: D 158 VAL cc_start: 0.8225 (t) cc_final: 0.7803 (m) REVERT: D 178 PHE cc_start: 0.9000 (m-80) cc_final: 0.8427 (m-80) REVERT: D 208 LEU cc_start: 0.9012 (mt) cc_final: 0.8725 (mt) REVERT: D 233 ASN cc_start: 0.8752 (m110) cc_final: 0.7962 (m110) outliers start: 0 outliers final: 0 residues processed: 657 average time/residue: 0.1346 time to fit residues: 132.3190 Evaluate side-chains 571 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 571 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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: 0.9980 chunk 133 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN B 218 ASN B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 HIS B 645 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.096441 restraints weight = 39057.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.099844 restraints weight = 20781.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.101989 restraints weight = 13020.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.103499 restraints weight = 9298.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104397 restraints weight = 7295.598| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.7180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 16386 Z= 0.139 Angle : 0.658 8.009 22134 Z= 0.345 Chirality : 0.044 0.214 2360 Planarity : 0.004 0.047 2818 Dihedral : 10.539 172.663 2242 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.12 % Allowed : 0.58 % Favored : 99.30 % 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 aren not related in a simple way. whole: 0.73 (0.19), residues: 1932 helix: 1.00 (0.15), residues: 1135 sheet: -0.28 (0.41), residues: 148 loop : -0.05 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 196 TYR 0.030 0.002 TYR D 162 PHE 0.025 0.002 PHE A 171 TRP 0.055 0.002 TRP D 124 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00311 (16386) covalent geometry : angle 0.65781 (22134) hydrogen bonds : bond 0.03958 ( 871) hydrogen bonds : angle 5.02220 ( 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 670 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 668 time to evaluate : 0.641 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 15 GLU cc_start: 0.9128 (tt0) cc_final: 0.8907 (tt0) REVERT: A 54 LYS cc_start: 0.9717 (ttmm) cc_final: 0.9417 (ttmm) REVERT: A 99 LYS cc_start: 0.9426 (mmmt) cc_final: 0.9147 (mmmm) REVERT: A 106 LEU cc_start: 0.9580 (tp) cc_final: 0.9290 (tp) REVERT: A 107 LYS cc_start: 0.9265 (mtpp) cc_final: 0.8782 (mtpp) REVERT: A 116 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8482 (mt-10) REVERT: A 135 GLU cc_start: 0.9242 (mm-30) cc_final: 0.9021 (mp0) REVERT: A 139 GLU cc_start: 0.9406 (mm-30) cc_final: 0.9119 (mm-30) REVERT: A 142 ASN cc_start: 0.9407 (m-40) cc_final: 0.9067 (m110) REVERT: A 150 GLN cc_start: 0.9385 (tm-30) cc_final: 0.8807 (tm-30) REVERT: A 213 ILE cc_start: 0.8938 (mp) cc_final: 0.8585 (tt) REVERT: A 223 VAL cc_start: 0.9513 (m) cc_final: 0.9105 (p) REVERT: A 227 MET cc_start: 0.9398 (mtp) cc_final: 0.8917 (mtp) REVERT: A 251 LEU cc_start: 0.9630 (tp) cc_final: 0.9360 (tp) REVERT: A 256 ARG cc_start: 0.9280 (tmt170) cc_final: 0.8671 (ttp80) REVERT: A 286 ASP cc_start: 0.8632 (m-30) cc_final: 0.8365 (m-30) REVERT: A 322 MET cc_start: 0.8656 (mmp) cc_final: 0.8261 (mmm) REVERT: A 333 LYS cc_start: 0.9543 (ttmt) cc_final: 0.9083 (ttmm) REVERT: A 345 LYS cc_start: 0.9417 (tttt) cc_final: 0.9192 (tttt) REVERT: A 349 LEU cc_start: 0.9554 (mt) cc_final: 0.9210 (mt) REVERT: A 361 GLN cc_start: 0.9279 (tp40) cc_final: 0.8959 (tp-100) REVERT: A 362 ASP cc_start: 0.8375 (m-30) cc_final: 0.7665 (m-30) REVERT: A 407 ILE cc_start: 0.9178 (mt) cc_final: 0.8936 (mt) REVERT: A 431 LEU cc_start: 0.9213 (mm) cc_final: 0.8970 (mm) REVERT: A 437 THR cc_start: 0.9608 (m) cc_final: 0.9366 (m) REVERT: A 441 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8604 (mt-10) REVERT: A 458 MET cc_start: 0.9134 (mmp) cc_final: 0.8606 (mmp) REVERT: A 466 MET cc_start: 0.8716 (ptt) cc_final: 0.8496 (ptt) REVERT: A 505 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8797 (mt-10) REVERT: A 570 MET cc_start: 0.9169 (mtp) cc_final: 0.8757 (mtp) REVERT: A 588 GLN cc_start: 0.8893 (tp40) cc_final: 0.8644 (mm-40) REVERT: A 615 MET cc_start: 0.8944 (mmp) cc_final: 0.8679 (mmp) REVERT: A 632 MET cc_start: 0.8798 (mtp) cc_final: 0.8527 (mtp) REVERT: A 634 MET cc_start: 0.9236 (mmm) cc_final: 0.9002 (mmt) REVERT: A 639 ASP cc_start: 0.9145 (m-30) cc_final: 0.8678 (m-30) REVERT: A 643 THR cc_start: 0.9556 (p) cc_final: 0.9202 (t) REVERT: A 646 GLN cc_start: 0.9166 (pt0) cc_final: 0.8948 (pt0) REVERT: A 664 THR cc_start: 0.9279 (p) cc_final: 0.8554 (p) REVERT: A 667 LEU cc_start: 0.9616 (tt) cc_final: 0.9347 (tt) REVERT: A 668 ASN cc_start: 0.9367 (m110) cc_final: 0.9056 (m110) REVERT: B 25 GLN cc_start: 0.9110 (mt0) cc_final: 0.8515 (mt0) REVERT: B 71 LEU cc_start: 0.9724 (mm) cc_final: 0.9495 (mp) REVERT: B 87 LYS cc_start: 0.9363 (tptp) cc_final: 0.9041 (tptp) REVERT: B 117 ARG cc_start: 0.8887 (mtt180) cc_final: 0.8555 (ttm110) REVERT: B 120 ASP cc_start: 0.8840 (m-30) cc_final: 0.8625 (m-30) REVERT: B 147 GLN cc_start: 0.9153 (mt0) cc_final: 0.8831 (mt0) REVERT: B 149 TYR cc_start: 0.9423 (t80) cc_final: 0.8724 (t80) REVERT: B 172 LEU cc_start: 0.9449 (mp) cc_final: 0.8941 (mp) REVERT: B 174 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7927 (mm-30) REVERT: B 227 MET cc_start: 0.9381 (mtp) cc_final: 0.9096 (mtp) REVERT: B 232 ASN cc_start: 0.9097 (t0) cc_final: 0.8588 (t0) REVERT: B 278 LEU cc_start: 0.9268 (tp) cc_final: 0.9048 (tp) REVERT: B 279 SER cc_start: 0.8011 (m) cc_final: 0.7659 (p) REVERT: B 286 ASP cc_start: 0.8692 (m-30) cc_final: 0.8430 (m-30) REVERT: B 312 GLN cc_start: 0.9131 (pm20) cc_final: 0.8342 (pm20) REVERT: B 333 LYS cc_start: 0.9281 (tptp) cc_final: 0.9067 (tttp) REVERT: B 398 ASP cc_start: 0.8761 (t0) cc_final: 0.8556 (t0) REVERT: B 407 ILE cc_start: 0.9502 (mt) cc_final: 0.8999 (mt) REVERT: B 415 ASN cc_start: 0.9503 (t0) cc_final: 0.8924 (t0) REVERT: B 459 LYS cc_start: 0.9278 (mttp) cc_final: 0.8632 (mtmm) REVERT: B 472 LEU cc_start: 0.9636 (mm) cc_final: 0.9410 (mm) REVERT: B 493 MET cc_start: 0.9422 (tmm) cc_final: 0.9111 (tmm) REVERT: B 516 GLN cc_start: 0.9236 (mp10) cc_final: 0.8907 (mp10) REVERT: B 570 MET cc_start: 0.8804 (mtp) cc_final: 0.8379 (mtp) REVERT: B 585 SER cc_start: 0.9233 (p) cc_final: 0.8935 (t) REVERT: B 588 GLN cc_start: 0.9426 (mm-40) cc_final: 0.8755 (mm-40) REVERT: B 591 THR cc_start: 0.9440 (p) cc_final: 0.9232 (p) REVERT: B 628 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8359 (mm-30) REVERT: B 645 GLN cc_start: 0.9354 (tp40) cc_final: 0.9033 (tp-100) REVERT: B 646 GLN cc_start: 0.9530 (pt0) cc_final: 0.9246 (pt0) REVERT: B 650 GLN cc_start: 0.8014 (mt0) cc_final: 0.7470 (mm-40) REVERT: B 683 TYR cc_start: 0.8912 (t80) cc_final: 0.8583 (t80) REVERT: C 16 ASP cc_start: 0.6700 (p0) cc_final: 0.6159 (p0) REVERT: C 42 LEU cc_start: 0.8790 (pt) cc_final: 0.8543 (pt) REVERT: C 179 TYR cc_start: 0.8790 (t80) cc_final: 0.8556 (t80) REVERT: D 158 VAL cc_start: 0.8306 (t) cc_final: 0.7119 (m) REVERT: D 162 TYR cc_start: 0.8135 (m-80) cc_final: 0.7638 (m-80) REVERT: D 178 PHE cc_start: 0.9150 (m-80) cc_final: 0.8712 (m-80) REVERT: D 233 ASN cc_start: 0.8632 (m110) cc_final: 0.8309 (m-40) outliers start: 2 outliers final: 0 residues processed: 669 average time/residue: 0.1261 time to fit residues: 127.3507 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 : 0.551 ------------------------------------------------------------------------------- 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: 3.9990 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 189 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 165 optimal weight: 0.0170 chunk 16 optimal weight: 0.5980 chunk 54 optimal weight: 0.3980 chunk 132 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 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 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.140651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.098958 restraints weight = 39096.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.102443 restraints weight = 20696.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.104634 restraints weight = 12963.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.106047 restraints weight = 9238.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.107082 restraints weight = 7288.652| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.7369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16386 Z= 0.139 Angle : 0.663 7.794 22134 Z= 0.349 Chirality : 0.044 0.279 2360 Planarity : 0.004 0.047 2818 Dihedral : 10.272 162.558 2242 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.06 % Allowed : 0.17 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.19), residues: 1932 helix: 0.93 (0.15), residues: 1147 sheet: -0.03 (0.43), residues: 132 loop : -0.15 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 235 TYR 0.034 0.002 TYR A 498 PHE 0.031 0.002 PHE A 360 TRP 0.047 0.002 TRP D 124 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00311 (16386) covalent geometry : angle 0.66350 (22134) hydrogen bonds : bond 0.03953 ( 871) hydrogen bonds : angle 4.99709 ( 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 649 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 648 time to evaluate : 0.903 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 15 GLU cc_start: 0.9081 (tt0) cc_final: 0.8838 (tt0) REVERT: A 54 LYS cc_start: 0.9696 (ttmm) cc_final: 0.9390 (ttmm) REVERT: A 99 LYS cc_start: 0.9392 (mmmt) cc_final: 0.9145 (mmmm) REVERT: A 106 LEU cc_start: 0.9561 (tp) cc_final: 0.9278 (tp) REVERT: A 107 LYS cc_start: 0.9266 (mtpp) cc_final: 0.8803 (mtpp) REVERT: A 116 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8573 (mt-10) REVERT: A 135 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8992 (mp0) REVERT: A 139 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9117 (mm-30) REVERT: A 142 ASN cc_start: 0.9389 (m-40) cc_final: 0.9079 (m110) REVERT: A 150 GLN cc_start: 0.9360 (tm-30) cc_final: 0.9075 (tm-30) REVERT: A 213 ILE cc_start: 0.8878 (mp) cc_final: 0.8497 (tt) REVERT: A 223 VAL cc_start: 0.9484 (m) cc_final: 0.9089 (p) REVERT: A 227 MET cc_start: 0.9335 (mtp) cc_final: 0.8895 (mtp) REVERT: A 251 LEU cc_start: 0.9661 (tp) cc_final: 0.9409 (tp) REVERT: A 256 ARG cc_start: 0.9246 (tmt170) cc_final: 0.8653 (ttp80) REVERT: A 286 ASP cc_start: 0.8469 (m-30) cc_final: 0.8184 (m-30) REVERT: A 321 GLU cc_start: 0.8623 (pp20) cc_final: 0.7760 (pp20) REVERT: A 322 MET cc_start: 0.8553 (mmp) cc_final: 0.7223 (mmm) REVERT: A 333 LYS cc_start: 0.9554 (ttmt) cc_final: 0.9190 (ttmm) REVERT: A 349 LEU cc_start: 0.9541 (mt) cc_final: 0.9245 (mt) REVERT: A 361 GLN cc_start: 0.9316 (tp40) cc_final: 0.8912 (tp-100) REVERT: A 362 ASP cc_start: 0.8347 (m-30) cc_final: 0.7612 (m-30) REVERT: A 407 ILE cc_start: 0.9220 (mt) cc_final: 0.8969 (mt) REVERT: A 431 LEU cc_start: 0.9185 (mm) cc_final: 0.8954 (mm) REVERT: A 437 THR cc_start: 0.9608 (m) cc_final: 0.9285 (p) REVERT: A 458 MET cc_start: 0.9107 (mmp) cc_final: 0.8663 (mmm) REVERT: A 505 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8680 (mt-10) REVERT: A 570 MET cc_start: 0.9000 (mtp) cc_final: 0.8633 (mtp) REVERT: A 615 MET cc_start: 0.8855 (mmp) cc_final: 0.8599 (mmp) REVERT: A 636 LYS cc_start: 0.9549 (mmmm) cc_final: 0.8909 (mmmm) REVERT: A 639 ASP cc_start: 0.9114 (m-30) cc_final: 0.8797 (m-30) REVERT: A 643 THR cc_start: 0.9475 (p) cc_final: 0.9230 (t) REVERT: A 646 GLN cc_start: 0.9090 (pt0) cc_final: 0.8873 (pt0) REVERT: A 650 GLN cc_start: 0.8470 (mt0) cc_final: 0.8223 (mt0) REVERT: A 664 THR cc_start: 0.9263 (p) cc_final: 0.8559 (p) REVERT: A 667 LEU cc_start: 0.9618 (tt) cc_final: 0.9338 (tt) REVERT: B 87 LYS cc_start: 0.9360 (tptp) cc_final: 0.9056 (tptp) REVERT: B 116 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8949 (mt-10) REVERT: B 117 ARG cc_start: 0.8860 (mtt180) cc_final: 0.8539 (ttm110) REVERT: B 147 GLN cc_start: 0.9138 (mt0) cc_final: 0.8907 (mt0) REVERT: B 149 TYR cc_start: 0.9434 (t80) cc_final: 0.8713 (t80) REVERT: B 172 LEU cc_start: 0.9456 (mp) cc_final: 0.9174 (mp) REVERT: B 174 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7943 (mm-30) REVERT: B 227 MET cc_start: 0.9384 (mtp) cc_final: 0.9067 (mtp) REVERT: B 232 ASN cc_start: 0.9017 (t160) cc_final: 0.8640 (t0) REVERT: B 257 ASP cc_start: 0.8971 (m-30) cc_final: 0.8749 (m-30) REVERT: B 278 LEU cc_start: 0.9291 (tp) cc_final: 0.9087 (tp) REVERT: B 286 ASP cc_start: 0.8610 (m-30) cc_final: 0.8375 (m-30) REVERT: B 291 LEU cc_start: 0.9797 (mt) cc_final: 0.9462 (mt) REVERT: B 312 GLN cc_start: 0.9095 (pm20) cc_final: 0.8488 (pm20) REVERT: B 345 LYS cc_start: 0.9282 (tttt) cc_final: 0.9061 (tttt) REVERT: B 348 MET cc_start: 0.8821 (pmm) cc_final: 0.8555 (pmm) REVERT: B 378 PHE cc_start: 0.9334 (p90) cc_final: 0.9005 (p90) REVERT: B 415 ASN cc_start: 0.9549 (t0) cc_final: 0.9067 (t0) REVERT: B 441 GLU cc_start: 0.9131 (pt0) cc_final: 0.8917 (pt0) REVERT: B 459 LYS cc_start: 0.9282 (mttp) cc_final: 0.8723 (mtmm) REVERT: B 493 MET cc_start: 0.9399 (tmm) cc_final: 0.9085 (tmm) REVERT: B 501 GLN cc_start: 0.9640 (tt0) cc_final: 0.9118 (tt0) REVERT: B 516 GLN cc_start: 0.9201 (mp10) cc_final: 0.8841 (mp10) REVERT: B 550 MET cc_start: 0.8662 (ptt) cc_final: 0.8264 (ptp) REVERT: B 570 MET cc_start: 0.8731 (mtp) cc_final: 0.8135 (mtp) REVERT: B 585 SER cc_start: 0.9262 (p) cc_final: 0.8945 (t) REVERT: B 588 GLN cc_start: 0.9390 (mm-40) cc_final: 0.8631 (mm-40) REVERT: B 591 THR cc_start: 0.9238 (p) cc_final: 0.8965 (p) REVERT: B 615 MET cc_start: 0.9312 (mmp) cc_final: 0.9078 (mmp) REVERT: B 628 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8290 (mm-30) REVERT: B 646 GLN cc_start: 0.9477 (pt0) cc_final: 0.9199 (pt0) REVERT: B 650 GLN cc_start: 0.8341 (mt0) cc_final: 0.7856 (mm-40) REVERT: B 667 LEU cc_start: 0.9382 (tp) cc_final: 0.8951 (tp) REVERT: B 677 ARG cc_start: 0.9358 (mmm-85) cc_final: 0.8436 (mmm-85) REVERT: C 16 ASP cc_start: 0.6503 (p0) cc_final: 0.5933 (p0) REVERT: C 42 LEU cc_start: 0.8790 (pt) cc_final: 0.8552 (pt) REVERT: C 179 TYR cc_start: 0.8816 (t80) cc_final: 0.8545 (t80) REVERT: C 214 ASN cc_start: 0.8192 (p0) cc_final: 0.7985 (p0) REVERT: D 158 VAL cc_start: 0.8260 (t) cc_final: 0.7807 (m) REVERT: D 162 TYR cc_start: 0.8133 (m-80) cc_final: 0.7730 (m-80) REVERT: D 178 PHE cc_start: 0.9123 (m-80) cc_final: 0.8476 (m-80) REVERT: D 208 LEU cc_start: 0.8785 (mt) cc_final: 0.8414 (mt) REVERT: D 233 ASN cc_start: 0.8795 (m110) cc_final: 0.8233 (m-40) outliers start: 1 outliers final: 0 residues processed: 648 average time/residue: 0.1209 time to fit residues: 118.6015 Evaluate side-chains 581 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 581 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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: 1.9990 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.136680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.094784 restraints weight = 40043.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.098058 restraints weight = 21559.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.100200 restraints weight = 13726.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.101537 restraints weight = 9868.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.102442 restraints weight = 7818.538| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.7461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16386 Z= 0.209 Angle : 0.704 9.558 22134 Z= 0.373 Chirality : 0.045 0.300 2360 Planarity : 0.004 0.041 2818 Dihedral : 10.291 162.979 2242 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.06 % Allowed : 0.23 % 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 aren not related in a simple way. whole: 0.43 (0.19), residues: 1932 helix: 0.78 (0.15), residues: 1147 sheet: -0.55 (0.39), residues: 162 loop : -0.18 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 235 TYR 0.030 0.002 TYR A 498 PHE 0.024 0.002 PHE A 360 TRP 0.042 0.002 TRP D 124 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00456 (16386) covalent geometry : angle 0.70411 (22134) hydrogen bonds : bond 0.04067 ( 871) hydrogen bonds : angle 5.13278 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3361.78 seconds wall clock time: 58 minutes 58.13 seconds (3538.13 seconds total)