Starting phenix.real_space_refine on Wed Mar 4 11:06:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ek2_31166/03_2026/7ek2_31166.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ek2_31166/03_2026/7ek2_31166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ek2_31166/03_2026/7ek2_31166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ek2_31166/03_2026/7ek2_31166.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ek2_31166/03_2026/7ek2_31166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ek2_31166/03_2026/7ek2_31166.map" } resolution = 2.7 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= 0.001 sd= 0.020 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 8730 2.51 5 N 2360 2.21 5 O 2395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13540 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2708 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 16, 'TRANS': 324} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.04, per 1000 atoms: 0.15 Number of scatterers: 13540 At special positions: 0 Unit cell: (110.224, 112.88, 112.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 2395 8.00 N 2360 7.00 C 8730 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: 0.91 Conformation dependent library (CDL) restraints added in 651.7 milliseconds 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3290 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 86.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 89 through 101 Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.551A pdb=" N LEU A 127 " --> pdb=" O HIS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 139 through 162 Processing helix chain 'A' and resid 176 through 226 Proline residue: A 184 - end of helix Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 231 through 254 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 268 through 277 removed outlier: 3.879A pdb=" N VAL A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'A' and resid 310 through 326 removed outlier: 3.513A pdb=" N ILE A 324 " --> pdb=" O CYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 356 removed outlier: 3.759A pdb=" N THR A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Proline residue: A 348 - end of helix removed outlier: 4.940A pdb=" N ASP A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 380 removed outlier: 3.547A pdb=" N ILE A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 388 through 418 removed outlier: 3.640A pdb=" N VAL A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 417 " --> pdb=" O ARG A 413 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 88 Processing helix chain 'B' and resid 89 through 101 Processing helix chain 'B' and resid 110 through 118 Processing helix chain 'B' and resid 121 through 129 removed outlier: 3.551A pdb=" N LEU B 127 " --> pdb=" O HIS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 139 Processing helix chain 'B' and resid 139 through 162 Processing helix chain 'B' and resid 176 through 226 Proline residue: B 184 - end of helix Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 231 through 254 Proline residue: B 246 - end of helix Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.879A pdb=" N VAL B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 Processing helix chain 'B' and resid 299 through 308 Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.513A pdb=" N ILE B 324 " --> pdb=" O CYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 356 removed outlier: 3.759A pdb=" N THR B 336 " --> pdb=" O TYR B 332 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Proline residue: B 348 - end of helix removed outlier: 4.939A pdb=" N ASP B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP B 354 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 380 removed outlier: 3.547A pdb=" N ILE B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 388 through 418 removed outlier: 3.639A pdb=" N VAL B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 417 " --> pdb=" O ARG B 413 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 88 Processing helix chain 'C' and resid 89 through 101 Processing helix chain 'C' and resid 110 through 118 Processing helix chain 'C' and resid 121 through 129 removed outlier: 3.552A pdb=" N LEU C 127 " --> pdb=" O HIS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 Processing helix chain 'C' and resid 139 through 162 Processing helix chain 'C' and resid 176 through 226 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 231 through 254 Proline residue: C 246 - end of helix Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 268 through 277 removed outlier: 3.879A pdb=" N VAL C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 Processing helix chain 'C' and resid 299 through 308 Processing helix chain 'C' and resid 310 through 326 removed outlier: 3.513A pdb=" N ILE C 324 " --> pdb=" O CYS C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 356 removed outlier: 3.759A pdb=" N THR C 336 " --> pdb=" O TYR C 332 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Proline residue: C 348 - end of helix removed outlier: 4.940A pdb=" N ASP C 353 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP C 354 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 380 removed outlier: 3.546A pdb=" N ILE C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 388 through 418 removed outlier: 3.640A pdb=" N VAL C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 417 " --> pdb=" O ARG C 413 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 88 Processing helix chain 'D' and resid 89 through 101 Processing helix chain 'D' and resid 110 through 118 Processing helix chain 'D' and resid 121 through 129 removed outlier: 3.551A pdb=" N LEU D 127 " --> pdb=" O HIS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 139 Processing helix chain 'D' and resid 139 through 162 Processing helix chain 'D' and resid 176 through 226 Proline residue: D 184 - end of helix Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 231 through 254 Proline residue: D 246 - end of helix Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 268 through 277 removed outlier: 3.879A pdb=" N VAL D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 Processing helix chain 'D' and resid 299 through 308 Processing helix chain 'D' and resid 310 through 326 removed outlier: 3.513A pdb=" N ILE D 324 " --> pdb=" O CYS D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 356 removed outlier: 3.759A pdb=" N THR D 336 " --> pdb=" O TYR D 332 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) Proline residue: D 348 - end of helix removed outlier: 4.940A pdb=" N ASP D 353 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP D 354 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 380 removed outlier: 3.547A pdb=" N ILE D 373 " --> pdb=" O SER D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 Processing helix chain 'D' and resid 388 through 418 removed outlier: 3.640A pdb=" N VAL D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS D 417 " --> pdb=" O ARG D 413 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 88 Processing helix chain 'E' and resid 89 through 101 Processing helix chain 'E' and resid 110 through 118 Processing helix chain 'E' and resid 121 through 129 removed outlier: 3.551A pdb=" N LEU E 127 " --> pdb=" O HIS E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 139 Processing helix chain 'E' and resid 139 through 162 Processing helix chain 'E' and resid 176 through 226 Proline residue: E 184 - end of helix Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 231 through 254 Proline residue: E 246 - end of helix Processing helix chain 'E' and resid 258 through 263 Processing helix chain 'E' and resid 268 through 277 removed outlier: 3.880A pdb=" N VAL E 274 " --> pdb=" O ASP E 270 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL E 275 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 Processing helix chain 'E' and resid 299 through 308 Processing helix chain 'E' and resid 310 through 326 removed outlier: 3.513A pdb=" N ILE E 324 " --> pdb=" O CYS E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 356 removed outlier: 3.759A pdb=" N THR E 336 " --> pdb=" O TYR E 332 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) Proline residue: E 348 - end of helix removed outlier: 4.940A pdb=" N ASP E 353 " --> pdb=" O ILE E 349 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP E 354 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 380 removed outlier: 3.547A pdb=" N ILE E 373 " --> pdb=" O SER E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 Processing helix chain 'E' and resid 388 through 418 removed outlier: 3.639A pdb=" N VAL E 396 " --> pdb=" O LEU E 392 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS E 408 " --> pdb=" O LEU E 404 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU E 409 " --> pdb=" O ALA E 405 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS E 417 " --> pdb=" O ARG E 413 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY E 418 " --> pdb=" O LEU E 414 " (cutoff:3.500A) 1015 hydrogen bonds defined for protein. 3015 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: 2.47 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2110 1.29 - 1.42: 3527 1.42 - 1.55: 8102 1.55 - 1.68: 16 1.68 - 1.81: 75 Bond restraints: 13830 Sorted by residual: bond pdb=" C GLN B 401 " pdb=" O GLN B 401 " ideal model delta sigma weight residual 1.236 1.345 -0.109 1.15e-02 7.56e+03 8.93e+01 bond pdb=" C GLN D 401 " pdb=" O GLN D 401 " ideal model delta sigma weight residual 1.236 1.345 -0.109 1.15e-02 7.56e+03 8.93e+01 bond pdb=" C GLN E 401 " pdb=" O GLN E 401 " ideal model delta sigma weight residual 1.236 1.345 -0.109 1.15e-02 7.56e+03 8.92e+01 bond pdb=" C GLN A 401 " pdb=" O GLN A 401 " ideal model delta sigma weight residual 1.236 1.345 -0.108 1.15e-02 7.56e+03 8.89e+01 bond pdb=" C GLN C 401 " pdb=" O GLN C 401 " ideal model delta sigma weight residual 1.236 1.345 -0.108 1.15e-02 7.56e+03 8.83e+01 ... (remaining 13825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 14836 2.17 - 4.34: 3654 4.34 - 6.51: 285 6.51 - 8.69: 27 8.69 - 10.86: 8 Bond angle restraints: 18810 Sorted by residual: angle pdb=" C GLU A 382 " pdb=" CA GLU A 382 " pdb=" CB GLU A 382 " ideal model delta sigma weight residual 110.33 118.26 -7.93 1.02e+00 9.61e-01 6.04e+01 angle pdb=" C GLU B 382 " pdb=" CA GLU B 382 " pdb=" CB GLU B 382 " ideal model delta sigma weight residual 110.33 118.26 -7.93 1.02e+00 9.61e-01 6.04e+01 angle pdb=" C GLU E 382 " pdb=" CA GLU E 382 " pdb=" CB GLU E 382 " ideal model delta sigma weight residual 110.33 118.26 -7.93 1.02e+00 9.61e-01 6.04e+01 angle pdb=" C GLU D 382 " pdb=" CA GLU D 382 " pdb=" CB GLU D 382 " ideal model delta sigma weight residual 110.33 118.26 -7.93 1.02e+00 9.61e-01 6.04e+01 angle pdb=" C GLU C 382 " pdb=" CA GLU C 382 " pdb=" CB GLU C 382 " ideal model delta sigma weight residual 110.33 118.23 -7.90 1.02e+00 9.61e-01 5.99e+01 ... (remaining 18805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 7550 16.77 - 33.54: 645 33.54 - 50.31: 160 50.31 - 67.07: 20 67.07 - 83.84: 15 Dihedral angle restraints: 8390 sinusoidal: 3360 harmonic: 5030 Sorted by residual: dihedral pdb=" CA GLU B 382 " pdb=" C GLU B 382 " pdb=" N PRO B 383 " pdb=" CA PRO B 383 " ideal model delta harmonic sigma weight residual 180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA GLU C 382 " pdb=" C GLU C 382 " pdb=" N PRO C 383 " pdb=" CA PRO C 383 " ideal model delta harmonic sigma weight residual -180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA GLU D 382 " pdb=" C GLU D 382 " pdb=" N PRO D 383 " pdb=" CA PRO D 383 " ideal model delta harmonic sigma weight residual -180.00 -159.75 -20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 8387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1068 0.058 - 0.116: 774 0.116 - 0.175: 358 0.175 - 0.233: 35 0.233 - 0.291: 10 Chirality restraints: 2245 Sorted by residual: chirality pdb=" CB VAL E 378 " pdb=" CA VAL E 378 " pdb=" CG1 VAL E 378 " pdb=" CG2 VAL E 378 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB VAL C 378 " pdb=" CA VAL C 378 " pdb=" CG1 VAL C 378 " pdb=" CG2 VAL C 378 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB VAL A 378 " pdb=" CA VAL A 378 " pdb=" CG1 VAL A 378 " pdb=" CG2 VAL A 378 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 2242 not shown) Planarity restraints: 2345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 343 " 0.034 2.00e-02 2.50e+03 1.58e-02 6.26e+00 pdb=" CG TRP B 343 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP B 343 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 343 " -0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP B 343 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 343 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 343 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 343 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 343 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 343 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 343 " 0.033 2.00e-02 2.50e+03 1.58e-02 6.26e+00 pdb=" CG TRP C 343 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP C 343 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 343 " -0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP C 343 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 343 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 343 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 343 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 343 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 343 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 343 " 0.033 2.00e-02 2.50e+03 1.58e-02 6.25e+00 pdb=" CG TRP A 343 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP A 343 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 343 " -0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP A 343 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 343 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 343 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 343 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 343 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 343 " 0.016 2.00e-02 2.50e+03 ... (remaining 2342 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1360 2.77 - 3.31: 14132 3.31 - 3.84: 22770 3.84 - 4.37: 28598 4.37 - 4.90: 47163 Nonbonded interactions: 114023 Sorted by model distance: nonbonded pdb=" OH TYR C 179 " pdb=" OG1 THR C 346 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR D 179 " pdb=" OG1 THR D 346 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR A 179 " pdb=" OG1 THR A 346 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR B 179 " pdb=" OG1 THR B 346 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR E 179 " pdb=" OG1 THR E 346 " model vdw 2.245 3.040 ... (remaining 114018 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.540 Find NCS groups from input model: 0.150 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:7.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 : 0.017 0.109 13830 Z= 1.263 Angle : 1.769 10.857 18810 Z= 1.322 Chirality : 0.083 0.291 2245 Planarity : 0.005 0.019 2345 Dihedral : 13.886 83.843 5100 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.99 % Allowed : 3.63 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.19), residues: 1695 helix: 0.27 (0.13), residues: 1385 sheet: None (None), residues: 0 loop : -0.70 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 200 TYR 0.014 0.005 TYR B 179 PHE 0.022 0.004 PHE E 192 TRP 0.034 0.006 TRP B 343 HIS 0.009 0.003 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.01692 (13830) covalent geometry : angle 1.76938 (18810) hydrogen bonds : bond 0.19026 ( 1015) hydrogen bonds : angle 5.72028 ( 3015) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 240 time to evaluate : 0.533 Fit side-chains REVERT: A 88 ARG cc_start: 0.6747 (ttm-80) cc_final: 0.6392 (ttm110) REVERT: A 100 ARG cc_start: 0.7434 (ttp-110) cc_final: 0.7143 (ttm110) REVERT: A 103 ARG cc_start: 0.7337 (mtp85) cc_final: 0.7091 (mmm-85) REVERT: A 104 GLN cc_start: 0.7018 (mm110) cc_final: 0.6223 (pt0) REVERT: A 148 LEU cc_start: 0.8085 (mp) cc_final: 0.7877 (mt) REVERT: A 206 LYS cc_start: 0.8608 (mttp) cc_final: 0.8172 (mttp) REVERT: A 233 GLN cc_start: 0.7230 (mm-40) cc_final: 0.7008 (tp40) REVERT: A 332 TYR cc_start: 0.8763 (t80) cc_final: 0.8440 (t80) REVERT: A 354 ASP cc_start: 0.7033 (m-30) cc_final: 0.6431 (p0) REVERT: A 397 ARG cc_start: 0.8240 (ttp80) cc_final: 0.8022 (ttm170) REVERT: A 402 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6178 (mt-10) REVERT: B 104 GLN cc_start: 0.6832 (mm110) cc_final: 0.5923 (pt0) REVERT: B 206 LYS cc_start: 0.8356 (mttp) cc_final: 0.8094 (mmtp) REVERT: B 233 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6981 (mm110) REVERT: B 264 GLN cc_start: 0.8535 (tt0) cc_final: 0.8261 (tt0) REVERT: B 265 ASN cc_start: 0.8407 (m-40) cc_final: 0.8170 (m-40) REVERT: B 300 GLU cc_start: 0.8081 (tp30) cc_final: 0.7745 (mm-30) REVERT: B 397 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7674 (ttp80) REVERT: B 402 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6130 (mt-10) REVERT: C 92 ASP cc_start: 0.7190 (m-30) cc_final: 0.6810 (m-30) REVERT: C 103 ARG cc_start: 0.7385 (mtp85) cc_final: 0.7172 (mmm-85) REVERT: C 206 LYS cc_start: 0.8335 (mttp) cc_final: 0.7599 (mttp) REVERT: C 210 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7702 (mt-10) REVERT: C 217 ASP cc_start: 0.8729 (t70) cc_final: 0.8517 (t70) REVERT: C 233 GLN cc_start: 0.7384 (mm-40) cc_final: 0.7152 (mm-40) REVERT: C 264 GLN cc_start: 0.8148 (tt0) cc_final: 0.7834 (tt0) REVERT: C 297 LYS cc_start: 0.8575 (mmtp) cc_final: 0.8079 (mmtm) REVERT: C 315 GLU cc_start: 0.8224 (tt0) cc_final: 0.7586 (mt-10) REVERT: C 354 ASP cc_start: 0.7717 (m-30) cc_final: 0.7098 (p0) REVERT: C 391 ASP cc_start: 0.7968 (m-30) cc_final: 0.7449 (m-30) REVERT: C 401 GLN cc_start: 0.7959 (mt0) cc_final: 0.7701 (mt0) REVERT: C 402 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6144 (mt-10) REVERT: D 104 GLN cc_start: 0.7569 (mm110) cc_final: 0.7295 (mm110) REVERT: D 106 ARG cc_start: 0.7458 (mtt-85) cc_final: 0.7202 (mtp85) REVERT: D 206 LYS cc_start: 0.8400 (mttp) cc_final: 0.7929 (mttp) REVERT: D 210 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7843 (mt-10) REVERT: D 264 GLN cc_start: 0.8599 (tt0) cc_final: 0.8365 (tt0) REVERT: D 299 GLU cc_start: 0.8020 (tt0) cc_final: 0.7810 (tt0) REVERT: D 315 GLU cc_start: 0.8312 (tt0) cc_final: 0.7591 (mt-10) REVERT: D 397 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7770 (ttp80) REVERT: D 401 GLN cc_start: 0.7997 (mt0) cc_final: 0.7754 (mt0) REVERT: D 402 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6695 (mt-10) REVERT: E 163 ASP cc_start: 0.6697 (m-30) cc_final: 0.6432 (t0) REVERT: E 206 LYS cc_start: 0.8219 (mttp) cc_final: 0.7702 (mttp) REVERT: E 264 GLN cc_start: 0.8315 (tt0) cc_final: 0.8081 (tt0) REVERT: E 265 ASN cc_start: 0.8248 (m-40) cc_final: 0.7805 (m110) REVERT: E 397 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7925 (ttp80) REVERT: E 402 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6084 (mt-10) outliers start: 15 outliers final: 0 residues processed: 251 average time/residue: 0.8787 time to fit residues: 233.6930 Evaluate side-chains 184 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 179 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS A 401 GLN B 98 GLN B 123 HIS C 123 HIS D 98 GLN D 394 ASN E 123 HIS E 307 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.122375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.097879 restraints weight = 14510.360| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.40 r_work: 0.2774 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13830 Z= 0.140 Angle : 0.559 6.871 18810 Z= 0.290 Chirality : 0.039 0.150 2245 Planarity : 0.005 0.066 2345 Dihedral : 5.614 47.629 1875 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.57 % Allowed : 7.99 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.20), residues: 1695 helix: 1.54 (0.14), residues: 1430 sheet: None (None), residues: 0 loop : -0.39 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 200 TYR 0.012 0.001 TYR B 241 PHE 0.013 0.002 PHE D 245 TRP 0.016 0.002 TRP D 352 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00300 (13830) covalent geometry : angle 0.55922 (18810) hydrogen bonds : bond 0.05057 ( 1015) hydrogen bonds : angle 4.12884 ( 3015) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 0.495 Fit side-chains REVERT: A 88 ARG cc_start: 0.7160 (ttm-80) cc_final: 0.6801 (ttm110) REVERT: A 100 ARG cc_start: 0.8123 (ttp-110) cc_final: 0.7766 (ttm110) REVERT: A 104 GLN cc_start: 0.7511 (mm110) cc_final: 0.6909 (pt0) REVERT: A 162 LEU cc_start: 0.7825 (mt) cc_final: 0.7623 (mt) REVERT: A 206 LYS cc_start: 0.8905 (mttp) cc_final: 0.8437 (mtmt) REVERT: A 233 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7767 (mm110) REVERT: A 354 ASP cc_start: 0.7880 (m-30) cc_final: 0.7569 (p0) REVERT: A 390 ASP cc_start: 0.8305 (m-30) cc_final: 0.7882 (m-30) REVERT: B 98 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: B 104 GLN cc_start: 0.7458 (mm110) cc_final: 0.6671 (pt0) REVERT: B 206 LYS cc_start: 0.8800 (mttp) cc_final: 0.8431 (mttp) REVERT: B 233 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7573 (mm110) REVERT: B 264 GLN cc_start: 0.8608 (tt0) cc_final: 0.8347 (tt0) REVERT: B 297 LYS cc_start: 0.8396 (mmtp) cc_final: 0.8109 (mmtm) REVERT: B 390 ASP cc_start: 0.8183 (m-30) cc_final: 0.7946 (m-30) REVERT: C 116 HIS cc_start: 0.8392 (t-90) cc_final: 0.7980 (t70) REVERT: C 206 LYS cc_start: 0.8922 (mttp) cc_final: 0.8265 (mttp) REVERT: C 210 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8290 (mt-10) REVERT: C 262 ASP cc_start: 0.8537 (m-30) cc_final: 0.8190 (m-30) REVERT: C 264 GLN cc_start: 0.8355 (tt0) cc_final: 0.8036 (tt0) REVERT: C 297 LYS cc_start: 0.8558 (mmtp) cc_final: 0.8346 (tppt) REVERT: C 315 GLU cc_start: 0.8663 (tt0) cc_final: 0.8196 (mt-10) REVERT: C 354 ASP cc_start: 0.7963 (m-30) cc_final: 0.7644 (p0) REVERT: C 390 ASP cc_start: 0.8252 (m-30) cc_final: 0.7875 (m-30) REVERT: C 391 ASP cc_start: 0.8393 (m-30) cc_final: 0.8093 (m-30) REVERT: C 402 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.6852 (mt-10) REVERT: D 100 ARG cc_start: 0.8017 (ttm-80) cc_final: 0.7685 (ttm110) REVERT: D 104 GLN cc_start: 0.7933 (mm110) cc_final: 0.7706 (mm110) REVERT: D 206 LYS cc_start: 0.8750 (mttp) cc_final: 0.8230 (mttp) REVERT: D 210 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8262 (mt-10) REVERT: D 264 GLN cc_start: 0.8796 (tt0) cc_final: 0.8501 (tt0) REVERT: D 300 GLU cc_start: 0.8331 (tp30) cc_final: 0.7891 (mm-30) REVERT: D 315 GLU cc_start: 0.8655 (tt0) cc_final: 0.8108 (mt-10) REVERT: D 390 ASP cc_start: 0.8621 (m-30) cc_final: 0.8291 (m-30) REVERT: D 408 LYS cc_start: 0.7909 (tptp) cc_final: 0.7697 (tttm) REVERT: E 106 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7287 (mtt-85) REVERT: E 206 LYS cc_start: 0.8890 (mttp) cc_final: 0.8335 (mttp) REVERT: E 264 GLN cc_start: 0.8600 (tt0) cc_final: 0.8355 (tt0) REVERT: E 265 ASN cc_start: 0.8505 (m-40) cc_final: 0.8155 (m110) REVERT: E 390 ASP cc_start: 0.8404 (m-30) cc_final: 0.8149 (m-30) REVERT: E 402 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.6936 (mt-10) REVERT: E 417 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.5227 (mptt) outliers start: 39 outliers final: 12 residues processed: 217 average time/residue: 0.8266 time to fit residues: 190.7478 Evaluate side-chains 183 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 417 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 165 optimal weight: 10.0000 chunk 23 optimal weight: 0.3980 chunk 152 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN D 98 GLN D 123 HIS D 401 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.119975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.094657 restraints weight = 14133.726| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.39 r_work: 0.2781 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13830 Z= 0.145 Angle : 0.540 7.034 18810 Z= 0.277 Chirality : 0.039 0.156 2245 Planarity : 0.005 0.065 2345 Dihedral : 5.458 48.875 1875 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.30 % Allowed : 8.58 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.20), residues: 1695 helix: 1.78 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -0.33 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 200 TYR 0.013 0.001 TYR E 156 PHE 0.014 0.002 PHE D 245 TRP 0.013 0.002 TRP E 208 HIS 0.004 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00337 (13830) covalent geometry : angle 0.53995 (18810) hydrogen bonds : bond 0.05004 ( 1015) hydrogen bonds : angle 3.96921 ( 3015) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 181 time to evaluate : 0.448 Fit side-chains REVERT: A 88 ARG cc_start: 0.7124 (ttm-80) cc_final: 0.6673 (ttm110) REVERT: A 100 ARG cc_start: 0.8101 (ttp-110) cc_final: 0.7597 (ttm110) REVERT: A 104 GLN cc_start: 0.7476 (mm110) cc_final: 0.6834 (pt0) REVERT: A 162 LEU cc_start: 0.7883 (mt) cc_final: 0.7473 (mt) REVERT: A 206 LYS cc_start: 0.8907 (mttp) cc_final: 0.8489 (mttp) REVERT: A 233 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7763 (mm110) REVERT: A 306 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8369 (mt) REVERT: A 390 ASP cc_start: 0.8317 (m-30) cc_final: 0.7870 (m-30) REVERT: B 98 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: B 104 GLN cc_start: 0.7463 (mm110) cc_final: 0.6717 (pt0) REVERT: B 206 LYS cc_start: 0.8794 (mttp) cc_final: 0.8390 (mttp) REVERT: B 233 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7575 (mm110) REVERT: B 264 GLN cc_start: 0.8585 (tt0) cc_final: 0.8354 (tt0) REVERT: B 297 LYS cc_start: 0.8315 (mmtp) cc_final: 0.8009 (mmtm) REVERT: B 390 ASP cc_start: 0.8340 (m-30) cc_final: 0.7930 (m-30) REVERT: C 115 MET cc_start: 0.8277 (mtt) cc_final: 0.8045 (mtp) REVERT: C 116 HIS cc_start: 0.8471 (t-90) cc_final: 0.8159 (t70) REVERT: C 206 LYS cc_start: 0.8908 (mttp) cc_final: 0.8321 (mttp) REVERT: C 264 GLN cc_start: 0.8363 (tt0) cc_final: 0.8052 (tt0) REVERT: C 315 GLU cc_start: 0.8649 (tt0) cc_final: 0.8206 (mt-10) REVERT: C 390 ASP cc_start: 0.8327 (m-30) cc_final: 0.7937 (m-30) REVERT: C 402 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.6852 (mt-10) REVERT: D 100 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7825 (ttm110) REVERT: D 206 LYS cc_start: 0.8755 (mttp) cc_final: 0.8327 (mttp) REVERT: D 235 LYS cc_start: 0.8767 (tttt) cc_final: 0.8555 (tttt) REVERT: D 264 GLN cc_start: 0.8802 (tt0) cc_final: 0.8484 (tt0) REVERT: D 300 GLU cc_start: 0.8301 (tp30) cc_final: 0.7865 (mm-30) REVERT: D 315 GLU cc_start: 0.8582 (tt0) cc_final: 0.8077 (mt-10) REVERT: D 350 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8677 (pp) REVERT: D 390 ASP cc_start: 0.8608 (m-30) cc_final: 0.8219 (m-30) REVERT: E 106 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7370 (mtt-85) REVERT: E 115 MET cc_start: 0.8265 (mtm) cc_final: 0.8012 (mtp) REVERT: E 206 LYS cc_start: 0.8913 (mttp) cc_final: 0.8323 (mttp) REVERT: E 264 GLN cc_start: 0.8608 (tt0) cc_final: 0.8369 (tt0) REVERT: E 265 ASN cc_start: 0.8531 (m-40) cc_final: 0.8234 (m110) REVERT: E 390 ASP cc_start: 0.8492 (m-30) cc_final: 0.8106 (m-30) REVERT: E 402 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6785 (mt-10) outliers start: 50 outliers final: 18 residues processed: 218 average time/residue: 0.7758 time to fit residues: 180.6901 Evaluate side-chains 195 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 108 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN D 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.120401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.095641 restraints weight = 14905.162| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.46 r_work: 0.2782 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13830 Z= 0.148 Angle : 0.535 7.057 18810 Z= 0.274 Chirality : 0.039 0.155 2245 Planarity : 0.005 0.062 2345 Dihedral : 5.448 49.372 1875 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.84 % Allowed : 10.10 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.20), residues: 1695 helix: 1.83 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -0.29 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 397 TYR 0.009 0.001 TYR A 109 PHE 0.014 0.002 PHE B 146 TRP 0.012 0.002 TRP D 343 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00350 (13830) covalent geometry : angle 0.53545 (18810) hydrogen bonds : bond 0.04918 ( 1015) hydrogen bonds : angle 3.92067 ( 3015) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 0.528 Fit side-chains REVERT: A 88 ARG cc_start: 0.7146 (ttm-80) cc_final: 0.6836 (ttm110) REVERT: A 100 ARG cc_start: 0.8165 (ttp-110) cc_final: 0.7670 (ttm110) REVERT: A 104 GLN cc_start: 0.7552 (mm110) cc_final: 0.6981 (pt0) REVERT: A 162 LEU cc_start: 0.7852 (mt) cc_final: 0.7609 (mt) REVERT: A 206 LYS cc_start: 0.8826 (mttp) cc_final: 0.8384 (mttp) REVERT: A 233 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7595 (mm110) REVERT: A 306 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8302 (mt) REVERT: A 390 ASP cc_start: 0.8297 (m-30) cc_final: 0.7831 (m-30) REVERT: B 98 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: B 100 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7830 (ttm110) REVERT: B 104 GLN cc_start: 0.7417 (mm110) cc_final: 0.6586 (pt0) REVERT: B 206 LYS cc_start: 0.8758 (mttp) cc_final: 0.8320 (mttp) REVERT: B 233 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7493 (mm110) REVERT: B 264 GLN cc_start: 0.8567 (tt0) cc_final: 0.8326 (tt0) REVERT: B 297 LYS cc_start: 0.8253 (mmtp) cc_final: 0.7954 (mmtm) REVERT: B 390 ASP cc_start: 0.8326 (m-30) cc_final: 0.7918 (m-30) REVERT: C 104 GLN cc_start: 0.7522 (mm110) cc_final: 0.6503 (pt0) REVERT: C 115 MET cc_start: 0.8171 (mtt) cc_final: 0.7903 (mtp) REVERT: C 116 HIS cc_start: 0.8496 (t-90) cc_final: 0.8249 (t70) REVERT: C 132 SER cc_start: 0.8977 (p) cc_final: 0.8628 (m) REVERT: C 206 LYS cc_start: 0.8864 (mttp) cc_final: 0.8290 (mttp) REVERT: C 264 GLN cc_start: 0.8370 (tt0) cc_final: 0.8053 (tt0) REVERT: C 315 GLU cc_start: 0.8750 (tt0) cc_final: 0.8223 (mt-10) REVERT: C 390 ASP cc_start: 0.8360 (m-30) cc_final: 0.7931 (m-30) REVERT: C 402 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.6784 (mt-10) REVERT: D 88 ARG cc_start: 0.7153 (ttm-80) cc_final: 0.6899 (ttm110) REVERT: D 100 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7890 (ttm110) REVERT: D 206 LYS cc_start: 0.8709 (mttp) cc_final: 0.8252 (mttp) REVERT: D 235 LYS cc_start: 0.8733 (tttt) cc_final: 0.8465 (ttmt) REVERT: D 264 GLN cc_start: 0.8737 (tt0) cc_final: 0.8398 (tt0) REVERT: D 300 GLU cc_start: 0.8254 (tp30) cc_final: 0.7805 (mm-30) REVERT: D 315 GLU cc_start: 0.8739 (tt0) cc_final: 0.8208 (mt-10) REVERT: D 382 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: D 390 ASP cc_start: 0.8520 (m-30) cc_final: 0.8171 (m-30) REVERT: E 88 ARG cc_start: 0.7149 (ttm-80) cc_final: 0.6941 (mtp85) REVERT: E 99 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6604 (mm-30) REVERT: E 106 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7361 (mtt-85) REVERT: E 115 MET cc_start: 0.8186 (mtm) cc_final: 0.7916 (mtp) REVERT: E 206 LYS cc_start: 0.8818 (mttp) cc_final: 0.8294 (mttp) REVERT: E 264 GLN cc_start: 0.8586 (tt0) cc_final: 0.8349 (tt0) REVERT: E 300 GLU cc_start: 0.8586 (tp30) cc_final: 0.8113 (mm-30) REVERT: E 390 ASP cc_start: 0.8480 (m-30) cc_final: 0.8098 (m-30) REVERT: E 402 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.6651 (mt-10) outliers start: 43 outliers final: 20 residues processed: 214 average time/residue: 0.8151 time to fit residues: 186.1864 Evaluate side-chains 203 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN D 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.122279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.097733 restraints weight = 14894.707| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.45 r_work: 0.2810 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13830 Z= 0.124 Angle : 0.500 6.990 18810 Z= 0.255 Chirality : 0.038 0.154 2245 Planarity : 0.005 0.054 2345 Dihedral : 5.307 49.605 1875 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.71 % Allowed : 10.83 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.21), residues: 1695 helix: 2.04 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -0.21 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 200 TYR 0.012 0.001 TYR E 156 PHE 0.012 0.002 PHE A 146 TRP 0.012 0.002 TRP A 343 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00274 (13830) covalent geometry : angle 0.50041 (18810) hydrogen bonds : bond 0.04448 ( 1015) hydrogen bonds : angle 3.80553 ( 3015) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.467 Fit side-chains REVERT: A 88 ARG cc_start: 0.7156 (ttm-80) cc_final: 0.6785 (ttm110) REVERT: A 100 ARG cc_start: 0.8113 (ttp-110) cc_final: 0.7617 (ttm110) REVERT: A 104 GLN cc_start: 0.7518 (mm110) cc_final: 0.6987 (pt0) REVERT: A 206 LYS cc_start: 0.8835 (mttp) cc_final: 0.8393 (mttp) REVERT: A 233 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7549 (mm110) REVERT: A 306 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8296 (mt) REVERT: A 390 ASP cc_start: 0.8280 (m-30) cc_final: 0.7821 (m-30) REVERT: B 104 GLN cc_start: 0.7397 (mm110) cc_final: 0.6592 (pt0) REVERT: B 206 LYS cc_start: 0.8762 (mttp) cc_final: 0.8320 (mttp) REVERT: B 233 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7446 (mm110) REVERT: B 264 GLN cc_start: 0.8569 (tt0) cc_final: 0.8332 (tt0) REVERT: B 390 ASP cc_start: 0.8318 (m-30) cc_final: 0.7937 (m-30) REVERT: C 104 GLN cc_start: 0.7541 (mm110) cc_final: 0.6533 (pt0) REVERT: C 113 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8579 (mtpt) REVERT: C 115 MET cc_start: 0.8159 (mtt) cc_final: 0.7892 (mtp) REVERT: C 116 HIS cc_start: 0.8497 (t-90) cc_final: 0.8255 (t70) REVERT: C 132 SER cc_start: 0.8910 (p) cc_final: 0.8608 (m) REVERT: C 206 LYS cc_start: 0.8883 (mttp) cc_final: 0.8313 (mttp) REVERT: C 264 GLN cc_start: 0.8357 (tt0) cc_final: 0.8028 (tt0) REVERT: C 315 GLU cc_start: 0.8693 (tt0) cc_final: 0.8292 (mt-10) REVERT: C 390 ASP cc_start: 0.8329 (m-30) cc_final: 0.7916 (m-30) REVERT: C 402 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.6764 (mt-10) REVERT: D 100 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7855 (ttm110) REVERT: D 104 GLN cc_start: 0.7701 (mm110) cc_final: 0.6957 (pt0) REVERT: D 206 LYS cc_start: 0.8705 (mttp) cc_final: 0.8234 (mttp) REVERT: D 235 LYS cc_start: 0.8701 (tttt) cc_final: 0.8424 (ttmt) REVERT: D 264 GLN cc_start: 0.8674 (tt0) cc_final: 0.8345 (tt0) REVERT: D 300 GLU cc_start: 0.8319 (tp30) cc_final: 0.7927 (mm-30) REVERT: D 382 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7853 (tm-30) REVERT: D 390 ASP cc_start: 0.8517 (m-30) cc_final: 0.8185 (m-30) REVERT: E 99 GLU cc_start: 0.7470 (mm-30) cc_final: 0.6790 (mm-30) REVERT: E 106 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7357 (mtt-85) REVERT: E 115 MET cc_start: 0.8118 (mtm) cc_final: 0.7837 (mtp) REVERT: E 206 LYS cc_start: 0.8759 (mttp) cc_final: 0.8295 (mttp) REVERT: E 264 GLN cc_start: 0.8578 (tt0) cc_final: 0.8333 (tt0) REVERT: E 300 GLU cc_start: 0.8508 (tp30) cc_final: 0.8115 (mm-30) REVERT: E 390 ASP cc_start: 0.8456 (m-30) cc_final: 0.8086 (m-30) REVERT: E 402 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6659 (mt-10) outliers start: 41 outliers final: 20 residues processed: 211 average time/residue: 0.8139 time to fit residues: 183.1618 Evaluate side-chains 200 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 73 optimal weight: 0.2980 chunk 30 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 144 optimal weight: 0.0050 chunk 17 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 overall best weight: 3.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN D 98 GLN D 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.120164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.095338 restraints weight = 14888.520| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.45 r_work: 0.2778 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13830 Z= 0.160 Angle : 0.548 7.091 18810 Z= 0.279 Chirality : 0.040 0.158 2245 Planarity : 0.005 0.060 2345 Dihedral : 5.466 49.250 1875 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.10 % Allowed : 10.76 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.20), residues: 1695 helix: 1.86 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -0.32 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 397 TYR 0.011 0.002 TYR C 156 PHE 0.016 0.002 PHE B 146 TRP 0.011 0.002 TRP B 208 HIS 0.005 0.001 HIS D 344 Details of bonding type rmsd covalent geometry : bond 0.00388 (13830) covalent geometry : angle 0.54798 (18810) hydrogen bonds : bond 0.05040 ( 1015) hydrogen bonds : angle 3.90613 ( 3015) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 183 time to evaluate : 0.499 Fit side-chains REVERT: A 88 ARG cc_start: 0.7241 (ttm-80) cc_final: 0.6942 (ttm110) REVERT: A 100 ARG cc_start: 0.8139 (ttp-110) cc_final: 0.7641 (ttm110) REVERT: A 104 GLN cc_start: 0.7516 (mm110) cc_final: 0.7009 (pt0) REVERT: A 155 SER cc_start: 0.8748 (m) cc_final: 0.8455 (m) REVERT: A 206 LYS cc_start: 0.8806 (mttp) cc_final: 0.8355 (mttp) REVERT: A 233 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7584 (mm110) REVERT: A 306 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8353 (mt) REVERT: A 390 ASP cc_start: 0.8329 (m-30) cc_final: 0.7830 (m-30) REVERT: B 98 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: B 104 GLN cc_start: 0.7450 (mm110) cc_final: 0.6686 (pt0) REVERT: B 206 LYS cc_start: 0.8756 (mttp) cc_final: 0.8312 (mttp) REVERT: B 233 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7527 (mm110) REVERT: B 264 GLN cc_start: 0.8578 (tt0) cc_final: 0.8334 (tt0) REVERT: B 390 ASP cc_start: 0.8352 (m-30) cc_final: 0.7945 (m-30) REVERT: C 88 ARG cc_start: 0.6863 (ttm-80) cc_final: 0.6291 (ttm110) REVERT: C 104 GLN cc_start: 0.7590 (mm110) cc_final: 0.6534 (pt0) REVERT: C 115 MET cc_start: 0.8158 (mtt) cc_final: 0.7892 (mtp) REVERT: C 116 HIS cc_start: 0.8553 (t-90) cc_final: 0.8281 (t70) REVERT: C 132 SER cc_start: 0.8904 (p) cc_final: 0.8602 (m) REVERT: C 206 LYS cc_start: 0.8874 (mttp) cc_final: 0.8289 (mttp) REVERT: C 264 GLN cc_start: 0.8390 (tt0) cc_final: 0.8058 (tt0) REVERT: C 315 GLU cc_start: 0.8716 (tt0) cc_final: 0.8355 (mt-10) REVERT: C 390 ASP cc_start: 0.8353 (m-30) cc_final: 0.7912 (m-30) REVERT: C 402 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.6780 (mt-10) REVERT: D 88 ARG cc_start: 0.7241 (ttm-80) cc_final: 0.6982 (ttm110) REVERT: D 100 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7813 (ttm110) REVERT: D 104 GLN cc_start: 0.7767 (mm110) cc_final: 0.7024 (pt0) REVERT: D 206 LYS cc_start: 0.8710 (mttp) cc_final: 0.8249 (mttp) REVERT: D 235 LYS cc_start: 0.8731 (tttt) cc_final: 0.8467 (ttmt) REVERT: D 264 GLN cc_start: 0.8734 (tt0) cc_final: 0.8387 (tt0) REVERT: D 300 GLU cc_start: 0.8338 (tp30) cc_final: 0.7929 (mm-30) REVERT: D 382 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7936 (tm-30) REVERT: D 390 ASP cc_start: 0.8566 (m-30) cc_final: 0.8179 (m-30) REVERT: D 397 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8194 (ttp80) REVERT: E 88 ARG cc_start: 0.7267 (ttm-80) cc_final: 0.7024 (mtp85) REVERT: E 99 GLU cc_start: 0.7484 (mm-30) cc_final: 0.6762 (mm-30) REVERT: E 106 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7333 (mtt-85) REVERT: E 115 MET cc_start: 0.8202 (mtm) cc_final: 0.7939 (mtp) REVERT: E 206 LYS cc_start: 0.8754 (mttp) cc_final: 0.8283 (mttp) REVERT: E 264 GLN cc_start: 0.8595 (tt0) cc_final: 0.8354 (tt0) REVERT: E 300 GLU cc_start: 0.8512 (tp30) cc_final: 0.8111 (mm-30) REVERT: E 390 ASP cc_start: 0.8403 (m-30) cc_final: 0.8020 (m-30) REVERT: E 402 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6687 (mt-10) REVERT: E 408 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7706 (tppt) outliers start: 47 outliers final: 23 residues processed: 216 average time/residue: 0.8152 time to fit residues: 187.6381 Evaluate side-chains 204 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 408 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 128 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 98 optimal weight: 0.0770 chunk 124 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.123776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.099313 restraints weight = 14790.832| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.46 r_work: 0.2841 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13830 Z= 0.113 Angle : 0.484 6.949 18810 Z= 0.244 Chirality : 0.037 0.154 2245 Planarity : 0.005 0.040 2345 Dihedral : 5.201 48.678 1875 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.64 % Allowed : 11.62 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.21), residues: 1695 helix: 2.22 (0.14), residues: 1430 sheet: None (None), residues: 0 loop : -0.13 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 100 TYR 0.007 0.001 TYR C 241 PHE 0.010 0.002 PHE A 146 TRP 0.014 0.001 TRP A 343 HIS 0.003 0.001 HIS C 344 Details of bonding type rmsd covalent geometry : bond 0.00240 (13830) covalent geometry : angle 0.48391 (18810) hydrogen bonds : bond 0.04084 ( 1015) hydrogen bonds : angle 3.72528 ( 3015) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 0.565 Fit side-chains REVERT: A 88 ARG cc_start: 0.7248 (ttm-80) cc_final: 0.6883 (ttm110) REVERT: A 100 ARG cc_start: 0.8189 (ttp-110) cc_final: 0.7707 (ttm110) REVERT: A 104 GLN cc_start: 0.7505 (mm110) cc_final: 0.7010 (pt0) REVERT: A 155 SER cc_start: 0.8758 (m) cc_final: 0.8534 (m) REVERT: A 206 LYS cc_start: 0.8856 (mttp) cc_final: 0.8409 (mttp) REVERT: A 233 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7647 (mm110) REVERT: A 390 ASP cc_start: 0.8215 (m-30) cc_final: 0.7737 (m-30) REVERT: B 100 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7649 (ttp-110) REVERT: B 103 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7541 (mtm180) REVERT: B 104 GLN cc_start: 0.7453 (mm110) cc_final: 0.6717 (pt0) REVERT: B 206 LYS cc_start: 0.8746 (mttp) cc_final: 0.8291 (mttp) REVERT: B 233 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7457 (mm110) REVERT: B 264 GLN cc_start: 0.8689 (tt0) cc_final: 0.8408 (tt0) REVERT: B 390 ASP cc_start: 0.8367 (m-30) cc_final: 0.7939 (m-30) REVERT: B 402 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.6935 (mt-10) REVERT: C 104 GLN cc_start: 0.7596 (mm110) cc_final: 0.6560 (pt0) REVERT: C 115 MET cc_start: 0.8142 (mtt) cc_final: 0.7886 (mtp) REVERT: C 116 HIS cc_start: 0.8494 (t-90) cc_final: 0.8240 (t70) REVERT: C 132 SER cc_start: 0.8905 (p) cc_final: 0.8620 (m) REVERT: C 206 LYS cc_start: 0.8891 (mttp) cc_final: 0.8313 (mttp) REVERT: C 264 GLN cc_start: 0.8372 (tt0) cc_final: 0.8040 (tt0) REVERT: C 315 GLU cc_start: 0.8602 (tt0) cc_final: 0.8161 (mt-10) REVERT: C 390 ASP cc_start: 0.8276 (m-30) cc_final: 0.7873 (m-30) REVERT: C 402 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6738 (mt-10) REVERT: D 88 ARG cc_start: 0.7199 (ttm-80) cc_final: 0.6953 (ttm110) REVERT: D 100 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7794 (ttm110) REVERT: D 104 GLN cc_start: 0.7770 (mm110) cc_final: 0.7039 (pt0) REVERT: D 206 LYS cc_start: 0.8705 (mttp) cc_final: 0.8226 (mttp) REVERT: D 235 LYS cc_start: 0.8677 (tttt) cc_final: 0.8407 (ttmt) REVERT: D 264 GLN cc_start: 0.8661 (tt0) cc_final: 0.8326 (tt0) REVERT: D 300 GLU cc_start: 0.8273 (tp30) cc_final: 0.7884 (mm-30) REVERT: D 390 ASP cc_start: 0.8511 (m-30) cc_final: 0.8181 (m-30) REVERT: E 88 ARG cc_start: 0.7210 (ttm-80) cc_final: 0.6967 (mtp85) REVERT: E 99 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6822 (mm-30) REVERT: E 106 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7248 (mtt-85) REVERT: E 115 MET cc_start: 0.8160 (mtm) cc_final: 0.7872 (mtp) REVERT: E 206 LYS cc_start: 0.8763 (mttp) cc_final: 0.8285 (mttp) REVERT: E 264 GLN cc_start: 0.8592 (tt0) cc_final: 0.8347 (tt0) REVERT: E 300 GLU cc_start: 0.8470 (tp30) cc_final: 0.8091 (mm-30) REVERT: E 390 ASP cc_start: 0.8334 (m-30) cc_final: 0.7972 (m-30) REVERT: E 402 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6654 (mt-10) outliers start: 40 outliers final: 14 residues processed: 210 average time/residue: 0.8084 time to fit residues: 180.7877 Evaluate side-chains 192 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 124 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.120085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.095794 restraints weight = 14822.735| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.37 r_work: 0.2802 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13830 Z= 0.164 Angle : 0.551 7.255 18810 Z= 0.280 Chirality : 0.040 0.159 2245 Planarity : 0.005 0.058 2345 Dihedral : 5.441 49.307 1875 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.31 % Allowed : 12.08 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.21), residues: 1695 helix: 1.95 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -0.25 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 100 TYR 0.010 0.002 TYR B 241 PHE 0.016 0.002 PHE B 146 TRP 0.011 0.002 TRP A 343 HIS 0.004 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00399 (13830) covalent geometry : angle 0.55064 (18810) hydrogen bonds : bond 0.05010 ( 1015) hydrogen bonds : angle 3.88095 ( 3015) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.511 Fit side-chains REVERT: A 88 ARG cc_start: 0.7404 (ttm-80) cc_final: 0.7040 (ttm110) REVERT: A 100 ARG cc_start: 0.8230 (ttp-110) cc_final: 0.7751 (ttm110) REVERT: A 104 GLN cc_start: 0.7656 (mm110) cc_final: 0.7131 (pt0) REVERT: A 155 SER cc_start: 0.8742 (m) cc_final: 0.8463 (m) REVERT: A 206 LYS cc_start: 0.8822 (mttp) cc_final: 0.8396 (mttp) REVERT: A 233 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7661 (mm110) REVERT: A 374 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: A 390 ASP cc_start: 0.8315 (m-30) cc_final: 0.7829 (m-30) REVERT: B 100 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.7736 (ttp-110) REVERT: B 104 GLN cc_start: 0.7487 (mm110) cc_final: 0.6779 (pt0) REVERT: B 206 LYS cc_start: 0.8796 (mttp) cc_final: 0.8362 (mttp) REVERT: B 233 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7522 (mm110) REVERT: B 264 GLN cc_start: 0.8598 (tt0) cc_final: 0.8356 (tt0) REVERT: B 390 ASP cc_start: 0.8358 (m-30) cc_final: 0.7954 (m-30) REVERT: B 402 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7037 (mt-10) REVERT: C 88 ARG cc_start: 0.6983 (ttm-80) cc_final: 0.6430 (ttm110) REVERT: C 104 GLN cc_start: 0.7650 (mm110) cc_final: 0.6615 (pt0) REVERT: C 115 MET cc_start: 0.8242 (mtt) cc_final: 0.7993 (mtp) REVERT: C 116 HIS cc_start: 0.8609 (t-90) cc_final: 0.8346 (t70) REVERT: C 132 SER cc_start: 0.8936 (p) cc_final: 0.8653 (m) REVERT: C 206 LYS cc_start: 0.8900 (mttp) cc_final: 0.8362 (mttp) REVERT: C 264 GLN cc_start: 0.8421 (tt0) cc_final: 0.8112 (tt0) REVERT: C 315 GLU cc_start: 0.8702 (tt0) cc_final: 0.8369 (mt-10) REVERT: C 390 ASP cc_start: 0.8387 (m-30) cc_final: 0.7962 (m-30) REVERT: C 402 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.6902 (mt-10) REVERT: D 88 ARG cc_start: 0.7421 (ttm-80) cc_final: 0.7184 (ttm110) REVERT: D 100 ARG cc_start: 0.8054 (ttm-80) cc_final: 0.7724 (ttm110) REVERT: D 104 GLN cc_start: 0.7878 (mm110) cc_final: 0.7145 (pt0) REVERT: D 206 LYS cc_start: 0.8736 (mttp) cc_final: 0.8303 (mttp) REVERT: D 235 LYS cc_start: 0.8810 (tttt) cc_final: 0.8548 (ttmt) REVERT: D 264 GLN cc_start: 0.8731 (tt0) cc_final: 0.8400 (tt0) REVERT: D 300 GLU cc_start: 0.8347 (tp30) cc_final: 0.7933 (mm-30) REVERT: D 390 ASP cc_start: 0.8582 (m-30) cc_final: 0.8209 (m-30) REVERT: E 88 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.7276 (mtp85) REVERT: E 99 GLU cc_start: 0.7429 (mm-30) cc_final: 0.6694 (mm-30) REVERT: E 106 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7380 (mtt-85) REVERT: E 115 MET cc_start: 0.8298 (mtm) cc_final: 0.8024 (mtp) REVERT: E 206 LYS cc_start: 0.8803 (mttp) cc_final: 0.8357 (mttp) REVERT: E 264 GLN cc_start: 0.8630 (tt0) cc_final: 0.8416 (tt0) REVERT: E 300 GLU cc_start: 0.8526 (tp30) cc_final: 0.8145 (mm-30) REVERT: E 390 ASP cc_start: 0.8426 (m-30) cc_final: 0.8059 (m-30) REVERT: E 402 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6788 (mt-10) outliers start: 35 outliers final: 19 residues processed: 209 average time/residue: 0.8192 time to fit residues: 182.5253 Evaluate side-chains 199 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 48 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.120428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.095605 restraints weight = 14924.862| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.45 r_work: 0.2775 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13830 Z= 0.164 Angle : 0.556 7.565 18810 Z= 0.282 Chirality : 0.040 0.157 2245 Planarity : 0.005 0.058 2345 Dihedral : 5.526 49.746 1875 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.24 % Allowed : 12.41 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.20), residues: 1695 helix: 1.88 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -0.43 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 397 TYR 0.011 0.002 TYR E 156 PHE 0.016 0.002 PHE B 146 TRP 0.011 0.002 TRP A 343 HIS 0.005 0.001 HIS D 344 Details of bonding type rmsd covalent geometry : bond 0.00402 (13830) covalent geometry : angle 0.55557 (18810) hydrogen bonds : bond 0.05029 ( 1015) hydrogen bonds : angle 3.91422 ( 3015) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.542 Fit side-chains REVERT: A 88 ARG cc_start: 0.7311 (ttm-80) cc_final: 0.6920 (ttm110) REVERT: A 100 ARG cc_start: 0.8193 (ttp-110) cc_final: 0.7714 (ttm110) REVERT: A 104 GLN cc_start: 0.7610 (mm110) cc_final: 0.7074 (pt0) REVERT: A 155 SER cc_start: 0.8727 (m) cc_final: 0.8446 (m) REVERT: A 206 LYS cc_start: 0.8811 (mttp) cc_final: 0.8362 (mttp) REVERT: A 233 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7653 (mm110) REVERT: A 374 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8236 (tm-30) REVERT: A 390 ASP cc_start: 0.8281 (m-30) cc_final: 0.7757 (m-30) REVERT: B 100 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7650 (ttp-110) REVERT: B 104 GLN cc_start: 0.7439 (mm110) cc_final: 0.6716 (pt0) REVERT: B 206 LYS cc_start: 0.8762 (mttp) cc_final: 0.8309 (mttp) REVERT: B 233 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7449 (mm110) REVERT: B 264 GLN cc_start: 0.8645 (tt0) cc_final: 0.8405 (tt0) REVERT: B 297 LYS cc_start: 0.8320 (mmtp) cc_final: 0.7989 (mmtm) REVERT: B 390 ASP cc_start: 0.8342 (m-30) cc_final: 0.7921 (m-30) REVERT: B 402 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.6957 (mt-10) REVERT: C 88 ARG cc_start: 0.6917 (ttm-80) cc_final: 0.6468 (ttm110) REVERT: C 104 GLN cc_start: 0.7482 (mm110) cc_final: 0.6529 (pt0) REVERT: C 115 MET cc_start: 0.8168 (mtt) cc_final: 0.7904 (mtp) REVERT: C 116 HIS cc_start: 0.8577 (t-90) cc_final: 0.8305 (t70) REVERT: C 132 SER cc_start: 0.8914 (p) cc_final: 0.8634 (m) REVERT: C 206 LYS cc_start: 0.8882 (mttp) cc_final: 0.8307 (mttp) REVERT: C 264 GLN cc_start: 0.8393 (tt0) cc_final: 0.8077 (tt0) REVERT: C 315 GLU cc_start: 0.8714 (tt0) cc_final: 0.8367 (mt-10) REVERT: C 390 ASP cc_start: 0.8357 (m-30) cc_final: 0.7905 (m-30) REVERT: C 402 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.6807 (mt-10) REVERT: D 88 ARG cc_start: 0.7376 (ttm-80) cc_final: 0.7096 (ttm110) REVERT: D 100 ARG cc_start: 0.8110 (ttm-80) cc_final: 0.7810 (ttm110) REVERT: D 104 GLN cc_start: 0.7847 (mm110) cc_final: 0.7097 (pt0) REVERT: D 206 LYS cc_start: 0.8707 (mttp) cc_final: 0.8251 (mttp) REVERT: D 235 LYS cc_start: 0.8751 (tttt) cc_final: 0.8293 (tttp) REVERT: D 264 GLN cc_start: 0.8731 (tt0) cc_final: 0.8390 (tt0) REVERT: D 300 GLU cc_start: 0.8237 (tp30) cc_final: 0.7805 (mm-30) REVERT: D 390 ASP cc_start: 0.8578 (m-30) cc_final: 0.8155 (m-30) REVERT: E 88 ARG cc_start: 0.7527 (ttm-80) cc_final: 0.7234 (mtp85) REVERT: E 99 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6665 (mm-30) REVERT: E 106 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7330 (mtt-85) REVERT: E 115 MET cc_start: 0.8232 (mtm) cc_final: 0.7944 (mtp) REVERT: E 206 LYS cc_start: 0.8769 (mttp) cc_final: 0.8294 (mttp) REVERT: E 264 GLN cc_start: 0.8611 (tt0) cc_final: 0.8365 (tt0) REVERT: E 300 GLU cc_start: 0.8510 (tp30) cc_final: 0.8118 (mm-30) REVERT: E 390 ASP cc_start: 0.8401 (m-30) cc_final: 0.8017 (m-30) REVERT: E 402 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6678 (mt-10) outliers start: 34 outliers final: 20 residues processed: 208 average time/residue: 0.8010 time to fit residues: 177.6862 Evaluate side-chains 205 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN D 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.120654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.095846 restraints weight = 14808.134| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.46 r_work: 0.2752 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13830 Z= 0.152 Angle : 0.541 7.700 18810 Z= 0.276 Chirality : 0.039 0.157 2245 Planarity : 0.005 0.054 2345 Dihedral : 5.493 50.211 1875 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.98 % Allowed : 12.87 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.20), residues: 1695 helix: 1.92 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -0.39 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 100 TYR 0.012 0.001 TYR E 156 PHE 0.014 0.002 PHE B 146 TRP 0.012 0.002 TRP A 343 HIS 0.005 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00365 (13830) covalent geometry : angle 0.54095 (18810) hydrogen bonds : bond 0.04881 ( 1015) hydrogen bonds : angle 3.89096 ( 3015) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.539 Fit side-chains REVERT: A 88 ARG cc_start: 0.7265 (ttm-80) cc_final: 0.6845 (ttm110) REVERT: A 100 ARG cc_start: 0.8149 (ttp-110) cc_final: 0.7669 (ttm110) REVERT: A 104 GLN cc_start: 0.7549 (mm110) cc_final: 0.6982 (pt0) REVERT: A 155 SER cc_start: 0.8705 (m) cc_final: 0.8424 (m) REVERT: A 206 LYS cc_start: 0.8801 (mttp) cc_final: 0.8338 (mttp) REVERT: A 233 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7588 (mm110) REVERT: A 374 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: A 390 ASP cc_start: 0.8249 (m-30) cc_final: 0.7725 (m-30) REVERT: B 100 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7563 (ttp-110) REVERT: B 104 GLN cc_start: 0.7375 (mm110) cc_final: 0.6624 (pt0) REVERT: B 206 LYS cc_start: 0.8729 (mttp) cc_final: 0.8258 (mttp) REVERT: B 233 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7476 (mm110) REVERT: B 264 GLN cc_start: 0.8658 (tt0) cc_final: 0.8415 (tt0) REVERT: B 390 ASP cc_start: 0.8323 (m-30) cc_final: 0.7900 (m-30) REVERT: C 88 ARG cc_start: 0.6782 (ttm-80) cc_final: 0.6341 (ttm110) REVERT: C 104 GLN cc_start: 0.7422 (mm110) cc_final: 0.6431 (pt0) REVERT: C 115 MET cc_start: 0.8088 (mtt) cc_final: 0.7821 (mtp) REVERT: C 116 HIS cc_start: 0.8525 (t-90) cc_final: 0.8248 (t70) REVERT: C 132 SER cc_start: 0.8930 (p) cc_final: 0.8636 (m) REVERT: C 206 LYS cc_start: 0.8865 (mttp) cc_final: 0.8262 (mttp) REVERT: C 264 GLN cc_start: 0.8362 (tt0) cc_final: 0.8032 (tt0) REVERT: C 315 GLU cc_start: 0.8721 (tt0) cc_final: 0.8323 (mt-10) REVERT: C 390 ASP cc_start: 0.8310 (m-30) cc_final: 0.7849 (m-30) REVERT: C 402 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.6704 (mt-10) REVERT: D 88 ARG cc_start: 0.7339 (ttm-80) cc_final: 0.7028 (ttm110) REVERT: D 100 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7747 (ttm110) REVERT: D 104 GLN cc_start: 0.7804 (mm110) cc_final: 0.7022 (pt0) REVERT: D 206 LYS cc_start: 0.8683 (mttp) cc_final: 0.8208 (mttp) REVERT: D 235 LYS cc_start: 0.8696 (tttt) cc_final: 0.8458 (ttmt) REVERT: D 264 GLN cc_start: 0.8736 (tt0) cc_final: 0.8389 (tt0) REVERT: D 300 GLU cc_start: 0.8320 (tp30) cc_final: 0.7914 (mm-30) REVERT: D 390 ASP cc_start: 0.8529 (m-30) cc_final: 0.8141 (m-30) REVERT: E 88 ARG cc_start: 0.7471 (ttm-80) cc_final: 0.7177 (mtp85) REVERT: E 99 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6530 (mm-30) REVERT: E 106 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7292 (mtt-85) REVERT: E 115 MET cc_start: 0.8177 (mtm) cc_final: 0.7890 (mtp) REVERT: E 206 LYS cc_start: 0.8731 (mttp) cc_final: 0.8231 (mttp) REVERT: E 264 GLN cc_start: 0.8605 (tt0) cc_final: 0.8353 (tt0) REVERT: E 300 GLU cc_start: 0.8476 (tp30) cc_final: 0.8082 (mm-30) REVERT: E 390 ASP cc_start: 0.8381 (m-30) cc_final: 0.7998 (m-30) REVERT: E 402 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6577 (mt-10) outliers start: 30 outliers final: 21 residues processed: 205 average time/residue: 0.8035 time to fit residues: 175.6998 Evaluate side-chains 205 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 31 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 99 optimal weight: 10.0000 chunk 168 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.124031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.099499 restraints weight = 14868.075| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.47 r_work: 0.2817 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13830 Z= 0.111 Angle : 0.485 7.589 18810 Z= 0.245 Chirality : 0.037 0.157 2245 Planarity : 0.005 0.041 2345 Dihedral : 5.194 49.240 1875 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.72 % Allowed : 13.27 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.21), residues: 1695 helix: 2.26 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -0.16 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 100 TYR 0.009 0.001 TYR E 156 PHE 0.009 0.002 PHE A 364 TRP 0.014 0.001 TRP A 343 HIS 0.003 0.001 HIS D 344 Details of bonding type rmsd covalent geometry : bond 0.00232 (13830) covalent geometry : angle 0.48459 (18810) hydrogen bonds : bond 0.03983 ( 1015) hydrogen bonds : angle 3.71207 ( 3015) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4700.55 seconds wall clock time: 80 minutes 38.55 seconds (4838.55 seconds total)