Starting phenix.real_space_refine on Thu Jul 31 04:45:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ek2_31166/07_2025/7ek2_31166.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ek2_31166/07_2025/7ek2_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ek2_31166/07_2025/7ek2_31166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ek2_31166/07_2025/7ek2_31166.map" model { file = "/net/cci-nas-00/data/ceres_data/7ek2_31166/07_2025/7ek2_31166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ek2_31166/07_2025/7ek2_31166.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, E, D Time building chain proxies: 7.25, per 1000 atoms: 0.54 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: 3.26 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 1.02 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: 4.88 Time building geometry restraints manager: 3.95 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 49.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.170 Process input model: 35.120 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:133.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 219.720 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (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 TRP 0.034 0.006 TRP B 343 HIS 0.009 0.003 HIS B 126 PHE 0.022 0.004 PHE E 192 TYR 0.014 0.005 TYR B 179 ARG 0.011 0.001 ARG D 200 Details of bonding type rmsd hydrogen bonds : bond 0.19026 ( 1015) hydrogen bonds : angle 5.72028 ( 3015) covalent geometry : bond 0.01692 (13830) covalent geometry : angle 1.76938 (18810) *********************** 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 : 1.881 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: 0.8080 (tp30) cc_final: 0.7744 (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: 0.7173 (mmm-85) REVERT: C 206 LYS cc_start: 0.8335 (mttp) cc_final: 0.7689 (mttp) REVERT: C 217 ASP cc_start: 0.8729 (t70) cc_final: 0.8518 (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: 0.8080 (mmtm) REVERT: C 315 GLU cc_start: 0.8224 (tt0) cc_final: 0.7582 (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: 0.7450 (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: 0.7294 (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: 0.7927 (mttp) REVERT: D 210 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7896 (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: 0.7584 (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: 0.6704 (mt-10) REVERT: E 163 ASP cc_start: 0.6698 (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: 0.6092 (mt-10) outliers start: 15 outliers final: 0 residues processed: 251 average time/residue: 2.3292 time to fit residues: 621.8785 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 : 1.690 ------------------------------------------------------------------------------- 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 143 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.121443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.097289 restraints weight = 14482.557| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.35 r_work: 0.2765 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13830 Z= 0.157 Angle : 0.578 6.874 18810 Z= 0.299 Chirality : 0.040 0.152 2245 Planarity : 0.006 0.070 2345 Dihedral : 5.658 48.242 1875 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.71 % Allowed : 7.92 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.20), residues: 1695 helix: 1.46 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -0.29 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 352 HIS 0.005 0.001 HIS A 344 PHE 0.014 0.002 PHE D 245 TYR 0.013 0.001 TYR B 241 ARG 0.009 0.001 ARG C 200 Details of bonding type rmsd hydrogen bonds : bond 0.05324 ( 1015) hydrogen bonds : angle 4.15901 ( 3015) covalent geometry : bond 0.00352 (13830) covalent geometry : angle 0.57789 (18810) *********************** 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 230 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 1.574 Fit side-chains REVERT: A 88 ARG cc_start: 0.7273 (ttm-80) cc_final: 0.6733 (ttm110) REVERT: A 100 ARG cc_start: 0.8150 (ttp-110) cc_final: 0.7820 (ttm110) REVERT: A 104 GLN cc_start: 0.7501 (mm110) cc_final: 0.6882 (pt0) REVERT: A 162 LEU cc_start: 0.7916 (mt) cc_final: 0.7715 (mt) REVERT: A 164 LEU cc_start: 0.7798 (mp) cc_final: 0.7583 (mp) REVERT: A 206 LYS cc_start: 0.8913 (mttp) cc_final: 0.8526 (mttp) REVERT: A 233 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7846 (mm110) REVERT: A 354 ASP cc_start: 0.7963 (m-30) cc_final: 0.7697 (p0) REVERT: A 390 ASP cc_start: 0.8355 (m-30) cc_final: 0.7940 (m-30) REVERT: B 104 GLN cc_start: 0.7501 (mm110) cc_final: 0.6731 (pt0) REVERT: B 115 MET cc_start: 0.8579 (mtm) cc_final: 0.8326 (ttm) REVERT: B 206 LYS cc_start: 0.8843 (mttp) cc_final: 0.8477 (mttp) REVERT: B 233 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7648 (mm110) REVERT: B 264 GLN cc_start: 0.8621 (tt0) cc_final: 0.8367 (tt0) REVERT: B 297 LYS cc_start: 0.8425 (mmtp) cc_final: 0.8146 (mmtm) REVERT: B 390 ASP cc_start: 0.8242 (m-30) cc_final: 0.8013 (m-30) REVERT: C 116 HIS cc_start: 0.8509 (t-90) cc_final: 0.8121 (t70) REVERT: C 206 LYS cc_start: 0.8905 (mttp) cc_final: 0.8383 (mttp) REVERT: C 264 GLN cc_start: 0.8407 (tt0) cc_final: 0.8106 (tt0) REVERT: C 315 GLU cc_start: 0.8725 (tt0) cc_final: 0.8305 (mt-10) REVERT: C 354 ASP cc_start: 0.8021 (m-30) cc_final: 0.7782 (p0) REVERT: C 390 ASP cc_start: 0.8372 (m-30) cc_final: 0.8014 (m-30) REVERT: C 391 ASP cc_start: 0.8430 (m-30) cc_final: 0.8168 (m-30) REVERT: C 402 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.6941 (mt-10) REVERT: D 100 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.7909 (ttm110) REVERT: D 104 GLN cc_start: 0.7989 (mm110) cc_final: 0.7743 (mm110) REVERT: D 206 LYS cc_start: 0.8787 (mttp) cc_final: 0.8331 (mttp) REVERT: D 264 GLN cc_start: 0.8836 (tt0) cc_final: 0.8546 (tt0) REVERT: D 300 GLU cc_start: 0.8371 (tp30) cc_final: 0.7952 (mm-30) REVERT: D 315 GLU cc_start: 0.8697 (tt0) cc_final: 0.8221 (mt-10) REVERT: D 390 ASP cc_start: 0.8654 (m-30) cc_final: 0.8327 (m-30) REVERT: D 408 LYS cc_start: 0.7978 (tptp) cc_final: 0.7771 (tttm) REVERT: E 106 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7443 (mtt-85) REVERT: E 206 LYS cc_start: 0.8944 (mttp) cc_final: 0.8417 (mttp) REVERT: E 264 GLN cc_start: 0.8651 (tt0) cc_final: 0.8420 (tt0) REVERT: E 265 ASN cc_start: 0.8557 (m-40) cc_final: 0.8205 (m110) REVERT: E 390 ASP cc_start: 0.8436 (m-30) cc_final: 0.8184 (m-30) REVERT: E 417 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.5234 (mptt) outliers start: 41 outliers final: 13 residues processed: 218 average time/residue: 1.7460 time to fit residues: 406.6069 Evaluate side-chains 180 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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 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 112 optimal weight: 0.1980 chunk 89 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 39 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN B 180 GLN D 98 GLN D 123 HIS D 401 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.117587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.091954 restraints weight = 14182.670| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.40 r_work: 0.2768 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13830 Z= 0.202 Angle : 0.617 7.170 18810 Z= 0.317 Chirality : 0.042 0.156 2245 Planarity : 0.006 0.077 2345 Dihedral : 5.731 49.742 1875 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.63 % Allowed : 8.98 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.20), residues: 1695 helix: 1.42 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -0.55 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP D 352 HIS 0.006 0.002 HIS D 344 PHE 0.019 0.003 PHE B 146 TYR 0.014 0.002 TYR E 156 ARG 0.008 0.001 ARG C 200 Details of bonding type rmsd hydrogen bonds : bond 0.05839 ( 1015) hydrogen bonds : angle 4.14187 ( 3015) covalent geometry : bond 0.00501 (13830) covalent geometry : angle 0.61652 (18810) *********************** 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 239 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 184 time to evaluate : 1.410 Fit side-chains REVERT: A 88 ARG cc_start: 0.7232 (ttm-80) cc_final: 0.6639 (ttm110) REVERT: A 100 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7700 (ttm110) REVERT: A 104 GLN cc_start: 0.7491 (mm110) cc_final: 0.6844 (pt0) REVERT: A 162 LEU cc_start: 0.7870 (mt) cc_final: 0.7641 (mt) REVERT: A 164 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7450 (mp) REVERT: A 206 LYS cc_start: 0.8872 (mttp) cc_final: 0.8459 (mttp) REVERT: A 233 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7781 (mm110) REVERT: A 354 ASP cc_start: 0.7877 (m-30) cc_final: 0.7575 (p0) REVERT: A 390 ASP cc_start: 0.8379 (m-30) cc_final: 0.7882 (m-30) REVERT: B 98 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: B 104 GLN cc_start: 0.7426 (mm110) cc_final: 0.6690 (pt0) REVERT: B 206 LYS cc_start: 0.8811 (mttp) cc_final: 0.8400 (mttp) REVERT: B 233 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7572 (mm110) REVERT: B 264 GLN cc_start: 0.8615 (tt0) cc_final: 0.8336 (tt0) REVERT: B 297 LYS cc_start: 0.8392 (mmtp) cc_final: 0.8071 (mmtm) REVERT: B 390 ASP cc_start: 0.8395 (m-30) cc_final: 0.7966 (m-30) REVERT: C 115 MET cc_start: 0.8259 (mtt) cc_final: 0.8003 (mtp) REVERT: C 116 HIS cc_start: 0.8479 (t-90) cc_final: 0.8196 (t70) REVERT: C 132 SER cc_start: 0.9042 (p) cc_final: 0.8662 (m) REVERT: C 206 LYS cc_start: 0.8895 (mttp) cc_final: 0.8317 (mttp) REVERT: C 264 GLN cc_start: 0.8415 (tt0) cc_final: 0.8112 (tt0) REVERT: C 315 GLU cc_start: 0.8696 (tt0) cc_final: 0.8164 (mt-10) REVERT: C 390 ASP cc_start: 0.8366 (m-30) cc_final: 0.7904 (m-30) REVERT: C 402 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.6917 (mt-10) REVERT: D 88 ARG cc_start: 0.7376 (ttm-80) cc_final: 0.7091 (ttm110) REVERT: D 100 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.7901 (ttm110) REVERT: D 104 GLN cc_start: 0.8056 (mm110) cc_final: 0.7842 (mm110) REVERT: D 206 LYS cc_start: 0.8769 (mttp) cc_final: 0.8346 (mttp) REVERT: D 235 LYS cc_start: 0.8828 (tttt) cc_final: 0.8377 (tttp) REVERT: D 264 GLN cc_start: 0.8862 (tt0) cc_final: 0.8535 (tt0) REVERT: D 300 GLU cc_start: 0.8359 (tp30) cc_final: 0.7908 (mm-30) REVERT: E 106 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7372 (mtt-85) REVERT: E 115 MET cc_start: 0.8320 (mtm) cc_final: 0.8053 (mtp) REVERT: E 206 LYS cc_start: 0.8922 (mttp) cc_final: 0.8325 (mttp) REVERT: E 264 GLN cc_start: 0.8624 (tt0) cc_final: 0.8411 (tt0) REVERT: E 402 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.6759 (mt-10) REVERT: E 417 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.5862 (mptt) outliers start: 55 outliers final: 25 residues processed: 224 average time/residue: 1.7236 time to fit residues: 413.5322 Evaluate side-chains 202 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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 164 LEU Chi-restraints excluded: chain A residue 264 GLN 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 89 ILE Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 131 LEU 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 402 GLU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 417 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 22 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 144 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 136 optimal weight: 40.0000 chunk 78 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.122216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.097813 restraints weight = 14782.437| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.44 r_work: 0.2814 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13830 Z= 0.119 Angle : 0.497 6.977 18810 Z= 0.254 Chirality : 0.038 0.152 2245 Planarity : 0.005 0.050 2345 Dihedral : 5.397 49.616 1875 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.51 % Allowed : 10.50 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.21), residues: 1695 helix: 1.92 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -0.31 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 343 HIS 0.004 0.001 HIS C 344 PHE 0.011 0.002 PHE A 146 TYR 0.009 0.001 TYR C 241 ARG 0.008 0.000 ARG D 397 Details of bonding type rmsd hydrogen bonds : bond 0.04392 ( 1015) hydrogen bonds : angle 3.86015 ( 3015) covalent geometry : bond 0.00252 (13830) covalent geometry : angle 0.49660 (18810) *********************** 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 221 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 1.448 Fit side-chains REVERT: A 88 ARG cc_start: 0.7307 (ttm-80) cc_final: 0.6716 (ttm110) REVERT: A 100 ARG cc_start: 0.8089 (ttp-110) cc_final: 0.7603 (ttm110) REVERT: A 104 GLN cc_start: 0.7567 (mm110) cc_final: 0.6990 (pt0) REVERT: A 164 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7953 (mp) REVERT: A 206 LYS cc_start: 0.8834 (mttp) cc_final: 0.8381 (mttp) REVERT: A 233 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7565 (mm110) REVERT: A 306 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8177 (mt) REVERT: A 390 ASP cc_start: 0.8254 (m-30) cc_final: 0.7774 (m-30) REVERT: B 100 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7757 (ttp-110) REVERT: B 104 GLN cc_start: 0.7437 (mm110) cc_final: 0.6755 (pt0) REVERT: B 156 TYR cc_start: 0.8776 (t80) cc_final: 0.8572 (t80) REVERT: B 206 LYS cc_start: 0.8759 (mttp) cc_final: 0.8317 (mttp) REVERT: B 233 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7420 (mm110) REVERT: B 264 GLN cc_start: 0.8551 (tt0) cc_final: 0.8330 (tt0) REVERT: B 297 LYS cc_start: 0.8225 (mmtp) cc_final: 0.7916 (mmtm) REVERT: B 390 ASP cc_start: 0.8314 (m-30) cc_final: 0.7920 (m-30) REVERT: C 104 GLN cc_start: 0.7393 (mm110) cc_final: 0.6414 (pt0) REVERT: C 113 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8541 (mtpt) REVERT: C 115 MET cc_start: 0.8162 (mtt) cc_final: 0.7897 (mtp) REVERT: C 116 HIS cc_start: 0.8493 (t-90) cc_final: 0.8261 (t70) REVERT: C 132 SER cc_start: 0.9012 (p) cc_final: 0.8639 (m) REVERT: C 206 LYS cc_start: 0.8884 (mttp) cc_final: 0.8305 (mttp) REVERT: C 264 GLN cc_start: 0.8365 (tt0) cc_final: 0.8020 (tt0) REVERT: C 315 GLU cc_start: 0.8718 (tt0) cc_final: 0.8308 (mt-10) REVERT: C 390 ASP cc_start: 0.8318 (m-30) cc_final: 0.7895 (m-30) REVERT: C 402 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.6777 (mt-10) REVERT: D 88 ARG cc_start: 0.7299 (ttm-80) cc_final: 0.7007 (ttm110) REVERT: D 100 ARG cc_start: 0.8101 (ttm-80) cc_final: 0.7784 (ttm110) REVERT: D 104 GLN cc_start: 0.8034 (mm110) cc_final: 0.7807 (mm110) REVERT: D 206 LYS cc_start: 0.8707 (mttp) cc_final: 0.8212 (mttp) REVERT: D 235 LYS cc_start: 0.8732 (tttt) cc_final: 0.8489 (ttmt) REVERT: D 264 GLN cc_start: 0.8769 (tt0) cc_final: 0.8417 (tt0) REVERT: D 300 GLU cc_start: 0.8345 (tp30) cc_final: 0.7950 (mm-30) REVERT: D 382 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7760 (tm-30) REVERT: E 106 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7309 (mtt-85) REVERT: E 115 MET cc_start: 0.8173 (mtm) cc_final: 0.7876 (mtp) REVERT: E 206 LYS cc_start: 0.8763 (mttp) cc_final: 0.8300 (mttp) REVERT: E 264 GLN cc_start: 0.8565 (tt0) cc_final: 0.8324 (tt0) REVERT: E 300 GLU cc_start: 0.8526 (tp30) cc_final: 0.8122 (mm-30) REVERT: E 390 ASP cc_start: 0.8410 (m-30) cc_final: 0.7995 (m-30) REVERT: E 402 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6654 (mt-10) REVERT: E 417 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7236 (mptt) outliers start: 38 outliers final: 16 residues processed: 209 average time/residue: 1.9345 time to fit residues: 432.1830 Evaluate side-chains 197 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 264 GLN 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 402 GLU Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 171 LEU 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 148 LEU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 417 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 122 optimal weight: 4.9990 chunk 136 optimal weight: 40.0000 chunk 139 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN D 180 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 = 0.3241 r_free = 0.3241 target = 0.119176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.094546 restraints weight = 14929.470| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.44 r_work: 0.2720 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13830 Z= 0.198 Angle : 0.591 7.181 18810 Z= 0.303 Chirality : 0.042 0.163 2245 Planarity : 0.006 0.070 2345 Dihedral : 5.660 49.802 1875 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.10 % Allowed : 10.69 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.20), residues: 1695 helix: 1.59 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -0.48 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 343 HIS 0.006 0.002 HIS D 344 PHE 0.019 0.003 PHE B 146 TYR 0.013 0.002 TYR C 156 ARG 0.007 0.001 ARG D 397 Details of bonding type rmsd hydrogen bonds : bond 0.05557 ( 1015) hydrogen bonds : angle 4.03648 ( 3015) covalent geometry : bond 0.00494 (13830) covalent geometry : angle 0.59069 (18810) *********************** 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 232 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 1.546 Fit side-chains REVERT: A 88 ARG cc_start: 0.7275 (ttm-80) cc_final: 0.6629 (ttm110) REVERT: A 100 ARG cc_start: 0.8131 (ttp-110) cc_final: 0.7648 (ttm110) REVERT: A 104 GLN cc_start: 0.7540 (mm110) cc_final: 0.6966 (pt0) REVERT: A 162 LEU cc_start: 0.7802 (mt) cc_final: 0.7494 (mt) REVERT: A 164 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7438 (mp) REVERT: A 206 LYS cc_start: 0.8792 (mttp) cc_final: 0.8332 (mttp) REVERT: A 233 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7606 (mm110) REVERT: A 390 ASP cc_start: 0.8380 (m-30) cc_final: 0.7873 (m-30) REVERT: B 100 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7724 (ttp-110) REVERT: B 104 GLN cc_start: 0.7421 (mm110) cc_final: 0.6738 (pt0) REVERT: B 206 LYS cc_start: 0.8769 (mttp) cc_final: 0.8330 (mttp) REVERT: B 233 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7492 (mm110) REVERT: B 264 GLN cc_start: 0.8622 (tt0) cc_final: 0.8338 (tt0) REVERT: B 297 LYS cc_start: 0.8394 (mmtp) cc_final: 0.8034 (mmtm) REVERT: B 390 ASP cc_start: 0.8380 (m-30) cc_final: 0.7952 (m-30) REVERT: C 104 GLN cc_start: 0.7572 (mm110) cc_final: 0.6475 (pt0) REVERT: C 113 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8576 (mtpt) REVERT: C 115 MET cc_start: 0.8132 (mtt) cc_final: 0.7849 (mtp) REVERT: C 116 HIS cc_start: 0.8516 (t-90) cc_final: 0.8232 (t70) REVERT: C 132 SER cc_start: 0.8929 (p) cc_final: 0.8616 (m) REVERT: C 206 LYS cc_start: 0.8871 (mttp) cc_final: 0.8280 (mttp) REVERT: C 264 GLN cc_start: 0.8407 (tt0) cc_final: 0.8077 (tt0) REVERT: C 315 GLU cc_start: 0.8686 (tt0) cc_final: 0.8230 (mt-10) REVERT: C 390 ASP cc_start: 0.8345 (m-30) cc_final: 0.7881 (m-30) REVERT: C 402 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.6824 (mt-10) REVERT: D 88 ARG cc_start: 0.7404 (ttm-80) cc_final: 0.7090 (ttm110) REVERT: D 100 ARG cc_start: 0.8083 (ttm-80) cc_final: 0.7772 (ttm110) REVERT: D 104 GLN cc_start: 0.8023 (mm110) cc_final: 0.7798 (mm110) REVERT: D 206 LYS cc_start: 0.8694 (mttp) cc_final: 0.8228 (mttp) REVERT: D 235 LYS cc_start: 0.8761 (tttt) cc_final: 0.8290 (tttp) REVERT: D 264 GLN cc_start: 0.8761 (tt0) cc_final: 0.8419 (tt0) REVERT: D 300 GLU cc_start: 0.8264 (tp30) cc_final: 0.7806 (mm-30) REVERT: D 382 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7926 (tm-30) REVERT: E 106 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7320 (mtt-85) REVERT: E 115 MET cc_start: 0.8251 (mtm) cc_final: 0.7959 (mtp) REVERT: E 206 LYS cc_start: 0.8812 (mttp) cc_final: 0.8272 (mttp) REVERT: E 264 GLN cc_start: 0.8591 (tt0) cc_final: 0.8361 (tt0) REVERT: E 299 GLU cc_start: 0.8325 (tt0) cc_final: 0.7867 (tt0) REVERT: E 300 GLU cc_start: 0.8509 (tp30) cc_final: 0.8037 (mm-30) REVERT: E 402 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.6688 (mt-10) REVERT: E 408 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7711 (tppt) REVERT: E 417 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.5537 (mptt) outliers start: 47 outliers final: 25 residues processed: 218 average time/residue: 1.8724 time to fit residues: 437.9103 Evaluate side-chains 208 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 1.618 ------------------------------------------------------------------------------- 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 164 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 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 107 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 131 LEU 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 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 Chi-restraints excluded: chain E residue 417 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 49 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3261 r_free = 0.3261 target = 0.120873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.096038 restraints weight = 14983.128| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.48 r_work: 0.2757 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13830 Z= 0.136 Angle : 0.516 7.055 18810 Z= 0.264 Chirality : 0.038 0.155 2245 Planarity : 0.005 0.059 2345 Dihedral : 5.474 49.968 1875 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.77 % Allowed : 11.55 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.21), residues: 1695 helix: 1.87 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -0.40 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 343 HIS 0.004 0.001 HIS A 344 PHE 0.012 0.002 PHE D 245 TYR 0.011 0.001 TYR C 156 ARG 0.009 0.000 ARG D 397 Details of bonding type rmsd hydrogen bonds : bond 0.04677 ( 1015) hydrogen bonds : angle 3.88123 ( 3015) covalent geometry : bond 0.00316 (13830) covalent geometry : angle 0.51635 (18810) *********************** 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 228 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 1.621 Fit side-chains REVERT: A 88 ARG cc_start: 0.7259 (ttm-80) cc_final: 0.6600 (ttm110) REVERT: A 100 ARG cc_start: 0.8114 (ttp-110) cc_final: 0.7628 (ttm110) REVERT: A 104 GLN cc_start: 0.7495 (mm110) cc_final: 0.6959 (pt0) REVERT: A 155 SER cc_start: 0.8769 (m) cc_final: 0.8508 (m) REVERT: A 162 LEU cc_start: 0.7754 (mt) cc_final: 0.7431 (mt) REVERT: A 164 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7916 (mp) REVERT: A 206 LYS cc_start: 0.8825 (mttp) cc_final: 0.8376 (mttp) REVERT: A 233 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7562 (mm110) REVERT: A 306 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8273 (mt) REVERT: A 312 CYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8262 (p) REVERT: A 390 ASP cc_start: 0.8318 (m-30) cc_final: 0.7822 (m-30) REVERT: B 100 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7712 (ttp-110) REVERT: B 104 GLN cc_start: 0.7416 (mm110) cc_final: 0.6635 (pt0) REVERT: B 206 LYS cc_start: 0.8770 (mttp) cc_final: 0.8350 (mttp) REVERT: B 233 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7405 (mm110) REVERT: B 264 GLN cc_start: 0.8603 (tt0) cc_final: 0.8380 (tt0) REVERT: B 390 ASP cc_start: 0.8363 (m-30) cc_final: 0.7949 (m-30) REVERT: C 104 GLN cc_start: 0.7556 (mm110) cc_final: 0.6477 (pt0) REVERT: C 113 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8589 (mtpt) REVERT: C 115 MET cc_start: 0.8151 (mtt) cc_final: 0.7880 (mtp) REVERT: C 116 HIS cc_start: 0.8560 (t-90) cc_final: 0.8276 (t70) REVERT: C 132 SER cc_start: 0.8933 (p) cc_final: 0.8628 (m) REVERT: C 206 LYS cc_start: 0.8897 (mttp) cc_final: 0.8311 (mttp) REVERT: C 264 GLN cc_start: 0.8394 (tt0) cc_final: 0.8067 (tt0) REVERT: C 315 GLU cc_start: 0.8771 (tt0) cc_final: 0.8366 (mt-10) REVERT: C 390 ASP cc_start: 0.8343 (m-30) cc_final: 0.7898 (m-30) REVERT: C 402 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.6747 (mt-10) REVERT: D 88 ARG cc_start: 0.7400 (ttm-80) cc_final: 0.7081 (ttm110) REVERT: D 100 ARG cc_start: 0.8049 (ttm-80) cc_final: 0.7745 (ttm110) REVERT: D 206 LYS cc_start: 0.8715 (mttp) cc_final: 0.8254 (mttp) REVERT: D 235 LYS cc_start: 0.8720 (tttt) cc_final: 0.8477 (ttmt) REVERT: D 264 GLN cc_start: 0.8688 (tt0) cc_final: 0.8333 (tt0) REVERT: D 300 GLU cc_start: 0.8331 (tp30) cc_final: 0.7929 (mm-30) REVERT: D 382 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: E 106 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7302 (mtt-85) REVERT: E 115 MET cc_start: 0.8236 (mtm) cc_final: 0.7943 (mtp) REVERT: E 206 LYS cc_start: 0.8764 (mttp) cc_final: 0.8288 (mttp) REVERT: E 264 GLN cc_start: 0.8605 (tt0) cc_final: 0.8372 (tt0) REVERT: E 299 GLU cc_start: 0.8230 (tt0) cc_final: 0.7781 (tt0) REVERT: E 300 GLU cc_start: 0.8498 (tp30) cc_final: 0.8059 (mm-30) REVERT: E 402 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6677 (mt-10) REVERT: E 417 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.5247 (mptt) outliers start: 42 outliers final: 20 residues processed: 216 average time/residue: 2.0756 time to fit residues: 478.2176 Evaluate side-chains 208 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 2.929 ------------------------------------------------------------------------------- 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 164 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 312 CYS 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 102 MET Chi-restraints excluded: chain B residue 148 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 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 402 GLU Chi-restraints excluded: chain E residue 417 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 10 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3272 r_free = 0.3272 target = 0.121767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.097243 restraints weight = 14909.363| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.44 r_work: 0.2777 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13830 Z= 0.126 Angle : 0.503 7.017 18810 Z= 0.256 Chirality : 0.038 0.153 2245 Planarity : 0.005 0.054 2345 Dihedral : 5.360 49.967 1875 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.77 % Allowed : 11.55 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.21), residues: 1695 helix: 2.03 (0.14), residues: 1430 sheet: None (None), residues: 0 loop : -0.32 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 343 HIS 0.004 0.001 HIS A 344 PHE 0.011 0.002 PHE A 146 TYR 0.007 0.001 TYR C 241 ARG 0.008 0.000 ARG D 397 Details of bonding type rmsd hydrogen bonds : bond 0.04450 ( 1015) hydrogen bonds : angle 3.80482 ( 3015) covalent geometry : bond 0.00287 (13830) covalent geometry : angle 0.50343 (18810) *********************** 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 229 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 1.638 Fit side-chains REVERT: A 88 ARG cc_start: 0.7179 (ttm-80) cc_final: 0.6817 (ttm110) REVERT: A 100 ARG cc_start: 0.8150 (ttp-110) cc_final: 0.7673 (ttm110) REVERT: A 104 GLN cc_start: 0.7486 (mm110) cc_final: 0.6984 (pt0) REVERT: A 155 SER cc_start: 0.8736 (m) cc_final: 0.8480 (m) REVERT: A 162 LEU cc_start: 0.7753 (mt) cc_final: 0.7447 (mt) REVERT: A 164 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7945 (mp) REVERT: A 206 LYS cc_start: 0.8818 (mttp) cc_final: 0.8365 (mttp) REVERT: A 233 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7594 (mm110) REVERT: A 306 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8343 (mt) REVERT: A 390 ASP cc_start: 0.8252 (m-30) cc_final: 0.7759 (m-30) REVERT: B 100 ARG cc_start: 0.8041 (ttm-80) cc_final: 0.7682 (ttp-110) REVERT: B 104 GLN cc_start: 0.7418 (mm110) cc_final: 0.6667 (pt0) REVERT: B 206 LYS cc_start: 0.8743 (mttp) cc_final: 0.8315 (mttp) REVERT: B 233 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7366 (mm110) REVERT: B 264 GLN cc_start: 0.8584 (tt0) cc_final: 0.8356 (tt0) REVERT: B 390 ASP cc_start: 0.8344 (m-30) cc_final: 0.7958 (m-30) REVERT: B 402 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.6897 (mt-10) REVERT: C 104 GLN cc_start: 0.7710 (mm110) cc_final: 0.6542 (pt0) REVERT: C 113 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8574 (mtpt) REVERT: C 115 MET cc_start: 0.8118 (mtt) cc_final: 0.7850 (mtp) REVERT: C 116 HIS cc_start: 0.8503 (t-90) cc_final: 0.8254 (t70) REVERT: C 132 SER cc_start: 0.8911 (p) cc_final: 0.8626 (m) REVERT: C 206 LYS cc_start: 0.8887 (mttp) cc_final: 0.8302 (mttp) REVERT: C 264 GLN cc_start: 0.8380 (tt0) cc_final: 0.8054 (tt0) REVERT: C 315 GLU cc_start: 0.8679 (tt0) cc_final: 0.8255 (mt-10) REVERT: C 390 ASP cc_start: 0.8300 (m-30) cc_final: 0.7879 (m-30) REVERT: C 402 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6728 (mt-10) REVERT: D 88 ARG cc_start: 0.7339 (ttm-80) cc_final: 0.6990 (ttm110) REVERT: D 100 ARG cc_start: 0.8056 (ttm-80) cc_final: 0.7754 (ttm110) REVERT: D 112 GLU cc_start: 0.7909 (mp0) cc_final: 0.7699 (mp0) REVERT: D 171 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8220 (tp) REVERT: D 206 LYS cc_start: 0.8675 (mttp) cc_final: 0.8176 (mttp) REVERT: D 235 LYS cc_start: 0.8693 (tttt) cc_final: 0.8435 (ttmt) REVERT: D 264 GLN cc_start: 0.8667 (tt0) cc_final: 0.8308 (tt0) REVERT: D 300 GLU cc_start: 0.8287 (tp30) cc_final: 0.7883 (mm-30) REVERT: D 382 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: E 99 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6705 (mm-30) REVERT: E 106 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7310 (mtt-85) REVERT: E 115 MET cc_start: 0.8156 (mtm) cc_final: 0.7865 (mtp) REVERT: E 206 LYS cc_start: 0.8753 (mttp) cc_final: 0.8261 (mttp) REVERT: E 264 GLN cc_start: 0.8583 (tt0) cc_final: 0.8333 (tt0) REVERT: E 299 GLU cc_start: 0.8117 (tt0) cc_final: 0.7707 (tt0) REVERT: E 300 GLU cc_start: 0.8464 (tp30) cc_final: 0.8042 (mm-30) REVERT: E 390 ASP cc_start: 0.8456 (m-30) cc_final: 0.8038 (m-30) REVERT: E 402 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.6670 (mt-10) REVERT: E 417 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.4994 (mptt) outliers start: 42 outliers final: 21 residues processed: 218 average time/residue: 2.4105 time to fit residues: 564.4067 Evaluate side-chains 214 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 1.432 ------------------------------------------------------------------------------- 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 164 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 102 MET Chi-restraints excluded: chain B residue 148 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 171 LEU Chi-restraints excluded: chain D residue 382 GLU 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 382 GLU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 417 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 44 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 10 optimal weight: 0.0980 chunk 168 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- 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 = 0.3261 r_free = 0.3261 target = 0.120983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.096700 restraints weight = 14945.899| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.39 r_work: 0.2776 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13830 Z= 0.138 Angle : 0.519 7.111 18810 Z= 0.264 Chirality : 0.038 0.155 2245 Planarity : 0.005 0.056 2345 Dihedral : 5.401 50.072 1875 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.71 % Allowed : 12.08 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.21), residues: 1695 helix: 1.98 (0.14), residues: 1430 sheet: None (None), residues: 0 loop : -0.35 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 343 HIS 0.005 0.001 HIS A 344 PHE 0.012 0.002 PHE B 146 TYR 0.008 0.001 TYR B 241 ARG 0.005 0.000 ARG E 100 Details of bonding type rmsd hydrogen bonds : bond 0.04634 ( 1015) hydrogen bonds : angle 3.84086 ( 3015) covalent geometry : bond 0.00323 (13830) covalent geometry : angle 0.51941 (18810) *********************** 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 231 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 1.531 Fit side-chains REVERT: A 88 ARG cc_start: 0.7313 (ttm-80) cc_final: 0.6787 (ttm110) REVERT: A 100 ARG cc_start: 0.8181 (ttp-110) cc_final: 0.7707 (ttm110) REVERT: A 104 GLN cc_start: 0.7512 (mm110) cc_final: 0.7029 (pt0) REVERT: A 155 SER cc_start: 0.8735 (m) cc_final: 0.8482 (m) REVERT: A 162 LEU cc_start: 0.7810 (mt) cc_final: 0.7505 (mt) REVERT: A 164 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7950 (mp) REVERT: A 206 LYS cc_start: 0.8884 (mttp) cc_final: 0.8453 (mttp) REVERT: A 233 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7648 (mm110) REVERT: A 306 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8358 (mt) REVERT: A 312 CYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8291 (p) REVERT: A 390 ASP cc_start: 0.8285 (m-30) cc_final: 0.7809 (m-30) REVERT: B 100 ARG cc_start: 0.8079 (ttm-80) cc_final: 0.7703 (ttp-110) REVERT: B 104 GLN cc_start: 0.7448 (mm110) cc_final: 0.6729 (pt0) REVERT: B 206 LYS cc_start: 0.8777 (mttp) cc_final: 0.8362 (mttp) REVERT: B 233 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7502 (mm110) REVERT: B 264 GLN cc_start: 0.8610 (tt0) cc_final: 0.8391 (tt0) REVERT: B 390 ASP cc_start: 0.8355 (m-30) cc_final: 0.7962 (m-30) REVERT: B 402 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.6951 (mt-10) REVERT: C 104 GLN cc_start: 0.7578 (mm110) cc_final: 0.6576 (pt0) REVERT: C 115 MET cc_start: 0.8175 (mtt) cc_final: 0.7913 (mtp) REVERT: C 116 HIS cc_start: 0.8539 (t-90) cc_final: 0.8300 (t70) REVERT: C 132 SER cc_start: 0.8934 (p) cc_final: 0.8655 (m) REVERT: C 206 LYS cc_start: 0.8890 (mttp) cc_final: 0.8326 (mttp) REVERT: C 264 GLN cc_start: 0.8402 (tt0) cc_final: 0.8087 (tt0) REVERT: C 315 GLU cc_start: 0.8706 (tt0) cc_final: 0.8309 (mt-10) REVERT: C 390 ASP cc_start: 0.8261 (m-30) cc_final: 0.7828 (m-30) REVERT: C 402 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6796 (mt-10) REVERT: D 88 ARG cc_start: 0.7398 (ttm-80) cc_final: 0.7046 (ttm110) REVERT: D 100 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.7832 (ttm110) REVERT: D 104 GLN cc_start: 0.7778 (mm110) cc_final: 0.7052 (pt0) REVERT: D 112 GLU cc_start: 0.7957 (mp0) cc_final: 0.7748 (mp0) REVERT: D 206 LYS cc_start: 0.8691 (mttp) cc_final: 0.8213 (mttp) REVERT: D 235 LYS cc_start: 0.8764 (tttt) cc_final: 0.8527 (ttmt) REVERT: D 264 GLN cc_start: 0.8699 (tt0) cc_final: 0.8346 (tt0) REVERT: D 300 GLU cc_start: 0.8361 (tp30) cc_final: 0.7975 (mm-30) REVERT: D 382 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: E 99 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6746 (mm-30) REVERT: E 106 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7362 (mtt-85) REVERT: E 115 MET cc_start: 0.8215 (mtm) cc_final: 0.7923 (mtp) REVERT: E 206 LYS cc_start: 0.8779 (mttp) cc_final: 0.8306 (mttp) REVERT: E 264 GLN cc_start: 0.8609 (tt0) cc_final: 0.8356 (tt0) REVERT: E 299 GLU cc_start: 0.8132 (tt0) cc_final: 0.7733 (tt0) REVERT: E 300 GLU cc_start: 0.8500 (tp30) cc_final: 0.8084 (mm-30) REVERT: E 390 ASP cc_start: 0.8464 (m-30) cc_final: 0.8047 (m-30) REVERT: E 402 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6731 (mt-10) REVERT: E 417 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.5083 (mptt) outliers start: 41 outliers final: 22 residues processed: 221 average time/residue: 1.6684 time to fit residues: 394.5766 Evaluate side-chains 215 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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 164 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 312 CYS 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 102 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 131 LEU 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 102 MET 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 Chi-restraints excluded: chain E residue 417 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 113 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3227 r_free = 0.3227 target = 0.118295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.094073 restraints weight = 14900.631| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.35 r_work: 0.2731 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13830 Z= 0.216 Angle : 0.608 7.582 18810 Z= 0.312 Chirality : 0.042 0.170 2245 Planarity : 0.006 0.058 2345 Dihedral : 5.700 51.648 1875 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.57 % Allowed : 12.15 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.20), residues: 1695 helix: 1.60 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -0.58 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 352 HIS 0.006 0.002 HIS D 344 PHE 0.021 0.003 PHE B 146 TYR 0.013 0.002 TYR E 156 ARG 0.006 0.001 ARG E 100 Details of bonding type rmsd hydrogen bonds : bond 0.05676 ( 1015) hydrogen bonds : angle 4.06120 ( 3015) covalent geometry : bond 0.00544 (13830) covalent geometry : angle 0.60840 (18810) *********************** 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 221 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 1.678 Fit side-chains REVERT: A 88 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.6919 (ttm110) REVERT: A 100 ARG cc_start: 0.8187 (ttp-110) cc_final: 0.7714 (ttm110) REVERT: A 104 GLN cc_start: 0.7653 (mm110) cc_final: 0.7112 (pt0) REVERT: A 162 LEU cc_start: 0.7948 (mt) cc_final: 0.7688 (mt) REVERT: A 164 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7556 (mp) REVERT: A 206 LYS cc_start: 0.8829 (mttp) cc_final: 0.8407 (mttp) REVERT: A 233 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7686 (mm110) REVERT: A 390 ASP cc_start: 0.8413 (m-30) cc_final: 0.7917 (m-30) REVERT: B 100 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7840 (ttp-110) REVERT: B 104 GLN cc_start: 0.7475 (mm110) cc_final: 0.6772 (pt0) REVERT: B 206 LYS cc_start: 0.8837 (mttp) cc_final: 0.8443 (mttp) REVERT: B 233 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7588 (mm110) REVERT: B 264 GLN cc_start: 0.8707 (tt0) cc_final: 0.8444 (tt0) REVERT: B 297 LYS cc_start: 0.8463 (mmtp) cc_final: 0.8116 (mmtm) REVERT: B 390 ASP cc_start: 0.8458 (m-30) cc_final: 0.8049 (m-30) REVERT: C 98 GLN cc_start: 0.7947 (tt0) cc_final: 0.7673 (tt0) REVERT: C 115 MET cc_start: 0.8292 (mtt) cc_final: 0.8038 (mtp) REVERT: C 116 HIS cc_start: 0.8628 (t-90) cc_final: 0.8348 (t70) REVERT: C 132 SER cc_start: 0.8991 (p) cc_final: 0.8707 (m) REVERT: C 206 LYS cc_start: 0.8917 (mttp) cc_final: 0.8307 (mttp) REVERT: C 264 GLN cc_start: 0.8452 (tt0) cc_final: 0.8159 (tt0) REVERT: C 315 GLU cc_start: 0.8807 (tt0) cc_final: 0.8449 (mt-10) REVERT: C 390 ASP cc_start: 0.8428 (m-30) cc_final: 0.7966 (m-30) REVERT: C 402 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7007 (mt-10) REVERT: D 88 ARG cc_start: 0.7495 (ttm-80) cc_final: 0.7181 (ttm110) REVERT: D 100 ARG cc_start: 0.8074 (ttm-80) cc_final: 0.7754 (ttm110) REVERT: D 104 GLN cc_start: 0.7837 (mm110) cc_final: 0.7125 (pt0) REVERT: D 112 GLU cc_start: 0.7974 (mp0) cc_final: 0.7762 (mp0) REVERT: D 206 LYS cc_start: 0.8785 (mttp) cc_final: 0.8371 (mttp) REVERT: D 235 LYS cc_start: 0.8916 (tttt) cc_final: 0.8452 (tttp) REVERT: D 264 GLN cc_start: 0.8753 (tt0) cc_final: 0.8413 (tt0) REVERT: D 300 GLU cc_start: 0.8313 (tp30) cc_final: 0.7883 (mm-30) REVERT: D 382 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: E 106 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7442 (mtt-85) REVERT: E 115 MET cc_start: 0.8406 (mtm) cc_final: 0.8111 (mtp) REVERT: E 206 LYS cc_start: 0.8825 (mttp) cc_final: 0.8392 (mttp) REVERT: E 264 GLN cc_start: 0.8622 (tt0) cc_final: 0.8373 (tt0) REVERT: E 299 GLU cc_start: 0.8363 (tt0) cc_final: 0.7948 (tt0) REVERT: E 300 GLU cc_start: 0.8572 (tp30) cc_final: 0.8197 (mm-30) REVERT: E 402 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.6867 (mt-10) REVERT: E 417 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.5141 (mptt) outliers start: 39 outliers final: 26 residues processed: 211 average time/residue: 1.7275 time to fit residues: 389.3204 Evaluate side-chains 213 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 312 CYS 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 102 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 131 LEU 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 102 MET Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 417 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 76 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 20.0000 chunk 162 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 70 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 HIS D 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.120339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.095808 restraints weight = 14831.946| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.41 r_work: 0.2758 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2420 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= 0.144 Angle : 0.532 7.834 18810 Z= 0.271 Chirality : 0.039 0.158 2245 Planarity : 0.005 0.054 2345 Dihedral : 5.529 50.974 1875 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.57 % Allowed : 12.15 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.20), residues: 1695 helix: 1.84 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -0.46 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 343 HIS 0.004 0.001 HIS A 344 PHE 0.013 0.002 PHE B 146 TYR 0.010 0.001 TYR E 121 ARG 0.006 0.000 ARG D 397 Details of bonding type rmsd hydrogen bonds : bond 0.04785 ( 1015) hydrogen bonds : angle 3.90911 ( 3015) covalent geometry : bond 0.00342 (13830) covalent geometry : angle 0.53176 (18810) ********************** 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 227 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 1.591 Fit side-chains REVERT: A 88 ARG cc_start: 0.7376 (ttm-80) cc_final: 0.7030 (ttm110) REVERT: A 100 ARG cc_start: 0.8166 (ttp-110) cc_final: 0.7713 (ttm110) REVERT: A 104 GLN cc_start: 0.7595 (mm110) cc_final: 0.7040 (pt0) REVERT: A 155 SER cc_start: 0.8735 (m) cc_final: 0.8473 (m) REVERT: A 162 LEU cc_start: 0.7884 (mt) cc_final: 0.7604 (mt) REVERT: A 164 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7951 (mp) REVERT: A 206 LYS cc_start: 0.8824 (mttp) cc_final: 0.8381 (mttp) REVERT: A 233 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7497 (mm110) REVERT: A 306 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8366 (mt) REVERT: A 312 CYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8245 (p) REVERT: A 390 ASP cc_start: 0.8301 (m-30) cc_final: 0.7794 (m-30) REVERT: B 104 GLN cc_start: 0.7412 (mm110) cc_final: 0.6672 (pt0) REVERT: B 206 LYS cc_start: 0.8780 (mttp) cc_final: 0.8346 (mttp) REVERT: B 233 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7513 (mm110) REVERT: B 264 GLN cc_start: 0.8674 (tt0) cc_final: 0.8450 (tt0) REVERT: B 390 ASP cc_start: 0.8357 (m-30) cc_final: 0.7945 (m-30) REVERT: C 104 GLN cc_start: 0.7482 (mm110) cc_final: 0.6525 (pt0) REVERT: C 115 MET cc_start: 0.8179 (mtt) cc_final: 0.7907 (mtp) REVERT: C 132 SER cc_start: 0.8963 (p) cc_final: 0.8661 (m) REVERT: C 206 LYS cc_start: 0.8890 (mttp) cc_final: 0.8314 (mttp) REVERT: C 264 GLN cc_start: 0.8382 (tt0) cc_final: 0.8055 (tt0) REVERT: C 315 GLU cc_start: 0.8769 (tt0) cc_final: 0.8394 (mt-10) REVERT: C 390 ASP cc_start: 0.8348 (m-30) cc_final: 0.7888 (m-30) REVERT: C 402 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6850 (mt-10) REVERT: D 88 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.7030 (ttm110) REVERT: D 100 ARG cc_start: 0.8093 (ttm-80) cc_final: 0.7807 (ttm110) REVERT: D 104 GLN cc_start: 0.7778 (mm110) cc_final: 0.7048 (pt0) REVERT: D 112 GLU cc_start: 0.7938 (mp0) cc_final: 0.7731 (mp0) REVERT: D 206 LYS cc_start: 0.8704 (mttp) cc_final: 0.8239 (mttp) REVERT: D 264 GLN cc_start: 0.8712 (tt0) cc_final: 0.8364 (tt0) REVERT: D 300 GLU cc_start: 0.8324 (tp30) cc_final: 0.7926 (mm-30) REVERT: D 382 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: E 106 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7339 (mtt-85) REVERT: E 115 MET cc_start: 0.8266 (mtm) cc_final: 0.7960 (mtp) REVERT: E 206 LYS cc_start: 0.8778 (mttp) cc_final: 0.8309 (mttp) REVERT: E 264 GLN cc_start: 0.8613 (tt0) cc_final: 0.8369 (tt0) REVERT: E 299 GLU cc_start: 0.8243 (tt0) cc_final: 0.7810 (tt0) REVERT: E 300 GLU cc_start: 0.8485 (tp30) cc_final: 0.8078 (mm-30) REVERT: E 402 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6713 (mt-10) REVERT: E 417 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.5011 (mptt) outliers start: 39 outliers final: 24 residues processed: 218 average time/residue: 1.6557 time to fit residues: 387.2035 Evaluate side-chains 213 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 312 CYS 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 102 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 402 GLU 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 102 MET Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 417 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 141 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 151 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3305 r_free = 0.3305 target = 0.124301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.099927 restraints weight = 14944.821| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.46 r_work: 0.2855 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2617 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= 0.110 Angle : 0.480 7.435 18810 Z= 0.244 Chirality : 0.037 0.158 2245 Planarity : 0.005 0.039 2345 Dihedral : 5.212 49.655 1875 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.31 % Allowed : 12.61 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.21), residues: 1695 helix: 2.22 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -0.26 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 343 HIS 0.003 0.001 HIS C 344 PHE 0.009 0.002 PHE D 192 TYR 0.008 0.001 TYR E 156 ARG 0.006 0.000 ARG D 261 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 1015) hydrogen bonds : angle 3.72286 ( 3015) covalent geometry : bond 0.00229 (13830) covalent geometry : angle 0.48007 (18810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11372.89 seconds wall clock time: 202 minutes 51.17 seconds (12171.17 seconds total)