Starting phenix.real_space_refine on Wed Mar 4 10:59:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ek3_31167/03_2026/7ek3_31167.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ek3_31167/03_2026/7ek3_31167.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/7ek3_31167/03_2026/7ek3_31167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ek3_31167/03_2026/7ek3_31167.map" model { file = "/net/cci-nas-00/data/ceres_data/7ek3_31167/03_2026/7ek3_31167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ek3_31167/03_2026/7ek3_31167.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 8700 2.51 5 N 2360 2.21 5 O 2390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13505 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2701 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 16, 'TRANS': 324} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.19, per 1000 atoms: 0.16 Number of scatterers: 13505 At special positions: 0 Unit cell: (108.896, 111.552, 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 2390 8.00 N 2360 7.00 C 8700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 457.0 milliseconds 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3290 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 0 sheets defined 88.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 82 through 87 removed outlier: 3.708A pdb=" N ILE A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 103 Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 162 Proline residue: A 141 - end of helix 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: 3.603A pdb=" N VAL A 274 " --> pdb=" O ASP A 270 " (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 Processing helix chain 'A' and resid 329 through 346 removed outlier: 3.513A pdb=" N THR A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 356 removed outlier: 5.140A pdb=" N ASP A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ASP A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 380 removed outlier: 3.557A pdb=" N ILE A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 388 through 406 removed outlier: 3.751A pdb=" N VAL A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 397 " --> pdb=" O CYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 418 removed outlier: 3.577A pdb=" N GLY A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.709A pdb=" N ILE B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 103 Processing helix chain 'B' and resid 110 through 118 Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 133 through 162 Proline residue: B 141 - end of helix 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: 3.603A pdb=" N VAL B 274 " --> pdb=" O ASP B 270 " (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 Processing helix chain 'B' and resid 329 through 346 removed outlier: 3.513A pdb=" N THR B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 356 removed outlier: 5.140A pdb=" N ASP B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASP B 354 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 380 removed outlier: 3.557A pdb=" N ILE B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 388 through 406 removed outlier: 3.751A pdb=" N VAL B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 397 " --> pdb=" O CYS B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 418 removed outlier: 3.577A pdb=" N GLY B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 87 removed outlier: 3.709A pdb=" N ILE C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 103 Processing helix chain 'C' and resid 110 through 118 Processing helix chain 'C' and resid 121 through 129 Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 133 through 162 Proline residue: C 141 - end of helix 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: 3.603A pdb=" N VAL C 274 " --> pdb=" O ASP C 270 " (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 Processing helix chain 'C' and resid 329 through 346 removed outlier: 3.513A pdb=" N THR C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 356 removed outlier: 5.140A pdb=" N ASP C 353 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASP C 354 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 380 removed outlier: 3.557A pdb=" N ILE C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C 374 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 388 through 406 removed outlier: 3.751A pdb=" N VAL C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG C 397 " --> pdb=" O CYS C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 418 removed outlier: 3.576A pdb=" N GLY C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 87 removed outlier: 3.708A pdb=" N ILE D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 103 Processing helix chain 'D' and resid 110 through 118 Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 162 Proline residue: D 141 - end of helix 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: 3.603A pdb=" N VAL D 274 " --> pdb=" O ASP D 270 " (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 Processing helix chain 'D' and resid 329 through 346 removed outlier: 3.513A pdb=" N THR D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 356 removed outlier: 5.140A pdb=" N ASP D 353 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ASP D 354 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 380 removed outlier: 3.557A pdb=" N ILE D 373 " --> pdb=" O SER D 369 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU D 374 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 Processing helix chain 'D' and resid 388 through 406 removed outlier: 3.752A pdb=" N VAL D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG D 397 " --> pdb=" O CYS D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 418 removed outlier: 3.577A pdb=" N GLY D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 87 removed outlier: 3.708A pdb=" N ILE E 86 " --> pdb=" O THR E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 103 Processing helix chain 'E' and resid 110 through 118 Processing helix chain 'E' and resid 121 through 129 Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 133 through 162 Proline residue: E 141 - end of helix 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: 3.604A pdb=" N VAL E 274 " --> pdb=" O ASP E 270 " (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 Processing helix chain 'E' and resid 329 through 346 removed outlier: 3.513A pdb=" N THR E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 356 removed outlier: 5.140A pdb=" N ASP E 353 " --> pdb=" O ILE E 349 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ASP E 354 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 380 removed outlier: 3.557A pdb=" N ILE E 373 " --> pdb=" O SER E 369 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU E 374 " --> pdb=" O LEU E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 Processing helix chain 'E' and resid 388 through 406 removed outlier: 3.752A pdb=" N VAL E 396 " --> pdb=" O LEU E 392 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG E 397 " --> pdb=" O CYS E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 418 removed outlier: 3.577A pdb=" N GLY E 418 " --> pdb=" O LEU E 414 " (cutoff:3.500A) 1020 hydrogen bonds defined for protein. 3030 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: 1.90 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1843 1.26 - 1.40: 3443 1.40 - 1.54: 7665 1.54 - 1.68: 764 1.68 - 1.81: 75 Bond restraints: 13790 Sorted by residual: bond pdb=" C PRO B 385 " pdb=" O PRO B 385 " ideal model delta sigma weight residual 1.238 1.122 0.116 1.37e-02 5.33e+03 7.20e+01 bond pdb=" C PRO A 385 " pdb=" O PRO A 385 " ideal model delta sigma weight residual 1.238 1.122 0.116 1.37e-02 5.33e+03 7.16e+01 bond pdb=" C PRO C 385 " pdb=" O PRO C 385 " ideal model delta sigma weight residual 1.238 1.122 0.116 1.37e-02 5.33e+03 7.13e+01 bond pdb=" C PRO D 385 " pdb=" O PRO D 385 " ideal model delta sigma weight residual 1.238 1.122 0.116 1.37e-02 5.33e+03 7.13e+01 bond pdb=" C PRO E 385 " pdb=" O PRO E 385 " ideal model delta sigma weight residual 1.238 1.122 0.116 1.37e-02 5.33e+03 7.12e+01 ... (remaining 13785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 15312 2.32 - 4.64: 3110 4.64 - 6.96: 278 6.96 - 9.28: 40 9.28 - 11.60: 15 Bond angle restraints: 18755 Sorted by residual: angle pdb=" CA ILE A 140 " pdb=" C ILE A 140 " pdb=" N PRO A 141 " ideal model delta sigma weight residual 120.83 130.60 -9.77 5.90e-01 2.87e+00 2.74e+02 angle pdb=" CA ILE D 140 " pdb=" C ILE D 140 " pdb=" N PRO D 141 " ideal model delta sigma weight residual 120.83 130.59 -9.76 5.90e-01 2.87e+00 2.74e+02 angle pdb=" CA ILE C 140 " pdb=" C ILE C 140 " pdb=" N PRO C 141 " ideal model delta sigma weight residual 120.83 130.59 -9.76 5.90e-01 2.87e+00 2.73e+02 angle pdb=" CA ILE B 140 " pdb=" C ILE B 140 " pdb=" N PRO B 141 " ideal model delta sigma weight residual 120.83 130.58 -9.75 5.90e-01 2.87e+00 2.73e+02 angle pdb=" CA ILE E 140 " pdb=" C ILE E 140 " pdb=" N PRO E 141 " ideal model delta sigma weight residual 120.83 130.58 -9.75 5.90e-01 2.87e+00 2.73e+02 ... (remaining 18750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 7538 17.25 - 34.49: 632 34.49 - 51.74: 136 51.74 - 68.98: 54 68.98 - 86.23: 15 Dihedral angle restraints: 8375 sinusoidal: 3350 harmonic: 5025 Sorted by residual: dihedral pdb=" N GLN D 401 " pdb=" C GLN D 401 " pdb=" CA GLN D 401 " pdb=" CB GLN D 401 " ideal model delta harmonic sigma weight residual 122.80 112.07 10.73 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" N GLN C 401 " pdb=" C GLN C 401 " pdb=" CA GLN C 401 " pdb=" CB GLN C 401 " ideal model delta harmonic sigma weight residual 122.80 112.07 10.73 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" N GLN B 401 " pdb=" C GLN B 401 " pdb=" CA GLN B 401 " pdb=" CB GLN B 401 " ideal model delta harmonic sigma weight residual 122.80 112.08 10.72 0 2.50e+00 1.60e-01 1.84e+01 ... (remaining 8372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 946 0.048 - 0.096: 637 0.096 - 0.144: 462 0.144 - 0.192: 160 0.192 - 0.240: 40 Chirality restraints: 2245 Sorted by residual: chirality pdb=" CB VAL C 359 " pdb=" CA VAL C 359 " pdb=" CG1 VAL C 359 " pdb=" CG2 VAL C 359 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL B 359 " pdb=" CA VAL B 359 " pdb=" CG1 VAL B 359 " pdb=" CG2 VAL B 359 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB VAL D 359 " pdb=" CA VAL D 359 " pdb=" CG1 VAL D 359 " pdb=" CG2 VAL D 359 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 2242 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 343 " 0.030 2.00e-02 2.50e+03 1.53e-02 5.86e+00 pdb=" CG TRP C 343 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP C 343 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP C 343 " -0.021 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 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 343 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 343 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 343 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 343 " 0.030 2.00e-02 2.50e+03 1.53e-02 5.86e+00 pdb=" CG TRP E 343 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP E 343 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP E 343 " -0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP E 343 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 343 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 343 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 343 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 343 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP E 343 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 343 " 0.030 2.00e-02 2.50e+03 1.53e-02 5.83e+00 pdb=" CG TRP D 343 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP D 343 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP D 343 " -0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP D 343 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 343 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 343 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 343 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 343 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 343 " 0.009 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1143 2.76 - 3.30: 14062 3.30 - 3.83: 22548 3.83 - 4.37: 28971 4.37 - 4.90: 46595 Nonbonded interactions: 113319 Sorted by model distance: nonbonded pdb=" OH TYR D 179 " pdb=" OG1 THR D 346 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR A 179 " pdb=" OG1 THR A 346 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR C 179 " pdb=" OG1 THR C 346 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR E 179 " pdb=" OG1 THR E 346 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR B 179 " pdb=" OG1 THR B 346 " model vdw 2.232 3.040 ... (remaining 113314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.990 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:7.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.018 0.116 13790 Z= 1.305 Angle : 1.847 11.599 18755 Z= 1.370 Chirality : 0.084 0.240 2245 Planarity : 0.006 0.022 2340 Dihedral : 14.915 86.230 5085 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.66 % Allowed : 4.64 % Favored : 93.71 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.19), residues: 1695 helix: -0.07 (0.13), residues: 1430 sheet: None (None), residues: 0 loop : -1.31 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG B 118 TYR 0.018 0.006 TYR D 179 PHE 0.023 0.007 PHE B 288 TRP 0.030 0.006 TRP E 343 HIS 0.011 0.004 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.01797 (13790) covalent geometry : angle 1.84651 (18755) hydrogen bonds : bond 0.23786 ( 1020) hydrogen bonds : angle 6.50299 ( 3030) *********************** 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 306 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 281 time to evaluate : 0.427 Fit side-chains REVERT: A 104 GLN cc_start: 0.7299 (tp40) cc_final: 0.6755 (pt0) REVERT: A 109 TYR cc_start: 0.9082 (m-10) cc_final: 0.8850 (m-10) REVERT: A 233 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8308 (mp10) REVERT: A 261 ARG cc_start: 0.8593 (ttp-170) cc_final: 0.8327 (tmm-80) REVERT: A 299 GLU cc_start: 0.8307 (tt0) cc_final: 0.7300 (pm20) REVERT: A 401 GLN cc_start: 0.8624 (tt0) cc_final: 0.8356 (tt0) REVERT: A 402 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: B 96 ARG cc_start: 0.6999 (mtm-85) cc_final: 0.6393 (mtm-85) REVERT: B 104 GLN cc_start: 0.7435 (tp40) cc_final: 0.6925 (pt0) REVERT: B 180 GLN cc_start: 0.9075 (mt0) cc_final: 0.8872 (mt0) REVERT: B 261 ARG cc_start: 0.8549 (ttp-170) cc_final: 0.8172 (ttp-170) REVERT: B 264 GLN cc_start: 0.8440 (tt0) cc_final: 0.7755 (pt0) REVERT: B 279 LYS cc_start: 0.8732 (mtmt) cc_final: 0.8526 (mtmp) REVERT: B 402 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8603 (tt0) REVERT: C 100 ARG cc_start: 0.6991 (ttp-110) cc_final: 0.6740 (ttp-110) REVERT: C 103 ARG cc_start: 0.6868 (mtt-85) cc_final: 0.5993 (mmm160) REVERT: C 104 GLN cc_start: 0.7308 (tp40) cc_final: 0.6629 (pt0) REVERT: C 255 TYR cc_start: 0.8318 (t80) cc_final: 0.7981 (t80) REVERT: C 265 ASN cc_start: 0.8803 (m-40) cc_final: 0.8544 (m-40) REVERT: C 315 GLU cc_start: 0.8628 (tt0) cc_final: 0.7557 (mm-30) REVERT: C 358 ILE cc_start: 0.8378 (mt) cc_final: 0.8147 (mm) REVERT: C 402 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8025 (tt0) REVERT: C 407 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: D 88 ARG cc_start: 0.6974 (mtp85) cc_final: 0.6601 (mtp-110) REVERT: D 99 GLU cc_start: 0.6614 (mm-30) cc_final: 0.6351 (mm-30) REVERT: D 103 ARG cc_start: 0.6891 (mtt-85) cc_final: 0.5915 (mmp-170) REVERT: D 104 GLN cc_start: 0.7341 (tp40) cc_final: 0.6654 (pt0) REVERT: D 113 LYS cc_start: 0.7739 (mttt) cc_final: 0.7138 (mtpt) REVERT: D 162 LEU cc_start: 0.8059 (mt) cc_final: 0.7772 (mp) REVERT: D 265 ASN cc_start: 0.8991 (m-40) cc_final: 0.8624 (m-40) REVERT: D 279 LYS cc_start: 0.8453 (mtmt) cc_final: 0.8022 (mmtt) REVERT: D 299 GLU cc_start: 0.8129 (tt0) cc_final: 0.7221 (pm20) REVERT: D 315 GLU cc_start: 0.8405 (tt0) cc_final: 0.7387 (mm-30) REVERT: D 390 ASP cc_start: 0.8879 (m-30) cc_final: 0.8340 (m-30) REVERT: D 402 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8423 (tt0) REVERT: D 408 LYS cc_start: 0.8186 (tttt) cc_final: 0.7811 (ttpt) REVERT: E 102 MET cc_start: 0.7622 (mmt) cc_final: 0.7160 (mpp) REVERT: E 104 GLN cc_start: 0.6861 (tp40) cc_final: 0.6401 (pt0) REVERT: E 125 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7217 (ptp90) REVERT: E 233 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8545 (mp10) REVERT: E 315 GLU cc_start: 0.8548 (tt0) cc_final: 0.7616 (mm-30) REVERT: E 354 ASP cc_start: 0.8331 (m-30) cc_final: 0.8113 (m-30) REVERT: E 379 LEU cc_start: 0.8714 (mt) cc_final: 0.7903 (tp) REVERT: E 408 LYS cc_start: 0.8005 (tttt) cc_final: 0.7569 (ttpt) outliers start: 25 outliers final: 3 residues processed: 299 average time/residue: 0.8103 time to fit residues: 258.0492 Evaluate side-chains 217 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 208 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE 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 C residue 407 GLU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 140 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN D 252 HIS D 264 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.113876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.089908 restraints weight = 14570.797| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.30 r_work: 0.2745 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13790 Z= 0.146 Angle : 0.594 6.769 18755 Z= 0.309 Chirality : 0.041 0.154 2245 Planarity : 0.005 0.037 2340 Dihedral : 5.878 58.260 1880 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.78 % Allowed : 10.07 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.21), residues: 1695 helix: 1.61 (0.14), residues: 1445 sheet: None (None), residues: 0 loop : -0.93 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 200 TYR 0.011 0.001 TYR B 241 PHE 0.012 0.002 PHE A 245 TRP 0.012 0.002 TRP E 208 HIS 0.004 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00302 (13790) covalent geometry : angle 0.59418 (18755) hydrogen bonds : bond 0.05142 ( 1020) hydrogen bonds : angle 4.10765 ( 3030) *********************** 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 266 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 0.558 Fit side-chains REVERT: A 162 LEU cc_start: 0.8359 (mt) cc_final: 0.8137 (mt) REVERT: A 261 ARG cc_start: 0.8582 (ttp-170) cc_final: 0.8255 (tmm-80) REVERT: A 297 LYS cc_start: 0.9003 (mptt) cc_final: 0.8797 (mmtm) REVERT: A 350 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9105 (pt) REVERT: A 379 LEU cc_start: 0.9015 (mt) cc_final: 0.8651 (tp) REVERT: B 96 ARG cc_start: 0.7215 (mtm-85) cc_final: 0.6751 (mtm-85) REVERT: B 264 GLN cc_start: 0.8456 (tt0) cc_final: 0.8047 (pt0) REVERT: B 379 LEU cc_start: 0.8947 (mt) cc_final: 0.8592 (tp) REVERT: C 100 ARG cc_start: 0.7306 (ttp-110) cc_final: 0.7002 (ttp-110) REVERT: C 112 GLU cc_start: 0.8340 (mp0) cc_final: 0.8097 (mp0) REVERT: C 315 GLU cc_start: 0.8834 (tt0) cc_final: 0.8285 (mm-30) REVERT: C 390 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8284 (m-30) REVERT: C 402 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: D 88 ARG cc_start: 0.7360 (mtp85) cc_final: 0.6963 (mtp-110) REVERT: D 113 LYS cc_start: 0.8336 (mttt) cc_final: 0.8028 (mtpt) REVERT: D 134 ARG cc_start: 0.7307 (mtt180) cc_final: 0.6921 (mtt-85) REVERT: D 265 ASN cc_start: 0.9168 (m-40) cc_final: 0.8967 (m-40) REVERT: D 315 GLU cc_start: 0.8691 (tt0) cc_final: 0.8307 (mm-30) REVERT: D 390 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8104 (m-30) REVERT: D 408 LYS cc_start: 0.8540 (tttt) cc_final: 0.8337 (ttpp) REVERT: E 233 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8568 (mp10) REVERT: E 315 GLU cc_start: 0.8601 (tt0) cc_final: 0.8324 (mm-30) REVERT: E 379 LEU cc_start: 0.9108 (mt) cc_final: 0.8516 (tp) REVERT: E 401 GLN cc_start: 0.8805 (tt0) cc_final: 0.8507 (mt0) outliers start: 42 outliers final: 6 residues processed: 249 average time/residue: 0.7734 time to fit residues: 207.0670 Evaluate side-chains 205 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 390 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 131 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 164 optimal weight: 0.5980 chunk 145 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN C 252 HIS D 264 GLN D 401 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.111823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.087786 restraints weight = 14703.436| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.30 r_work: 0.2667 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13790 Z= 0.160 Angle : 0.579 6.692 18755 Z= 0.298 Chirality : 0.041 0.152 2245 Planarity : 0.005 0.041 2340 Dihedral : 4.520 56.784 1860 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.72 % Allowed : 12.32 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.21), residues: 1695 helix: 1.83 (0.14), residues: 1445 sheet: None (None), residues: 0 loop : -0.82 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 413 TYR 0.010 0.002 TYR B 241 PHE 0.014 0.002 PHE A 245 TRP 0.011 0.001 TRP E 208 HIS 0.006 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00373 (13790) covalent geometry : angle 0.57888 (18755) hydrogen bonds : bond 0.05260 ( 1020) hydrogen bonds : angle 3.91845 ( 3030) *********************** 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 244 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 0.587 Fit side-chains REVERT: A 99 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6891 (mm-30) REVERT: A 162 LEU cc_start: 0.8381 (mt) cc_final: 0.8172 (mt) REVERT: A 261 ARG cc_start: 0.8603 (ttp-170) cc_final: 0.8262 (tmm-80) REVERT: A 350 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9081 (pt) REVERT: B 96 ARG cc_start: 0.7064 (mtm-85) cc_final: 0.6632 (mtm-85) REVERT: B 104 GLN cc_start: 0.7654 (pt0) cc_final: 0.7341 (pt0) REVERT: B 125 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7421 (mtm-85) REVERT: B 264 GLN cc_start: 0.8483 (tt0) cc_final: 0.7883 (pt0) REVERT: B 379 LEU cc_start: 0.8883 (mt) cc_final: 0.8545 (tp) REVERT: C 112 GLU cc_start: 0.8336 (mp0) cc_final: 0.8070 (mp0) REVERT: C 206 LYS cc_start: 0.9014 (mmtp) cc_final: 0.8381 (mttp) REVERT: C 315 GLU cc_start: 0.8822 (tt0) cc_final: 0.8264 (mm-30) REVERT: C 382 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: C 402 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: D 88 ARG cc_start: 0.7386 (mtp85) cc_final: 0.7022 (mtp-110) REVERT: D 104 GLN cc_start: 0.7255 (pt0) cc_final: 0.7046 (pt0) REVERT: D 113 LYS cc_start: 0.8218 (mttt) cc_final: 0.7763 (mtpt) REVERT: D 134 ARG cc_start: 0.7138 (mtt180) cc_final: 0.6740 (mtt-85) REVERT: D 148 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8438 (mm) REVERT: D 265 ASN cc_start: 0.9171 (m-40) cc_final: 0.8905 (m-40) REVERT: D 268 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7448 (tp30) REVERT: D 315 GLU cc_start: 0.8698 (tt0) cc_final: 0.8262 (mm-30) REVERT: D 390 ASP cc_start: 0.8688 (m-30) cc_final: 0.8123 (m-30) REVERT: E 233 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8660 (mp10) REVERT: E 315 GLU cc_start: 0.8603 (tt0) cc_final: 0.8293 (mm-30) REVERT: E 379 LEU cc_start: 0.9161 (mt) cc_final: 0.8484 (tp) REVERT: E 401 GLN cc_start: 0.8737 (tt0) cc_final: 0.8479 (mt0) outliers start: 41 outliers final: 21 residues processed: 228 average time/residue: 0.8082 time to fit residues: 197.3264 Evaluate side-chains 216 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 321 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 21 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 264 GLN D 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.111128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.087168 restraints weight = 14618.606| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 1.29 r_work: 0.2662 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13790 Z= 0.169 Angle : 0.579 6.678 18755 Z= 0.298 Chirality : 0.041 0.156 2245 Planarity : 0.005 0.044 2340 Dihedral : 4.546 58.050 1860 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.51 % Allowed : 12.19 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.20), residues: 1695 helix: 1.86 (0.14), residues: 1445 sheet: None (None), residues: 0 loop : -0.90 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 220 TYR 0.009 0.002 TYR B 121 PHE 0.014 0.002 PHE A 245 TRP 0.012 0.001 TRP E 208 HIS 0.005 0.002 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00405 (13790) covalent geometry : angle 0.57923 (18755) hydrogen bonds : bond 0.05230 ( 1020) hydrogen bonds : angle 3.87548 ( 3030) *********************** 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 249 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 196 time to evaluate : 0.544 Fit side-chains REVERT: A 233 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8229 (mp10) REVERT: A 261 ARG cc_start: 0.8579 (ttp-170) cc_final: 0.8186 (tmm-80) REVERT: A 350 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.9009 (pt) REVERT: B 96 ARG cc_start: 0.7193 (mtm-85) cc_final: 0.6713 (mtm-85) REVERT: B 125 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7841 (mtp180) REVERT: B 374 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: B 379 LEU cc_start: 0.8836 (mt) cc_final: 0.8478 (tp) REVERT: B 390 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8366 (m-30) REVERT: B 401 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8445 (tt0) REVERT: C 102 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7510 (mmt) REVERT: C 112 GLU cc_start: 0.8364 (mp0) cc_final: 0.8155 (mp0) REVERT: C 206 LYS cc_start: 0.9041 (mmtp) cc_final: 0.8507 (mtmp) REVERT: C 315 GLU cc_start: 0.8856 (tt0) cc_final: 0.8316 (mm-30) REVERT: C 382 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: C 402 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: D 88 ARG cc_start: 0.7458 (mtp85) cc_final: 0.7175 (mtp-110) REVERT: D 100 ARG cc_start: 0.7657 (ttm110) cc_final: 0.7455 (ttm110) REVERT: D 113 LYS cc_start: 0.8310 (mttt) cc_final: 0.7797 (mtpt) REVERT: D 134 ARG cc_start: 0.7089 (mtt180) cc_final: 0.6662 (mtt-85) REVERT: D 148 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8417 (mm) REVERT: D 265 ASN cc_start: 0.9144 (m-40) cc_final: 0.8780 (m-40) REVERT: D 268 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7393 (tp30) REVERT: D 315 GLU cc_start: 0.8686 (tt0) cc_final: 0.8264 (mm-30) REVERT: D 390 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8095 (m-30) REVERT: E 233 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8664 (mp10) REVERT: E 315 GLU cc_start: 0.8600 (tt0) cc_final: 0.8316 (mm-30) REVERT: E 379 LEU cc_start: 0.9158 (mt) cc_final: 0.8472 (tp) REVERT: E 382 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7539 (tm-30) outliers start: 53 outliers final: 22 residues processed: 219 average time/residue: 0.8374 time to fit residues: 196.0545 Evaluate side-chains 222 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 401 GLN Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain E residue 236 LYS Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 382 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 160 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN D 264 GLN D 401 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.113011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.089135 restraints weight = 14751.545| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.29 r_work: 0.2689 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13790 Z= 0.136 Angle : 0.529 6.600 18755 Z= 0.272 Chirality : 0.039 0.150 2245 Planarity : 0.005 0.043 2340 Dihedral : 4.386 56.347 1860 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.38 % Allowed : 12.72 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.21), residues: 1695 helix: 2.10 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -0.98 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 200 TYR 0.007 0.001 TYR B 121 PHE 0.011 0.002 PHE A 245 TRP 0.011 0.001 TRP E 208 HIS 0.004 0.001 HIS D 117 Details of bonding type rmsd covalent geometry : bond 0.00309 (13790) covalent geometry : angle 0.52935 (18755) hydrogen bonds : bond 0.04543 ( 1020) hydrogen bonds : angle 3.72662 ( 3030) *********************** 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 248 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 197 time to evaluate : 0.543 Fit side-chains REVERT: A 233 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8280 (mp10) REVERT: A 261 ARG cc_start: 0.8592 (ttp-170) cc_final: 0.8198 (tmm-80) REVERT: A 350 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8976 (pt) REVERT: B 96 ARG cc_start: 0.7171 (mtm-85) cc_final: 0.6689 (mtm-85) REVERT: B 374 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: B 379 LEU cc_start: 0.8817 (mt) cc_final: 0.8440 (tp) REVERT: B 390 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8377 (m-30) REVERT: C 102 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7469 (mmt) REVERT: C 112 GLU cc_start: 0.8373 (mp0) cc_final: 0.8142 (mp0) REVERT: C 315 GLU cc_start: 0.8847 (tt0) cc_final: 0.8299 (mm-30) REVERT: C 402 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: D 88 ARG cc_start: 0.7240 (mtp85) cc_final: 0.6976 (mtp-110) REVERT: D 113 LYS cc_start: 0.8293 (mttt) cc_final: 0.7772 (mtpt) REVERT: D 265 ASN cc_start: 0.9107 (m-40) cc_final: 0.8721 (m-40) REVERT: D 268 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: D 315 GLU cc_start: 0.8669 (tt0) cc_final: 0.8259 (mm-30) REVERT: D 390 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8118 (m-30) REVERT: E 315 GLU cc_start: 0.8643 (tt0) cc_final: 0.8305 (mm-30) REVERT: E 379 LEU cc_start: 0.9157 (mt) cc_final: 0.8478 (tp) REVERT: E 382 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7456 (tm-30) outliers start: 51 outliers final: 24 residues processed: 221 average time/residue: 0.7477 time to fit residues: 177.3341 Evaluate side-chains 219 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 236 LYS Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 382 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 68 optimal weight: 40.0000 chunk 123 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 264 GLN D 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.113026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.090023 restraints weight = 14526.444| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.21 r_work: 0.2699 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13790 Z= 0.155 Angle : 0.552 6.605 18755 Z= 0.283 Chirality : 0.040 0.154 2245 Planarity : 0.005 0.043 2340 Dihedral : 4.425 56.062 1860 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.72 % Allowed : 13.84 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.20), residues: 1695 helix: 2.07 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -0.99 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 200 TYR 0.011 0.001 TYR A 241 PHE 0.013 0.002 PHE A 245 TRP 0.011 0.001 TRP E 208 HIS 0.005 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00370 (13790) covalent geometry : angle 0.55236 (18755) hydrogen bonds : bond 0.04853 ( 1020) hydrogen bonds : angle 3.75784 ( 3030) *********************** 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 233 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 0.542 Fit side-chains REVERT: A 172 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8818 (mt) REVERT: A 233 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8330 (mp10) REVERT: A 315 GLU cc_start: 0.8610 (tt0) cc_final: 0.8073 (mm-30) REVERT: A 350 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.9015 (pt) REVERT: B 96 ARG cc_start: 0.7180 (mtm-85) cc_final: 0.6637 (mtm-85) REVERT: B 374 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: B 379 LEU cc_start: 0.8787 (mt) cc_final: 0.8559 (mm) REVERT: B 390 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8347 (m-30) REVERT: C 102 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7517 (mmt) REVERT: C 112 GLU cc_start: 0.8356 (mp0) cc_final: 0.8135 (mp0) REVERT: C 315 GLU cc_start: 0.8827 (tt0) cc_final: 0.8303 (mm-30) REVERT: C 382 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8170 (tm-30) REVERT: C 402 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: D 88 ARG cc_start: 0.7247 (mtp85) cc_final: 0.6970 (mtp-110) REVERT: D 113 LYS cc_start: 0.8296 (mttt) cc_final: 0.7783 (mtpt) REVERT: D 265 ASN cc_start: 0.9030 (m-40) cc_final: 0.8637 (m-40) REVERT: D 268 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7415 (mm-30) REVERT: D 315 GLU cc_start: 0.8624 (tt0) cc_final: 0.8285 (mm-30) REVERT: D 390 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8088 (m-30) REVERT: E 102 MET cc_start: 0.7944 (tpt) cc_final: 0.7679 (tpp) REVERT: E 315 GLU cc_start: 0.8596 (tt0) cc_final: 0.8292 (mm-30) REVERT: E 379 LEU cc_start: 0.9189 (mt) cc_final: 0.8486 (tp) REVERT: E 382 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7490 (tm-30) outliers start: 41 outliers final: 24 residues processed: 213 average time/residue: 0.7845 time to fit residues: 179.3295 Evaluate side-chains 223 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 382 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 34 optimal weight: 30.0000 chunk 146 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 264 GLN D 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.114785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.090575 restraints weight = 14688.579| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.36 r_work: 0.2721 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13790 Z= 0.121 Angle : 0.506 6.562 18755 Z= 0.259 Chirality : 0.038 0.149 2245 Planarity : 0.004 0.042 2340 Dihedral : 4.210 53.173 1860 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.12 % Allowed : 14.77 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.21), residues: 1695 helix: 2.31 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -0.85 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 100 TYR 0.010 0.001 TYR A 241 PHE 0.010 0.001 PHE A 245 TRP 0.010 0.001 TRP D 208 HIS 0.003 0.001 HIS D 117 Details of bonding type rmsd covalent geometry : bond 0.00267 (13790) covalent geometry : angle 0.50619 (18755) hydrogen bonds : bond 0.04025 ( 1020) hydrogen bonds : angle 3.59059 ( 3030) *********************** 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 236 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.592 Fit side-chains REVERT: A 172 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8672 (mt) REVERT: A 233 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8189 (mp10) REVERT: A 315 GLU cc_start: 0.8644 (tt0) cc_final: 0.7957 (mm-30) REVERT: A 350 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8861 (pt) REVERT: B 96 ARG cc_start: 0.6962 (mtm-85) cc_final: 0.6411 (mtm-85) REVERT: B 374 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8043 (tm-30) REVERT: B 379 LEU cc_start: 0.8676 (mt) cc_final: 0.8188 (tp) REVERT: B 390 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8350 (m-30) REVERT: C 102 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7411 (mmt) REVERT: C 112 GLU cc_start: 0.8285 (mp0) cc_final: 0.8044 (mp0) REVERT: C 315 GLU cc_start: 0.8803 (tt0) cc_final: 0.8150 (mm-30) REVERT: C 382 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: C 402 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: D 102 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7264 (mmt) REVERT: D 113 LYS cc_start: 0.8235 (mttt) cc_final: 0.7639 (mtpt) REVERT: D 265 ASN cc_start: 0.9069 (m-40) cc_final: 0.8664 (m-40) REVERT: D 268 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7452 (mm-30) REVERT: D 315 GLU cc_start: 0.8632 (tt0) cc_final: 0.8142 (mm-30) REVERT: D 390 ASP cc_start: 0.8643 (m-30) cc_final: 0.8027 (m-30) REVERT: D 408 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8266 (ttpt) REVERT: E 315 GLU cc_start: 0.8645 (tt0) cc_final: 0.8155 (mm-30) REVERT: E 379 LEU cc_start: 0.9119 (mt) cc_final: 0.8379 (tp) REVERT: E 382 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7538 (tm-30) outliers start: 32 outliers final: 15 residues processed: 218 average time/residue: 0.7820 time to fit residues: 183.0910 Evaluate side-chains 216 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 172 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 140 ILE Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 382 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 264 GLN D 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.113437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.089008 restraints weight = 14513.028| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.36 r_work: 0.2695 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13790 Z= 0.139 Angle : 0.532 6.561 18755 Z= 0.272 Chirality : 0.039 0.151 2245 Planarity : 0.005 0.042 2340 Dihedral : 4.263 52.513 1860 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.25 % Allowed : 14.90 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.21), residues: 1695 helix: 2.28 (0.14), residues: 1445 sheet: None (None), residues: 0 loop : -0.81 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 100 TYR 0.009 0.001 TYR D 109 PHE 0.012 0.002 PHE A 245 TRP 0.010 0.001 TRP E 208 HIS 0.004 0.001 HIS D 117 Details of bonding type rmsd covalent geometry : bond 0.00323 (13790) covalent geometry : angle 0.53192 (18755) hydrogen bonds : bond 0.04471 ( 1020) hydrogen bonds : angle 3.64488 ( 3030) *********************** 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 229 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.576 Fit side-chains REVERT: A 172 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8690 (mt) REVERT: A 233 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8160 (mp-120) REVERT: A 315 GLU cc_start: 0.8654 (tt0) cc_final: 0.7991 (mm-30) REVERT: A 350 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8915 (pt) REVERT: B 96 ARG cc_start: 0.6997 (mtm-85) cc_final: 0.6419 (mtm-85) REVERT: B 374 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: B 390 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8330 (m-30) REVERT: C 102 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7438 (mmt) REVERT: C 112 GLU cc_start: 0.8245 (mp0) cc_final: 0.8031 (mp0) REVERT: C 270 ASP cc_start: 0.8689 (m-30) cc_final: 0.8159 (m-30) REVERT: C 315 GLU cc_start: 0.8850 (tt0) cc_final: 0.8169 (mm-30) REVERT: C 382 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: C 402 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: D 102 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7357 (mmt) REVERT: D 113 LYS cc_start: 0.8257 (mttt) cc_final: 0.7654 (mtpt) REVERT: D 265 ASN cc_start: 0.9030 (m-40) cc_final: 0.8637 (m-40) REVERT: D 268 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7478 (mm-30) REVERT: D 315 GLU cc_start: 0.8657 (tt0) cc_final: 0.8073 (mm-30) REVERT: D 382 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7666 (mm-30) REVERT: D 390 ASP cc_start: 0.8657 (m-30) cc_final: 0.8033 (m-30) REVERT: D 408 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8275 (ttpt) REVERT: E 315 GLU cc_start: 0.8650 (tt0) cc_final: 0.8175 (mm-30) REVERT: E 379 LEU cc_start: 0.9139 (mt) cc_final: 0.8368 (tp) REVERT: E 382 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7581 (tm-30) outliers start: 34 outliers final: 20 residues processed: 211 average time/residue: 0.7759 time to fit residues: 175.8279 Evaluate side-chains 217 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 342 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 162 LEU Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 382 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 51 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 93 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 264 GLN D 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.114438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.090009 restraints weight = 14711.731| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 1.37 r_work: 0.2708 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13790 Z= 0.128 Angle : 0.519 6.544 18755 Z= 0.264 Chirality : 0.039 0.150 2245 Planarity : 0.004 0.042 2340 Dihedral : 4.211 51.369 1860 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.32 % Allowed : 14.77 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.21), residues: 1695 helix: 2.32 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -0.75 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 100 TYR 0.008 0.001 TYR D 109 PHE 0.010 0.002 PHE A 245 TRP 0.010 0.001 TRP D 208 HIS 0.004 0.001 HIS D 117 Details of bonding type rmsd covalent geometry : bond 0.00292 (13790) covalent geometry : angle 0.51898 (18755) hydrogen bonds : bond 0.04206 ( 1020) hydrogen bonds : angle 3.60102 ( 3030) *********************** 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 228 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.533 Fit side-chains REVERT: A 172 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8665 (mt) REVERT: A 233 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8193 (mp10) REVERT: A 315 GLU cc_start: 0.8642 (tt0) cc_final: 0.7968 (mm-30) REVERT: A 350 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8906 (pt) REVERT: B 96 ARG cc_start: 0.6988 (mtm-85) cc_final: 0.6603 (mtm-85) REVERT: B 374 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8085 (tm-30) REVERT: B 390 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8355 (m-30) REVERT: C 102 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7444 (mmt) REVERT: C 112 GLU cc_start: 0.8239 (mp0) cc_final: 0.8027 (mp0) REVERT: C 270 ASP cc_start: 0.8645 (m-30) cc_final: 0.8125 (m-30) REVERT: C 315 GLU cc_start: 0.8823 (tt0) cc_final: 0.8165 (mm-30) REVERT: C 397 ARG cc_start: 0.8740 (ttm110) cc_final: 0.8420 (ttp80) REVERT: C 402 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: D 102 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7368 (mmt) REVERT: D 113 LYS cc_start: 0.8257 (mttt) cc_final: 0.7659 (mtpt) REVERT: D 148 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8362 (mm) REVERT: D 265 ASN cc_start: 0.9024 (m-40) cc_final: 0.8632 (m-40) REVERT: D 315 GLU cc_start: 0.8611 (tt0) cc_final: 0.8060 (mm-30) REVERT: D 390 ASP cc_start: 0.8641 (m-30) cc_final: 0.8021 (m-30) REVERT: D 408 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8277 (ttpt) REVERT: E 315 GLU cc_start: 0.8649 (tt0) cc_final: 0.8188 (mm-30) REVERT: E 379 LEU cc_start: 0.9133 (mt) cc_final: 0.8366 (tp) REVERT: E 382 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7527 (tm-30) outliers start: 35 outliers final: 20 residues processed: 209 average time/residue: 0.7938 time to fit residues: 177.8410 Evaluate side-chains 218 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 172 LEU 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 162 LEU Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 382 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 108 optimal weight: 0.0670 chunk 13 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 264 GLN D 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.115185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.090721 restraints weight = 14546.936| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 1.37 r_work: 0.2717 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13790 Z= 0.125 Angle : 0.515 6.543 18755 Z= 0.262 Chirality : 0.039 0.149 2245 Planarity : 0.004 0.042 2340 Dihedral : 4.151 52.194 1860 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.92 % Allowed : 15.23 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.21), residues: 1695 helix: 2.38 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -0.70 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 100 TYR 0.014 0.001 TYR A 241 PHE 0.010 0.001 PHE A 245 TRP 0.009 0.001 TRP D 208 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00280 (13790) covalent geometry : angle 0.51505 (18755) hydrogen bonds : bond 0.04100 ( 1020) hydrogen bonds : angle 3.56894 ( 3030) ********************** 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 220 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.529 Fit side-chains REVERT: A 172 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8627 (mt) REVERT: A 233 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8186 (mp10) REVERT: A 315 GLU cc_start: 0.8638 (tt0) cc_final: 0.7974 (mm-30) REVERT: A 350 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8898 (pt) REVERT: B 96 ARG cc_start: 0.7009 (mtm-85) cc_final: 0.6595 (mtm-85) REVERT: B 374 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8072 (tm-30) REVERT: B 390 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8359 (m-30) REVERT: C 102 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7419 (mmt) REVERT: C 112 GLU cc_start: 0.8240 (mp0) cc_final: 0.8020 (mp0) REVERT: C 206 LYS cc_start: 0.8922 (mptt) cc_final: 0.8305 (mtmp) REVERT: C 270 ASP cc_start: 0.8592 (m-30) cc_final: 0.8070 (m-30) REVERT: C 315 GLU cc_start: 0.8819 (tt0) cc_final: 0.8171 (mm-30) REVERT: C 397 ARG cc_start: 0.8727 (ttm110) cc_final: 0.8427 (ttp80) REVERT: C 402 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: D 102 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7375 (mmt) REVERT: D 113 LYS cc_start: 0.8296 (mttt) cc_final: 0.7715 (mtpt) REVERT: D 148 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8360 (mm) REVERT: D 265 ASN cc_start: 0.9020 (m-40) cc_final: 0.8623 (m-40) REVERT: D 315 GLU cc_start: 0.8649 (tt0) cc_final: 0.8045 (mm-30) REVERT: D 390 ASP cc_start: 0.8647 (m-30) cc_final: 0.8021 (m-30) REVERT: D 408 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8278 (ttpt) REVERT: E 315 GLU cc_start: 0.8660 (tt0) cc_final: 0.8228 (mm-30) REVERT: E 379 LEU cc_start: 0.9144 (mt) cc_final: 0.8378 (tp) REVERT: E 382 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7435 (tm-30) outliers start: 29 outliers final: 15 residues processed: 203 average time/residue: 0.8105 time to fit residues: 176.2058 Evaluate side-chains 213 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 172 LEU 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 261 ARG Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 382 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 151 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 264 GLN D 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.112952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.088304 restraints weight = 14670.223| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.37 r_work: 0.2687 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13790 Z= 0.149 Angle : 0.548 6.552 18755 Z= 0.280 Chirality : 0.040 0.151 2245 Planarity : 0.005 0.042 2340 Dihedral : 4.282 52.632 1860 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.85 % Allowed : 15.17 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.21), residues: 1695 helix: 2.28 (0.14), residues: 1445 sheet: None (None), residues: 0 loop : -0.73 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 200 TYR 0.010 0.001 TYR D 109 PHE 0.012 0.002 PHE E 384 TRP 0.011 0.001 TRP E 208 HIS 0.004 0.001 HIS D 117 Details of bonding type rmsd covalent geometry : bond 0.00353 (13790) covalent geometry : angle 0.54833 (18755) hydrogen bonds : bond 0.04667 ( 1020) hydrogen bonds : angle 3.67992 ( 3030) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4990.23 seconds wall clock time: 85 minutes 45.68 seconds (5145.68 seconds total)