Starting phenix.real_space_refine on Thu Jul 31 04:02:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ek3_31167/07_2025/7ek3_31167.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ek3_31167/07_2025/7ek3_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_31167/07_2025/7ek3_31167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ek3_31167/07_2025/7ek3_31167.map" model { file = "/net/cci-nas-00/data/ceres_data/7ek3_31167/07_2025/7ek3_31167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ek3_31167/07_2025/7ek3_31167.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, E, D Time building chain proxies: 8.12, per 1000 atoms: 0.60 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: 3.61 Conformation dependent library (CDL) restraints added in 2.7 seconds 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3290 Finding SS restraints... Secondary structure from input PDB file: 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: 1.29 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: 5.63 Time building geometry restraints manager: 4.27 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 40.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.150 Set scattering table: 0.270 Process input model: 36.180 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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:28.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.360 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (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 TRP 0.030 0.006 TRP E 343 HIS 0.011 0.004 HIS B 344 PHE 0.023 0.007 PHE B 288 TYR 0.018 0.006 TYR D 179 ARG 0.024 0.002 ARG B 118 Details of bonding type rmsd hydrogen bonds : bond 0.23786 ( 1020) hydrogen bonds : angle 6.50299 ( 3030) covalent geometry : bond 0.01797 (13790) covalent geometry : angle 1.84651 (18755) *********************** 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 : 1.550 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: 0.8849 (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: 0.7309 (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: 0.6653 (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: 0.7388 (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: 0.7624 (mm-30) REVERT: E 354 ASP cc_start: 0.8331 (m-30) cc_final: 0.8113 (m-30) REVERT: E 379 LEU cc_start: 0.8713 (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: 2.0615 time to fit residues: 661.0208 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 : 1.707 ------------------------------------------------------------------------------- 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 143 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 68 optimal weight: 30.0000 chunk 133 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 HIS 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 = 0.3129 r_free = 0.3129 target = 0.110565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.086575 restraints weight = 14490.723| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 1.30 r_work: 0.2657 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13790 Z= 0.183 Angle : 0.644 6.948 18755 Z= 0.336 Chirality : 0.043 0.154 2245 Planarity : 0.005 0.040 2340 Dihedral : 6.056 59.424 1880 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.78 % Allowed : 9.80 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.21), residues: 1695 helix: 1.42 (0.14), residues: 1450 sheet: None (None), residues: 0 loop : -0.96 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 352 HIS 0.007 0.002 HIS A 314 PHE 0.016 0.002 PHE A 245 TYR 0.012 0.002 TYR B 121 ARG 0.005 0.001 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.06103 ( 1020) hydrogen bonds : angle 4.20702 ( 3030) covalent geometry : bond 0.00426 (13790) covalent geometry : angle 0.64428 (18755) *********************** 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 255 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 1.711 Fit side-chains REVERT: A 102 MET cc_start: 0.7533 (tpt) cc_final: 0.7281 (tpp) REVERT: A 162 LEU cc_start: 0.8375 (mt) cc_final: 0.8165 (mt) REVERT: A 233 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8256 (mp10) REVERT: A 261 ARG cc_start: 0.8588 (ttp-170) cc_final: 0.8263 (tmm-80) REVERT: A 297 LYS cc_start: 0.9053 (mptt) cc_final: 0.8849 (mmtm) REVERT: A 379 LEU cc_start: 0.9034 (mt) cc_final: 0.8656 (tp) REVERT: B 96 ARG cc_start: 0.7070 (mtm-85) cc_final: 0.6687 (mtm-85) REVERT: B 264 GLN cc_start: 0.8481 (tt0) cc_final: 0.8003 (pt0) REVERT: B 379 LEU cc_start: 0.8978 (mt) cc_final: 0.8573 (tp) REVERT: C 100 ARG cc_start: 0.7122 (ttp-110) cc_final: 0.6826 (ttp-110) REVERT: C 103 ARG cc_start: 0.6540 (mtt-85) cc_final: 0.6056 (mmm160) REVERT: C 315 GLU cc_start: 0.8815 (tt0) cc_final: 0.8273 (mm-30) REVERT: C 402 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: D 88 ARG cc_start: 0.7500 (mtp85) cc_final: 0.7088 (mtp-110) REVERT: D 113 LYS cc_start: 0.8249 (mttt) cc_final: 0.7849 (mtpt) REVERT: D 265 ASN cc_start: 0.9172 (m-40) cc_final: 0.8884 (m-40) REVERT: D 390 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: E 233 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8617 (mp10) REVERT: E 315 GLU cc_start: 0.8578 (tt0) cc_final: 0.8263 (mm-30) REVERT: E 379 LEU cc_start: 0.9138 (mt) cc_final: 0.8492 (tp) REVERT: E 401 GLN cc_start: 0.8680 (tt0) cc_final: 0.8357 (mt0) REVERT: E 417 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7482 (mttp) outliers start: 42 outliers final: 9 residues processed: 239 average time/residue: 1.6296 time to fit residues: 418.5498 Evaluate side-chains 202 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 1.765 ------------------------------------------------------------------------------- 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 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 342 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain E residue 417 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 125 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 77 optimal weight: 0.0670 chunk 63 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 overall best weight: 1.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 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 = 0.3151 r_free = 0.3151 target = 0.112275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.088403 restraints weight = 14654.189| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.29 r_work: 0.2694 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 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 : 0.003 0.037 13790 Z= 0.149 Angle : 0.560 6.676 18755 Z= 0.288 Chirality : 0.040 0.150 2245 Planarity : 0.005 0.042 2340 Dihedral : 4.523 57.504 1860 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.52 % Allowed : 12.45 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.21), residues: 1695 helix: 1.83 (0.14), residues: 1445 sheet: None (None), residues: 0 loop : -0.87 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 208 HIS 0.004 0.001 HIS A 314 PHE 0.012 0.002 PHE A 245 TYR 0.009 0.001 TYR C 241 ARG 0.003 0.000 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.05033 ( 1020) hydrogen bonds : angle 3.88887 ( 3030) covalent geometry : bond 0.00335 (13790) covalent geometry : angle 0.56009 (18755) *********************** 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 237 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 2.437 Fit side-chains REVERT: A 99 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6961 (mm-30) REVERT: A 162 LEU cc_start: 0.8387 (mt) cc_final: 0.8171 (mt) REVERT: A 261 ARG cc_start: 0.8591 (ttp-170) cc_final: 0.8250 (tmm-80) REVERT: A 379 LEU cc_start: 0.9121 (mt) cc_final: 0.8656 (tp) REVERT: B 96 ARG cc_start: 0.7093 (mtm-85) cc_final: 0.6662 (mtm-85) REVERT: B 125 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7414 (mtm-85) REVERT: B 264 GLN cc_start: 0.8406 (tt0) cc_final: 0.7847 (pt0) REVERT: B 379 LEU cc_start: 0.8844 (mt) cc_final: 0.8538 (tp) REVERT: B 382 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8254 (tm-30) REVERT: C 112 GLU cc_start: 0.8343 (mp0) cc_final: 0.8102 (mp0) REVERT: C 144 ILE cc_start: 0.8883 (mt) cc_final: 0.8649 (mm) REVERT: C 206 LYS cc_start: 0.9003 (mmtp) cc_final: 0.8371 (mttp) REVERT: C 315 GLU cc_start: 0.8815 (tt0) cc_final: 0.8267 (mm-30) REVERT: C 382 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: C 402 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: D 88 ARG cc_start: 0.7381 (mtp85) cc_final: 0.7013 (mtp-110) REVERT: D 113 LYS cc_start: 0.8207 (mttt) cc_final: 0.7757 (mtpt) REVERT: D 134 ARG cc_start: 0.7105 (mtt90) cc_final: 0.6852 (mtt-85) REVERT: D 148 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8430 (mm) REVERT: D 210 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8933 (mt-10) REVERT: D 265 ASN cc_start: 0.9170 (m-40) cc_final: 0.8898 (m-40) REVERT: D 268 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7474 (tp30) REVERT: D 315 GLU cc_start: 0.8660 (tt0) cc_final: 0.8259 (mm-30) REVERT: D 390 ASP cc_start: 0.8676 (m-30) cc_final: 0.8140 (m-30) REVERT: E 233 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8641 (mp10) REVERT: E 279 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8428 (mtpt) REVERT: E 315 GLU cc_start: 0.8554 (tt0) cc_final: 0.8274 (mm-30) REVERT: E 379 LEU cc_start: 0.9135 (mt) cc_final: 0.8499 (tp) REVERT: E 401 GLN cc_start: 0.8732 (tt0) cc_final: 0.8488 (mt0) outliers start: 38 outliers final: 15 residues processed: 222 average time/residue: 1.8282 time to fit residues: 436.5724 Evaluate side-chains 215 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 2.077 ------------------------------------------------------------------------------- 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 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 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 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 148 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 382 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 82 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 = 0.3175 r_free = 0.3175 target = 0.113681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.090831 restraints weight = 14449.625| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 1.21 r_work: 0.2704 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13790 Z= 0.146 Angle : 0.550 6.663 18755 Z= 0.282 Chirality : 0.040 0.153 2245 Planarity : 0.005 0.042 2340 Dihedral : 4.442 57.162 1860 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.85 % Allowed : 12.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.20), residues: 1695 helix: 1.94 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -0.95 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 208 HIS 0.004 0.001 HIS D 117 PHE 0.012 0.002 PHE A 245 TYR 0.009 0.001 TYR B 121 ARG 0.003 0.000 ARG B 118 Details of bonding type rmsd hydrogen bonds : bond 0.04807 ( 1020) hydrogen bonds : angle 3.79668 ( 3030) covalent geometry : bond 0.00340 (13790) covalent geometry : angle 0.54982 (18755) *********************** 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 240 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 3.604 Fit side-chains REVERT: A 99 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6862 (mm-30) REVERT: A 261 ARG cc_start: 0.8577 (ttp-170) cc_final: 0.8189 (tmm-80) REVERT: B 96 ARG cc_start: 0.7114 (mtm-85) cc_final: 0.6626 (mtm-85) REVERT: B 125 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7573 (mtm-85) REVERT: B 379 LEU cc_start: 0.8845 (mt) cc_final: 0.8529 (tp) REVERT: B 390 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8334 (m-30) REVERT: C 112 GLU cc_start: 0.8334 (mp0) cc_final: 0.8120 (mp0) REVERT: C 144 ILE cc_start: 0.8906 (mt) cc_final: 0.8653 (mm) REVERT: C 206 LYS cc_start: 0.9025 (mmtp) cc_final: 0.8515 (mtmp) REVERT: C 315 GLU cc_start: 0.8784 (tt0) cc_final: 0.8269 (mm-30) REVERT: C 401 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8225 (mt0) REVERT: C 402 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: D 88 ARG cc_start: 0.7394 (mtp85) cc_final: 0.7124 (mtp-110) REVERT: D 113 LYS cc_start: 0.8269 (mttt) cc_final: 0.7775 (mtpt) REVERT: D 134 ARG cc_start: 0.6975 (mtt90) cc_final: 0.6620 (mtt-85) REVERT: D 148 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8383 (mm) REVERT: D 265 ASN cc_start: 0.9147 (m-40) cc_final: 0.8797 (m-40) REVERT: D 268 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7384 (tp30) REVERT: D 315 GLU cc_start: 0.8653 (tt0) cc_final: 0.8243 (mm-30) REVERT: D 390 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8109 (m-30) REVERT: E 233 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8655 (mp10) REVERT: E 315 GLU cc_start: 0.8603 (tt0) cc_final: 0.8287 (mm-30) REVERT: E 379 LEU cc_start: 0.9156 (mt) cc_final: 0.8480 (tp) outliers start: 43 outliers final: 21 residues processed: 220 average time/residue: 1.6431 time to fit residues: 389.1944 Evaluate side-chains 216 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 382 GLU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 125 ARG 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 390 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 401 GLN 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 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 E residue 140 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 0.0020 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 307 GLN 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 = 0.3206 r_free = 0.3206 target = 0.116374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.092677 restraints weight = 14719.108| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.29 r_work: 0.2756 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13790 Z= 0.116 Angle : 0.500 6.569 18755 Z= 0.254 Chirality : 0.038 0.148 2245 Planarity : 0.004 0.041 2340 Dihedral : 4.172 54.128 1860 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.45 % Allowed : 14.04 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.21), residues: 1695 helix: 2.26 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -1.00 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 208 HIS 0.003 0.001 HIS A 344 PHE 0.008 0.001 PHE A 245 TYR 0.006 0.001 TYR C 241 ARG 0.003 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 1020) hydrogen bonds : angle 3.58632 ( 3030) covalent geometry : bond 0.00250 (13790) covalent geometry : angle 0.50019 (18755) *********************** 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 245 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 1.560 Fit side-chains REVERT: A 233 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8249 (mp10) REVERT: A 261 ARG cc_start: 0.8603 (ttp-170) cc_final: 0.8211 (tmm-80) REVERT: B 96 ARG cc_start: 0.7116 (mtm-85) cc_final: 0.6612 (mtm-85) REVERT: B 125 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7570 (mtm-85) REVERT: B 379 LEU cc_start: 0.8871 (mt) cc_final: 0.8580 (tp) REVERT: B 390 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8361 (m-30) REVERT: C 144 ILE cc_start: 0.8877 (mt) cc_final: 0.8622 (mm) REVERT: C 206 LYS cc_start: 0.9187 (mmtp) cc_final: 0.8544 (mttp) REVERT: C 315 GLU cc_start: 0.8795 (tt0) cc_final: 0.8265 (mm-30) REVERT: C 382 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7909 (tm-30) REVERT: C 397 ARG cc_start: 0.8760 (ttm110) cc_final: 0.8502 (ttp80) REVERT: C 402 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: D 113 LYS cc_start: 0.8292 (mttt) cc_final: 0.7791 (mtpt) REVERT: D 265 ASN cc_start: 0.9138 (m-40) cc_final: 0.8776 (m-40) REVERT: D 315 GLU cc_start: 0.8646 (tt0) cc_final: 0.8256 (mm-30) REVERT: D 390 ASP cc_start: 0.8692 (m-30) cc_final: 0.8157 (m-30) REVERT: E 102 MET cc_start: 0.7703 (tpt) cc_final: 0.7436 (tpp) REVERT: E 315 GLU cc_start: 0.8640 (tt0) cc_final: 0.8283 (mm-30) REVERT: E 379 LEU cc_start: 0.9147 (mt) cc_final: 0.8496 (tp) outliers start: 37 outliers final: 14 residues processed: 230 average time/residue: 1.4756 time to fit residues: 366.0652 Evaluate side-chains 205 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 1.703 ------------------------------------------------------------------------------- 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 382 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 342 LEU 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 162 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 140 ILE Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 321 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 74 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 145 optimal weight: 0.0770 chunk 166 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 252 HIS C 401 GLN D 264 GLN D 401 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.113528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.090497 restraints weight = 14872.626| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.23 r_work: 0.2732 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13790 Z= 0.145 Angle : 0.543 6.598 18755 Z= 0.277 Chirality : 0.040 0.154 2245 Planarity : 0.005 0.042 2340 Dihedral : 4.274 53.377 1860 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.38 % Allowed : 14.30 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.21), residues: 1695 helix: 2.19 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -0.96 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 208 HIS 0.004 0.001 HIS D 117 PHE 0.013 0.002 PHE A 245 TYR 0.009 0.001 TYR D 109 ARG 0.003 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.04577 ( 1020) hydrogen bonds : angle 3.66939 ( 3030) covalent geometry : bond 0.00343 (13790) covalent geometry : angle 0.54289 (18755) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 1.638 Fit side-chains REVERT: A 233 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8251 (mp-120) REVERT: A 261 ARG cc_start: 0.8601 (ttp-170) cc_final: 0.8211 (tmm-80) REVERT: A 315 GLU cc_start: 0.8599 (tt0) cc_final: 0.8108 (mm-30) REVERT: B 96 ARG cc_start: 0.7205 (mtm-85) cc_final: 0.6680 (mtm-85) REVERT: B 379 LEU cc_start: 0.8813 (mt) cc_final: 0.8438 (tp) REVERT: B 390 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8338 (m-30) REVERT: C 206 LYS cc_start: 0.9219 (mmtp) cc_final: 0.9003 (mptt) REVERT: C 315 GLU cc_start: 0.8797 (tt0) cc_final: 0.8291 (mm-30) REVERT: C 382 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: C 397 ARG cc_start: 0.8831 (ttm110) cc_final: 0.8563 (ttp80) REVERT: C 402 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: D 113 LYS cc_start: 0.8322 (mttt) cc_final: 0.7821 (mtpt) REVERT: D 265 ASN cc_start: 0.9101 (m-40) cc_final: 0.8708 (m-40) REVERT: D 315 GLU cc_start: 0.8646 (tt0) cc_final: 0.8207 (mm-30) REVERT: D 382 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7741 (mm-30) REVERT: D 390 ASP cc_start: 0.8661 (m-30) cc_final: 0.8092 (m-30) REVERT: E 315 GLU cc_start: 0.8628 (tt0) cc_final: 0.8291 (mm-30) REVERT: E 379 LEU cc_start: 0.9193 (mt) cc_final: 0.8497 (tp) outliers start: 36 outliers final: 23 residues processed: 208 average time/residue: 1.6825 time to fit residues: 376.6336 Evaluate side-chains 209 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 342 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 342 LEU Chi-restraints excluded: chain B residue 350 ILE 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 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 84 ILE 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 26 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 145 optimal weight: 0.0470 chunk 89 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 148 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 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 = 0.3196 r_free = 0.3196 target = 0.115524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.092334 restraints weight = 14733.281| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.26 r_work: 0.2751 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13790 Z= 0.118 Angle : 0.501 6.541 18755 Z= 0.255 Chirality : 0.038 0.149 2245 Planarity : 0.004 0.041 2340 Dihedral : 4.127 51.141 1860 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.72 % Allowed : 15.10 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.21), residues: 1695 helix: 2.38 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -0.87 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 208 HIS 0.003 0.001 HIS D 117 PHE 0.009 0.001 PHE A 245 TYR 0.007 0.001 TYR D 109 ARG 0.004 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 1020) hydrogen bonds : angle 3.54730 ( 3030) covalent geometry : bond 0.00259 (13790) covalent geometry : angle 0.50113 (18755) *********************** 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 217 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 2.677 Fit side-chains REVERT: A 172 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8764 (mt) REVERT: A 233 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8252 (mp10) REVERT: A 315 GLU cc_start: 0.8592 (tt0) cc_final: 0.8069 (mm-30) REVERT: B 96 ARG cc_start: 0.7122 (mtm-85) cc_final: 0.6571 (mtm-85) REVERT: B 125 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7714 (mtm-85) REVERT: B 379 LEU cc_start: 0.8820 (mt) cc_final: 0.8406 (tp) REVERT: B 390 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8370 (m-30) REVERT: B 417 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7531 (mttm) REVERT: C 206 LYS cc_start: 0.9188 (mmtp) cc_final: 0.8539 (mttp) REVERT: C 315 GLU cc_start: 0.8799 (tt0) cc_final: 0.8262 (mm-30) REVERT: C 382 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: C 402 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: D 113 LYS cc_start: 0.8291 (mttt) cc_final: 0.7780 (mtpt) REVERT: D 265 ASN cc_start: 0.9135 (m-40) cc_final: 0.8761 (m-40) REVERT: D 315 GLU cc_start: 0.8630 (tt0) cc_final: 0.8153 (mm-30) REVERT: D 390 ASP cc_start: 0.8637 (m-30) cc_final: 0.8068 (m-30) REVERT: E 315 GLU cc_start: 0.8621 (tt0) cc_final: 0.8281 (mm-30) REVERT: E 379 LEU cc_start: 0.9173 (mt) cc_final: 0.8493 (tp) outliers start: 26 outliers final: 14 residues processed: 203 average time/residue: 1.7684 time to fit residues: 386.5446 Evaluate side-chains 209 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 382 GLU 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 390 ASP Chi-restraints excluded: chain B residue 417 LYS 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 162 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 321 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 162 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 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 = 0.3159 r_free = 0.3159 target = 0.112666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.088639 restraints weight = 14976.778| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 1.37 r_work: 0.2677 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 13790 Z= 0.156 Angle : 0.552 6.574 18755 Z= 0.282 Chirality : 0.040 0.155 2245 Planarity : 0.005 0.042 2340 Dihedral : 4.298 52.361 1860 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.92 % Allowed : 14.83 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.20), residues: 1695 helix: 2.21 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -0.89 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 208 HIS 0.004 0.001 HIS D 117 PHE 0.013 0.002 PHE A 245 TYR 0.012 0.002 TYR A 241 ARG 0.004 0.000 ARG C 397 Details of bonding type rmsd hydrogen bonds : bond 0.04770 ( 1020) hydrogen bonds : angle 3.69063 ( 3030) covalent geometry : bond 0.00375 (13790) covalent geometry : angle 0.55229 (18755) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 1.648 Fit side-chains REVERT: A 172 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8725 (mt) REVERT: A 233 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8230 (mp-120) REVERT: A 315 GLU cc_start: 0.8650 (tt0) cc_final: 0.7942 (mm-30) REVERT: B 96 ARG cc_start: 0.6994 (mtm-85) cc_final: 0.6607 (mtm-85) REVERT: B 102 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7031 (mmt) REVERT: B 125 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7559 (mtm-85) REVERT: B 379 LEU cc_start: 0.8619 (mt) cc_final: 0.8414 (mm) REVERT: B 390 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8336 (m-30) REVERT: C 206 LYS cc_start: 0.9075 (mmtp) cc_final: 0.8435 (mtmp) REVERT: C 270 ASP cc_start: 0.8692 (m-30) cc_final: 0.8152 (m-30) REVERT: C 279 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7778 (mttm) REVERT: C 315 GLU cc_start: 0.8905 (tt0) cc_final: 0.8220 (mm-30) REVERT: C 382 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: C 402 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: D 113 LYS cc_start: 0.8284 (mttt) cc_final: 0.7701 (mtpt) REVERT: D 265 ASN cc_start: 0.9023 (m-40) cc_final: 0.8649 (m-40) REVERT: D 315 GLU cc_start: 0.8633 (tt0) cc_final: 0.8050 (mm-30) REVERT: D 390 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8081 (m-30) REVERT: E 315 GLU cc_start: 0.8701 (tt0) cc_final: 0.8065 (mm-30) REVERT: E 379 LEU cc_start: 0.9135 (mt) cc_final: 0.8348 (tp) outliers start: 29 outliers final: 21 residues processed: 204 average time/residue: 1.4621 time to fit residues: 321.8322 Evaluate side-chains 213 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain B residue 102 MET 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 350 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 417 LYS 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 140 ILE 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 390 ASP 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 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 = 0.3207 r_free = 0.3207 target = 0.116367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.092763 restraints weight = 14821.847| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.34 r_work: 0.2745 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13790 Z= 0.117 Angle : 0.498 6.540 18755 Z= 0.254 Chirality : 0.038 0.149 2245 Planarity : 0.004 0.042 2340 Dihedral : 4.099 53.232 1860 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.52 % Allowed : 15.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.21), residues: 1695 helix: 2.43 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -0.75 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 208 HIS 0.003 0.001 HIS D 117 PHE 0.009 0.001 PHE A 245 TYR 0.008 0.001 TYR D 109 ARG 0.006 0.000 ARG C 397 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 1020) hydrogen bonds : angle 3.53102 ( 3030) covalent geometry : bond 0.00257 (13790) covalent geometry : angle 0.49824 (18755) *********************** 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 217 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 4.801 Fit side-chains REVERT: A 172 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8680 (mt) REVERT: A 233 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8182 (mp10) REVERT: A 315 GLU cc_start: 0.8649 (tt0) cc_final: 0.8000 (mm-30) REVERT: B 96 ARG cc_start: 0.7033 (mtm-85) cc_final: 0.6641 (mtm-85) REVERT: B 102 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.7014 (mmt) REVERT: B 125 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7599 (mtm-85) REVERT: B 379 LEU cc_start: 0.8652 (mt) cc_final: 0.8179 (tp) REVERT: B 390 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8367 (m-30) REVERT: B 417 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7511 (mttm) REVERT: C 206 LYS cc_start: 0.9072 (mmtp) cc_final: 0.8459 (mtmp) REVERT: C 270 ASP cc_start: 0.8477 (m-30) cc_final: 0.7984 (m-30) REVERT: C 315 GLU cc_start: 0.8826 (tt0) cc_final: 0.8197 (mm-30) REVERT: C 382 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: C 397 ARG cc_start: 0.8551 (ttp80) cc_final: 0.8327 (ttp80) REVERT: C 402 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: D 113 LYS cc_start: 0.8323 (mttt) cc_final: 0.7762 (mtpt) REVERT: D 265 ASN cc_start: 0.9109 (m-40) cc_final: 0.8713 (m-40) REVERT: D 315 GLU cc_start: 0.8644 (tt0) cc_final: 0.8072 (mm-30) REVERT: D 390 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8053 (m-30) REVERT: E 315 GLU cc_start: 0.8668 (tt0) cc_final: 0.8181 (mm-30) REVERT: E 379 LEU cc_start: 0.9123 (mt) cc_final: 0.8399 (tp) outliers start: 23 outliers final: 11 residues processed: 206 average time/residue: 2.3680 time to fit residues: 524.6410 Evaluate side-chains 205 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain B residue 102 MET 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 342 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 321 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 29 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 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 = 0.3156 r_free = 0.3156 target = 0.112374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.088456 restraints weight = 14972.687| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.36 r_work: 0.2673 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 13790 Z= 0.166 Angle : 0.567 6.557 18755 Z= 0.290 Chirality : 0.041 0.156 2245 Planarity : 0.005 0.042 2340 Dihedral : 4.332 54.383 1860 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.39 % Allowed : 15.30 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.21), residues: 1695 helix: 2.24 (0.14), residues: 1445 sheet: None (None), residues: 0 loop : -0.75 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 208 HIS 0.005 0.001 HIS C 117 PHE 0.014 0.002 PHE A 245 TYR 0.013 0.002 TYR A 241 ARG 0.007 0.000 ARG C 397 Details of bonding type rmsd hydrogen bonds : bond 0.04934 ( 1020) hydrogen bonds : angle 3.72185 ( 3030) covalent geometry : bond 0.00403 (13790) covalent geometry : angle 0.56672 (18755) ********************** 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 208 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 1.754 Fit side-chains REVERT: A 172 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8700 (mt) REVERT: A 233 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8295 (mp10) REVERT: A 315 GLU cc_start: 0.8666 (tt0) cc_final: 0.7971 (mm-30) REVERT: B 96 ARG cc_start: 0.7019 (mtm-85) cc_final: 0.6594 (mtm-85) REVERT: B 102 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7121 (mmt) REVERT: B 390 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8283 (m-30) REVERT: B 401 GLN cc_start: 0.8561 (tt0) cc_final: 0.8340 (tt0) REVERT: C 206 LYS cc_start: 0.9078 (mmtp) cc_final: 0.8457 (mtmp) REVERT: C 270 ASP cc_start: 0.8720 (m-30) cc_final: 0.8157 (m-30) REVERT: C 315 GLU cc_start: 0.8892 (tt0) cc_final: 0.8202 (mm-30) REVERT: C 382 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8035 (tm-30) REVERT: C 402 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: D 113 LYS cc_start: 0.8403 (mttt) cc_final: 0.7792 (mtpt) REVERT: D 265 ASN cc_start: 0.9023 (m-40) cc_final: 0.8622 (m-40) REVERT: D 315 GLU cc_start: 0.8672 (tt0) cc_final: 0.8069 (mm-30) REVERT: D 390 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8059 (m-30) REVERT: E 315 GLU cc_start: 0.8711 (tt0) cc_final: 0.8093 (mm-30) REVERT: E 379 LEU cc_start: 0.9167 (mt) cc_final: 0.8377 (tp) outliers start: 21 outliers final: 17 residues processed: 200 average time/residue: 1.5920 time to fit residues: 343.7770 Evaluate side-chains 207 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain B residue 102 MET 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 382 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 321 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 160 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 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 = 0.3154 r_free = 0.3154 target = 0.112205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.088344 restraints weight = 15030.904| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.36 r_work: 0.2672 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 13790 Z= 0.168 Angle : 0.569 6.568 18755 Z= 0.291 Chirality : 0.041 0.157 2245 Planarity : 0.005 0.043 2340 Dihedral : 4.374 54.296 1860 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.92 % Allowed : 14.83 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.21), residues: 1695 helix: 2.17 (0.14), residues: 1445 sheet: None (None), residues: 0 loop : -0.77 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 208 HIS 0.006 0.001 HIS A 105 PHE 0.014 0.002 PHE A 245 TYR 0.013 0.002 TYR D 109 ARG 0.008 0.000 ARG C 397 Details of bonding type rmsd hydrogen bonds : bond 0.04931 ( 1020) hydrogen bonds : angle 3.74240 ( 3030) covalent geometry : bond 0.00411 (13790) covalent geometry : angle 0.56878 (18755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11164.03 seconds wall clock time: 201 minutes 57.36 seconds (12117.36 seconds total)