Starting phenix.real_space_refine on Thu Sep 26 12:09:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ek3_31167/09_2024/7ek3_31167.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ek3_31167/09_2024/7ek3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ek3_31167/09_2024/7ek3_31167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ek3_31167/09_2024/7ek3_31167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ek3_31167/09_2024/7ek3_31167.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ek3_31167/09_2024/7ek3_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.90, per 1000 atoms: 0.44 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: 3.41 Conformation dependent library (CDL) restraints added in 1.9 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: 3.84 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 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: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 29.510 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.540 ------------------------------------------------------------------------------- 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= 1.182 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 *********************** 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 fitting. rotamer outliers: 25 poor density : 281 time to evaluate : 1.574 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: 1.6396 time to fit residues: 523.8316 Evaluate side-chains 217 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 208 time to evaluate : 1.541 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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= 0.279 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 *********************** 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 fitting. rotamer outliers: 42 poor density : 213 time to evaluate : 1.620 Fit side-chains REVERT: A 102 MET cc_start: 0.6683 (tpt) cc_final: 0.6449 (tpp) REVERT: A 104 GLN cc_start: 0.6957 (tp40) cc_final: 0.6423 (pt0) REVERT: A 379 LEU cc_start: 0.8620 (mt) cc_final: 0.8099 (tp) REVERT: A 401 GLN cc_start: 0.8427 (tt0) cc_final: 0.8173 (mt0) REVERT: B 96 ARG cc_start: 0.6023 (mtm-85) cc_final: 0.5749 (mtm-85) REVERT: B 104 GLN cc_start: 0.7366 (tp40) cc_final: 0.6778 (pt0) REVERT: B 264 GLN cc_start: 0.8188 (tt0) cc_final: 0.7342 (pt0) REVERT: B 379 LEU cc_start: 0.8503 (mt) cc_final: 0.7968 (tp) REVERT: C 100 ARG cc_start: 0.6162 (ttp-110) cc_final: 0.5911 (ttp-110) REVERT: C 103 ARG cc_start: 0.5878 (mtt-85) cc_final: 0.5176 (mmm160) REVERT: C 315 GLU cc_start: 0.8675 (tt0) cc_final: 0.7479 (mm-30) REVERT: C 402 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: D 88 ARG cc_start: 0.6856 (mtp85) cc_final: 0.6523 (mtp-110) REVERT: D 113 LYS cc_start: 0.7391 (mttt) cc_final: 0.6789 (mtpt) REVERT: D 265 ASN cc_start: 0.8920 (m-40) cc_final: 0.8564 (m-40) REVERT: D 390 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.7967 (m-30) REVERT: D 408 LYS cc_start: 0.8209 (tttt) cc_final: 0.7994 (ttpt) REVERT: E 233 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8286 (mp10) REVERT: E 315 GLU cc_start: 0.8430 (tt0) cc_final: 0.7431 (mm-30) REVERT: E 354 ASP cc_start: 0.8095 (m-30) cc_final: 0.7832 (m-30) REVERT: E 379 LEU cc_start: 0.8577 (mt) cc_final: 0.7795 (tp) REVERT: E 401 GLN cc_start: 0.8460 (tt0) cc_final: 0.8050 (mt0) REVERT: E 408 LYS cc_start: 0.7879 (tttt) cc_final: 0.7639 (ttpp) REVERT: E 417 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6950 (mttp) outliers start: 42 outliers final: 9 residues processed: 239 average time/residue: 1.5123 time to fit residues: 388.7839 Evaluate side-chains 202 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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 85 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13790 Z= 0.195 Angle : 0.542 6.649 18755 Z= 0.279 Chirality : 0.039 0.149 2245 Planarity : 0.005 0.041 2340 Dihedral : 4.445 56.690 1860 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.72 % Allowed : 12.05 % Favored : 85.23 % 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: 2.27 (0.21), residues: 1695 helix: 1.91 (0.14), residues: 1445 sheet: None (None), residues: 0 loop : -0.86 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 208 HIS 0.003 0.001 HIS C 117 PHE 0.010 0.002 PHE A 245 TYR 0.010 0.001 TYR B 241 ARG 0.002 0.000 ARG C 200 *********************** 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 254 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 213 time to evaluate : 1.612 Fit side-chains REVERT: A 104 GLN cc_start: 0.6936 (tp40) cc_final: 0.6315 (pt0) REVERT: A 144 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7724 (mm) REVERT: A 379 LEU cc_start: 0.8716 (mt) cc_final: 0.8159 (tp) REVERT: A 401 GLN cc_start: 0.8393 (tt0) cc_final: 0.8048 (mt0) REVERT: B 96 ARG cc_start: 0.6004 (mtm-85) cc_final: 0.5696 (mtm-85) REVERT: B 104 GLN cc_start: 0.7335 (tp40) cc_final: 0.6697 (pt0) REVERT: B 125 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6727 (mtm-85) REVERT: B 264 GLN cc_start: 0.8073 (tt0) cc_final: 0.7248 (pt0) REVERT: B 379 LEU cc_start: 0.8421 (mt) cc_final: 0.8015 (tp) REVERT: C 112 GLU cc_start: 0.8235 (mp0) cc_final: 0.7979 (mp0) REVERT: C 144 ILE cc_start: 0.8245 (mt) cc_final: 0.8041 (mm) REVERT: C 206 LYS cc_start: 0.8304 (mmtp) cc_final: 0.7677 (mttp) REVERT: C 315 GLU cc_start: 0.8696 (tt0) cc_final: 0.7491 (mm-30) REVERT: C 382 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: C 402 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: D 88 ARG cc_start: 0.6736 (mtp85) cc_final: 0.6483 (mtp-110) REVERT: D 113 LYS cc_start: 0.7311 (mttt) cc_final: 0.6696 (mtpt) REVERT: D 134 ARG cc_start: 0.6652 (mtt90) cc_final: 0.6432 (mtt-85) REVERT: D 148 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7605 (mm) REVERT: D 265 ASN cc_start: 0.8883 (m-40) cc_final: 0.8538 (m-40) REVERT: D 268 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7598 (tp30) REVERT: D 315 GLU cc_start: 0.8355 (tt0) cc_final: 0.7304 (mm-30) REVERT: D 390 ASP cc_start: 0.8605 (m-30) cc_final: 0.8041 (m-30) REVERT: D 408 LYS cc_start: 0.8129 (tttt) cc_final: 0.7922 (tttp) REVERT: E 233 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8291 (mp10) REVERT: E 315 GLU cc_start: 0.8458 (tt0) cc_final: 0.7456 (mm-30) REVERT: E 354 ASP cc_start: 0.8148 (m-30) cc_final: 0.7890 (m-30) REVERT: E 379 LEU cc_start: 0.8557 (mt) cc_final: 0.7797 (tp) REVERT: E 401 GLN cc_start: 0.8474 (tt0) cc_final: 0.8102 (mt0) REVERT: E 408 LYS cc_start: 0.7900 (tttt) cc_final: 0.7655 (ttpp) outliers start: 41 outliers final: 16 residues processed: 234 average time/residue: 1.4594 time to fit residues: 367.8782 Evaluate side-chains 214 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 192 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 162 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 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 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 Chi-restraints excluded: chain E residue 140 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 164 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2316 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= 0.223 Angle : 0.550 6.660 18755 Z= 0.282 Chirality : 0.040 0.153 2245 Planarity : 0.005 0.042 2340 Dihedral : 4.412 56.609 1860 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: 2.34 (0.21), residues: 1695 helix: 1.98 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -0.93 (0.36), residues: 255 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 0.012 0.002 PHE A 245 TYR 0.008 0.001 TYR B 121 ARG 0.002 0.000 ARG B 220 *********************** 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 242 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 199 time to evaluate : 1.668 Fit side-chains REVERT: A 104 GLN cc_start: 0.6660 (tp40) cc_final: 0.5999 (pt0) REVERT: A 401 GLN cc_start: 0.8378 (tt0) cc_final: 0.8071 (mt0) REVERT: B 96 ARG cc_start: 0.6028 (mtm-85) cc_final: 0.5668 (mtm-85) REVERT: B 104 GLN cc_start: 0.7274 (tp40) cc_final: 0.6582 (pt0) REVERT: B 125 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6895 (mtm-85) REVERT: B 264 GLN cc_start: 0.8071 (tt0) cc_final: 0.7198 (pt0) REVERT: B 379 LEU cc_start: 0.8350 (mt) cc_final: 0.7901 (tp) REVERT: B 390 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8188 (m-30) REVERT: C 112 GLU cc_start: 0.8230 (mp0) cc_final: 0.7986 (mp0) REVERT: C 144 ILE cc_start: 0.8295 (mt) cc_final: 0.8063 (mm) REVERT: C 206 LYS cc_start: 0.8348 (mmtp) cc_final: 0.7898 (mtmp) REVERT: C 315 GLU cc_start: 0.8709 (tt0) cc_final: 0.7455 (mm-30) REVERT: C 401 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7611 (mt0) REVERT: C 402 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: D 88 ARG cc_start: 0.6717 (mtp85) cc_final: 0.6504 (mtp-110) REVERT: D 113 LYS cc_start: 0.7354 (mttt) cc_final: 0.6707 (mtpt) REVERT: D 148 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7561 (mm) REVERT: D 265 ASN cc_start: 0.8805 (m-40) cc_final: 0.8454 (m-40) REVERT: D 268 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7470 (tp30) REVERT: D 315 GLU cc_start: 0.8353 (tt0) cc_final: 0.7355 (mm-30) REVERT: D 390 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8022 (m-30) REVERT: D 408 LYS cc_start: 0.8206 (tttt) cc_final: 0.8002 (tttp) REVERT: E 315 GLU cc_start: 0.8479 (tt0) cc_final: 0.7442 (mm-30) REVERT: E 379 LEU cc_start: 0.8581 (mt) cc_final: 0.7749 (tp) REVERT: E 382 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: E 401 GLN cc_start: 0.8462 (tt0) cc_final: 0.8219 (mt0) REVERT: E 408 LYS cc_start: 0.7893 (tttt) cc_final: 0.7648 (ttpp) outliers start: 43 outliers final: 20 residues processed: 219 average time/residue: 1.5272 time to fit residues: 359.7185 Evaluate side-chains 221 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 193 time to evaluate : 1.559 ------------------------------------------------------------------------------- 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 84 ILE 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 321 GLU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 382 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13790 Z= 0.226 Angle : 0.544 6.612 18755 Z= 0.278 Chirality : 0.040 0.153 2245 Planarity : 0.005 0.043 2340 Dihedral : 4.385 56.401 1860 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.18 % Allowed : 12.85 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.43 (0.20), residues: 1695 helix: 2.07 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -1.02 (0.35), 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 0.012 0.002 PHE A 245 TYR 0.015 0.001 TYR A 241 ARG 0.005 0.000 ARG B 200 *********************** 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 237 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 189 time to evaluate : 1.856 Fit side-chains REVERT: A 104 GLN cc_start: 0.6633 (tp40) cc_final: 0.5824 (pt0) REVERT: A 401 GLN cc_start: 0.8286 (tt0) cc_final: 0.8018 (mt0) REVERT: B 96 ARG cc_start: 0.6083 (mtm-85) cc_final: 0.5726 (mtm-85) REVERT: B 104 GLN cc_start: 0.7224 (tp40) cc_final: 0.6508 (pt0) REVERT: B 374 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7852 (tm-30) REVERT: B 379 LEU cc_start: 0.8336 (mt) cc_final: 0.7892 (tp) REVERT: B 390 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8200 (m-30) REVERT: C 112 GLU cc_start: 0.8231 (mp0) cc_final: 0.8028 (mp0) REVERT: C 315 GLU cc_start: 0.8754 (tt0) cc_final: 0.7596 (mm-30) REVERT: C 382 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: C 402 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7622 (tt0) REVERT: D 113 LYS cc_start: 0.7363 (mttt) cc_final: 0.6731 (mtpt) REVERT: D 148 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7559 (mm) REVERT: D 200 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.8087 (mtp85) REVERT: D 265 ASN cc_start: 0.8771 (m-40) cc_final: 0.8349 (m-40) REVERT: D 268 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7473 (tp30) REVERT: D 315 GLU cc_start: 0.8353 (tt0) cc_final: 0.7350 (mm-30) REVERT: D 390 ASP cc_start: 0.8615 (m-30) cc_final: 0.7999 (m-30) REVERT: D 408 LYS cc_start: 0.8212 (tttt) cc_final: 0.8004 (tttp) REVERT: E 315 GLU cc_start: 0.8523 (tt0) cc_final: 0.7471 (mm-30) REVERT: E 379 LEU cc_start: 0.8588 (mt) cc_final: 0.7745 (tp) REVERT: E 382 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: E 401 GLN cc_start: 0.8463 (tt0) cc_final: 0.8231 (mt0) REVERT: E 408 LYS cc_start: 0.7891 (tttt) cc_final: 0.7646 (ttpp) outliers start: 48 outliers final: 25 residues processed: 214 average time/residue: 1.4583 time to fit residues: 337.0885 Evaluate side-chains 220 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 187 time to evaluate : 1.537 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 113 LYS 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 374 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 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 200 ARG Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 382 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13790 Z= 0.215 Angle : 0.534 6.591 18755 Z= 0.273 Chirality : 0.039 0.153 2245 Planarity : 0.005 0.043 2340 Dihedral : 4.328 55.237 1860 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.58 % Allowed : 13.77 % Favored : 83.64 % 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: 2.56 (0.20), residues: 1695 helix: 2.16 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -0.98 (0.35), 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 0.012 0.002 PHE A 245 TYR 0.010 0.001 TYR D 109 ARG 0.003 0.000 ARG B 200 *********************** 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 240 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 201 time to evaluate : 1.562 Fit side-chains REVERT: A 104 GLN cc_start: 0.6630 (tp40) cc_final: 0.5760 (pt0) REVERT: A 172 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8448 (mt) REVERT: A 401 GLN cc_start: 0.8383 (tt0) cc_final: 0.8128 (mt0) REVERT: B 96 ARG cc_start: 0.6039 (mtm-85) cc_final: 0.5624 (mtm-85) REVERT: B 104 GLN cc_start: 0.7193 (tp40) cc_final: 0.6452 (pt0) REVERT: B 125 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.7015 (mtm-85) REVERT: B 374 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: B 379 LEU cc_start: 0.8252 (mt) cc_final: 0.7768 (tp) REVERT: B 390 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8209 (m-30) REVERT: C 315 GLU cc_start: 0.8687 (tt0) cc_final: 0.7461 (mm-30) REVERT: C 382 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: C 397 ARG cc_start: 0.8521 (ttm110) cc_final: 0.8194 (ttp80) REVERT: C 402 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: D 113 LYS cc_start: 0.7356 (mttt) cc_final: 0.6725 (mtpt) REVERT: D 148 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7785 (mm) REVERT: D 265 ASN cc_start: 0.8672 (m-40) cc_final: 0.8230 (m-40) REVERT: D 315 GLU cc_start: 0.8406 (tt0) cc_final: 0.7361 (mm-30) REVERT: D 390 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: D 408 LYS cc_start: 0.8215 (tttt) cc_final: 0.8013 (tttp) REVERT: E 315 GLU cc_start: 0.8527 (tt0) cc_final: 0.7471 (mm-30) REVERT: E 379 LEU cc_start: 0.8616 (mt) cc_final: 0.7768 (tp) REVERT: E 382 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: E 408 LYS cc_start: 0.7888 (tttt) cc_final: 0.7643 (ttpp) outliers start: 39 outliers final: 23 residues processed: 221 average time/residue: 1.5321 time to fit residues: 363.8900 Evaluate side-chains 222 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 233 GLN 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 130 SER Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain 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 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 261 ARG 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 321 GLU Chi-restraints excluded: chain E residue 382 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 13790 Z= 0.350 Angle : 0.616 6.647 18755 Z= 0.315 Chirality : 0.043 0.162 2245 Planarity : 0.005 0.046 2340 Dihedral : 4.579 56.957 1860 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.58 % Allowed : 13.91 % 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: 2.25 (0.20), residues: 1695 helix: 1.92 (0.14), residues: 1445 sheet: None (None), residues: 0 loop : -1.03 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 352 HIS 0.006 0.002 HIS D 117 PHE 0.018 0.003 PHE E 384 TYR 0.015 0.002 TYR D 109 ARG 0.007 0.001 ARG E 220 *********************** 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 227 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 188 time to evaluate : 1.558 Fit side-chains REVERT: A 104 GLN cc_start: 0.6620 (tp40) cc_final: 0.5932 (tt0) REVERT: A 172 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8490 (mt) REVERT: A 401 GLN cc_start: 0.8326 (tt0) cc_final: 0.8036 (mt0) REVERT: B 96 ARG cc_start: 0.6072 (mtm-85) cc_final: 0.5788 (mtm-85) REVERT: B 125 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.7019 (mtm-85) REVERT: B 374 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: B 379 LEU cc_start: 0.8085 (mt) cc_final: 0.7876 (mm) REVERT: B 390 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8210 (m-30) REVERT: C 382 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7975 (tm-30) REVERT: C 397 ARG cc_start: 0.8622 (ttm110) cc_final: 0.8263 (ttp80) REVERT: C 402 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: D 113 LYS cc_start: 0.7444 (mttt) cc_final: 0.6791 (mtpt) REVERT: D 148 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7596 (mm) REVERT: D 265 ASN cc_start: 0.8509 (m-40) cc_final: 0.8098 (m-40) REVERT: D 315 GLU cc_start: 0.8422 (tt0) cc_final: 0.7334 (mm-30) REVERT: D 390 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.7924 (m-30) REVERT: D 408 LYS cc_start: 0.8232 (tttt) cc_final: 0.7883 (ttpp) REVERT: E 315 GLU cc_start: 0.8592 (tt0) cc_final: 0.7549 (mm-30) REVERT: E 379 LEU cc_start: 0.8623 (mt) cc_final: 0.7746 (tp) REVERT: E 382 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: E 408 LYS cc_start: 0.7900 (tttt) cc_final: 0.7654 (ttpp) outliers start: 39 outliers final: 26 residues processed: 210 average time/residue: 1.4941 time to fit residues: 338.2773 Evaluate side-chains 223 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 188 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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 233 GLN 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 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 374 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 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 148 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 261 ARG 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 102 MET Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 382 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 49 optimal weight: 0.0030 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13790 Z= 0.202 Angle : 0.527 6.568 18755 Z= 0.270 Chirality : 0.039 0.151 2245 Planarity : 0.005 0.043 2340 Dihedral : 4.351 55.044 1860 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.58 % Allowed : 13.91 % 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: 2.59 (0.21), residues: 1695 helix: 2.18 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -1.01 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 208 HIS 0.004 0.001 HIS D 117 PHE 0.011 0.002 PHE A 245 TYR 0.011 0.001 TYR D 109 ARG 0.003 0.000 ARG B 200 *********************** 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 236 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 197 time to evaluate : 1.841 Fit side-chains REVERT: A 84 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.7191 (pp) REVERT: A 104 GLN cc_start: 0.6680 (tp40) cc_final: 0.5979 (tt0) REVERT: A 172 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8414 (mt) REVERT: A 401 GLN cc_start: 0.8386 (tt0) cc_final: 0.8127 (mt0) REVERT: B 96 ARG cc_start: 0.6057 (mtm-85) cc_final: 0.5748 (mtm-85) REVERT: B 104 GLN cc_start: 0.7113 (tp40) cc_final: 0.6449 (tt0) REVERT: B 125 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7001 (mtm-85) REVERT: B 374 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: B 390 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8220 (m-30) REVERT: C 270 ASP cc_start: 0.8238 (m-30) cc_final: 0.7684 (m-30) REVERT: C 315 GLU cc_start: 0.8690 (tt0) cc_final: 0.7456 (mm-30) REVERT: C 382 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: C 397 ARG cc_start: 0.8583 (ttm110) cc_final: 0.8261 (ttp80) REVERT: C 402 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: D 113 LYS cc_start: 0.7397 (mttt) cc_final: 0.6766 (mtpt) REVERT: D 265 ASN cc_start: 0.8534 (m-40) cc_final: 0.8144 (m-40) REVERT: D 315 GLU cc_start: 0.8449 (tt0) cc_final: 0.7338 (mm-30) REVERT: D 390 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.7945 (m-30) REVERT: D 408 LYS cc_start: 0.8210 (tttt) cc_final: 0.7875 (ttpp) REVERT: E 315 GLU cc_start: 0.8542 (tt0) cc_final: 0.7500 (mm-30) REVERT: E 379 LEU cc_start: 0.8621 (mt) cc_final: 0.7784 (tp) REVERT: E 382 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7202 (tm-30) REVERT: E 408 LYS cc_start: 0.7880 (tttt) cc_final: 0.7633 (ttpp) outliers start: 39 outliers final: 24 residues processed: 216 average time/residue: 1.5198 time to fit residues: 353.5250 Evaluate side-chains 222 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 189 time to evaluate : 1.693 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 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 315 GLU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 261 ARG 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 102 MET Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 382 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.0980 chunk 143 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13790 Z= 0.201 Angle : 0.524 6.556 18755 Z= 0.267 Chirality : 0.039 0.151 2245 Planarity : 0.004 0.042 2340 Dihedral : 4.258 53.123 1860 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.45 % Allowed : 14.24 % 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: 2.72 (0.21), residues: 1695 helix: 2.27 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -0.93 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 208 HIS 0.004 0.001 HIS D 117 PHE 0.010 0.002 PHE A 245 TYR 0.011 0.001 TYR A 241 ARG 0.004 0.000 ARG B 200 *********************** 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 227 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 190 time to evaluate : 1.632 Fit side-chains REVERT: A 104 GLN cc_start: 0.6679 (tp40) cc_final: 0.5984 (tt0) REVERT: A 172 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8328 (mt) REVERT: A 315 GLU cc_start: 0.8539 (tt0) cc_final: 0.7242 (mm-30) REVERT: A 401 GLN cc_start: 0.8359 (tt0) cc_final: 0.8137 (mt0) REVERT: B 96 ARG cc_start: 0.6053 (mtm-85) cc_final: 0.5740 (mtm-85) REVERT: B 125 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7025 (mtm-85) REVERT: B 374 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7904 (tm-30) REVERT: B 390 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8216 (m-30) REVERT: C 270 ASP cc_start: 0.8286 (m-30) cc_final: 0.7738 (m-30) REVERT: C 315 GLU cc_start: 0.8777 (tt0) cc_final: 0.7586 (mm-30) REVERT: C 382 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: C 397 ARG cc_start: 0.8519 (ttm110) cc_final: 0.8208 (ttp80) REVERT: C 402 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: D 113 LYS cc_start: 0.7356 (mttt) cc_final: 0.6710 (mtpt) REVERT: D 125 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6829 (ptp90) REVERT: D 265 ASN cc_start: 0.8531 (m-40) cc_final: 0.8134 (m-40) REVERT: D 315 GLU cc_start: 0.8421 (tt0) cc_final: 0.7281 (mm-30) REVERT: D 390 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: D 408 LYS cc_start: 0.8216 (tttt) cc_final: 0.7983 (ttpt) REVERT: E 315 GLU cc_start: 0.8549 (tt0) cc_final: 0.7480 (mm-30) REVERT: E 379 LEU cc_start: 0.8627 (mt) cc_final: 0.7777 (tp) REVERT: E 382 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7259 (tm-30) REVERT: E 408 LYS cc_start: 0.7886 (tttt) cc_final: 0.7639 (ttpp) outliers start: 37 outliers final: 19 residues processed: 211 average time/residue: 1.4946 time to fit residues: 339.5108 Evaluate side-chains 213 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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 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 130 SER Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain C residue 162 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 125 ARG Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 382 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 401 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 13790 Z= 0.365 Angle : 0.631 6.622 18755 Z= 0.323 Chirality : 0.044 0.159 2245 Planarity : 0.005 0.049 2340 Dihedral : 4.595 55.824 1860 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.05 % Allowed : 14.77 % 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: 2.25 (0.20), residues: 1695 helix: 1.94 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -1.11 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 352 HIS 0.006 0.002 HIS D 117 PHE 0.019 0.003 PHE E 384 TYR 0.016 0.002 TYR D 109 ARG 0.007 0.001 ARG E 220 ********************** 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 223 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 192 time to evaluate : 1.518 Fit side-chains REVERT: A 104 GLN cc_start: 0.6611 (tp40) cc_final: 0.5898 (tt0) REVERT: A 172 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8394 (mt) REVERT: A 401 GLN cc_start: 0.8366 (tt0) cc_final: 0.8136 (mt0) REVERT: B 96 ARG cc_start: 0.6079 (mtm-85) cc_final: 0.5736 (mtm-85) REVERT: B 125 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7048 (mtm-85) REVERT: B 374 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: B 390 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8159 (m-30) REVERT: C 106 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6226 (mtt90) REVERT: C 270 ASP cc_start: 0.8248 (m-30) cc_final: 0.7683 (m-30) REVERT: C 382 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: C 397 ARG cc_start: 0.8639 (ttm110) cc_final: 0.8260 (ttp80) REVERT: C 402 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: D 113 LYS cc_start: 0.7535 (mttt) cc_final: 0.6864 (mtpt) REVERT: D 125 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6996 (ptp90) REVERT: D 265 ASN cc_start: 0.8580 (m-40) cc_final: 0.8230 (m-40) REVERT: D 315 GLU cc_start: 0.8485 (tt0) cc_final: 0.7366 (mm-30) REVERT: D 390 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: D 408 LYS cc_start: 0.8223 (tttt) cc_final: 0.7880 (ttpp) REVERT: E 315 GLU cc_start: 0.8593 (tt0) cc_final: 0.7551 (mm-30) REVERT: E 379 LEU cc_start: 0.8660 (mt) cc_final: 0.7753 (tp) REVERT: E 382 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: E 408 LYS cc_start: 0.7893 (tttt) cc_final: 0.7650 (ttpp) outliers start: 31 outliers final: 17 residues processed: 211 average time/residue: 1.6258 time to fit residues: 367.6302 Evaluate side-chains 214 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 187 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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 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 130 SER Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 162 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 125 ARG Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 382 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 135 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.114156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.089999 restraints weight = 14472.707| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.36 r_work: 0.2706 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13790 Z= 0.193 Angle : 0.521 6.558 18755 Z= 0.266 Chirality : 0.039 0.152 2245 Planarity : 0.004 0.043 2340 Dihedral : 4.292 52.875 1860 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.85 % Allowed : 15.03 % 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: 2.70 (0.21), residues: 1695 helix: 2.25 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -0.92 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 208 HIS 0.004 0.001 HIS D 117 PHE 0.010 0.002 PHE A 245 TYR 0.012 0.001 TYR D 109 ARG 0.004 0.000 ARG C 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5532.97 seconds wall clock time: 97 minutes 2.21 seconds (5822.21 seconds total)