Starting phenix.real_space_refine on Thu Sep 26 12:25:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ek2_31166/09_2024/7ek2_31166.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ek2_31166/09_2024/7ek2_31166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ek2_31166/09_2024/7ek2_31166.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ek2_31166/09_2024/7ek2_31166.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ek2_31166/09_2024/7ek2_31166.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ek2_31166/09_2024/7ek2_31166.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 8730 2.51 5 N 2360 2.21 5 O 2395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13540 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2708 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 16, 'TRANS': 324} Restraints were copied for chains: C, B, E, D Time building chain proxies: 5.63, per 1000 atoms: 0.42 Number of scatterers: 13540 At special positions: 0 Unit cell: (110.224, 112.88, 112.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 2395 8.00 N 2360 7.00 C 8730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.7 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: 90 helices and 0 sheets defined 86.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 89 through 101 Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.551A pdb=" N LEU A 127 " --> pdb=" O HIS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 139 through 162 Processing helix chain 'A' and resid 176 through 226 Proline residue: A 184 - end of helix Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 231 through 254 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 268 through 277 removed outlier: 3.879A pdb=" N VAL A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'A' and resid 310 through 326 removed outlier: 3.513A pdb=" N ILE A 324 " --> pdb=" O CYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 356 removed outlier: 3.759A pdb=" N THR A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Proline residue: A 348 - end of helix removed outlier: 4.940A pdb=" N ASP A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 380 removed outlier: 3.547A pdb=" N ILE A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 388 through 418 removed outlier: 3.640A pdb=" N VAL A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 417 " --> pdb=" O ARG A 413 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 88 Processing helix chain 'B' and resid 89 through 101 Processing helix chain 'B' and resid 110 through 118 Processing helix chain 'B' and resid 121 through 129 removed outlier: 3.551A pdb=" N LEU B 127 " --> pdb=" O HIS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 139 Processing helix chain 'B' and resid 139 through 162 Processing helix chain 'B' and resid 176 through 226 Proline residue: B 184 - end of helix Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 231 through 254 Proline residue: B 246 - end of helix Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.879A pdb=" N VAL B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 Processing helix chain 'B' and resid 299 through 308 Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.513A pdb=" N ILE B 324 " --> pdb=" O CYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 356 removed outlier: 3.759A pdb=" N THR B 336 " --> pdb=" O TYR B 332 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Proline residue: B 348 - end of helix removed outlier: 4.939A pdb=" N ASP B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP B 354 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 380 removed outlier: 3.547A pdb=" N ILE B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 388 through 418 removed outlier: 3.639A pdb=" N VAL B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 417 " --> pdb=" O ARG B 413 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 88 Processing helix chain 'C' and resid 89 through 101 Processing helix chain 'C' and resid 110 through 118 Processing helix chain 'C' and resid 121 through 129 removed outlier: 3.552A pdb=" N LEU C 127 " --> pdb=" O HIS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 Processing helix chain 'C' and resid 139 through 162 Processing helix chain 'C' and resid 176 through 226 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 231 through 254 Proline residue: C 246 - end of helix Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 268 through 277 removed outlier: 3.879A pdb=" N VAL C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 Processing helix chain 'C' and resid 299 through 308 Processing helix chain 'C' and resid 310 through 326 removed outlier: 3.513A pdb=" N ILE C 324 " --> pdb=" O CYS C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 356 removed outlier: 3.759A pdb=" N THR C 336 " --> pdb=" O TYR C 332 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Proline residue: C 348 - end of helix removed outlier: 4.940A pdb=" N ASP C 353 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP C 354 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 380 removed outlier: 3.546A pdb=" N ILE C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 388 through 418 removed outlier: 3.640A pdb=" N VAL C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 417 " --> pdb=" O ARG C 413 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 88 Processing helix chain 'D' and resid 89 through 101 Processing helix chain 'D' and resid 110 through 118 Processing helix chain 'D' and resid 121 through 129 removed outlier: 3.551A pdb=" N LEU D 127 " --> pdb=" O HIS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 139 Processing helix chain 'D' and resid 139 through 162 Processing helix chain 'D' and resid 176 through 226 Proline residue: D 184 - end of helix Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 231 through 254 Proline residue: D 246 - end of helix Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 268 through 277 removed outlier: 3.879A pdb=" N VAL D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 Processing helix chain 'D' and resid 299 through 308 Processing helix chain 'D' and resid 310 through 326 removed outlier: 3.513A pdb=" N ILE D 324 " --> pdb=" O CYS D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 356 removed outlier: 3.759A pdb=" N THR D 336 " --> pdb=" O TYR D 332 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) Proline residue: D 348 - end of helix removed outlier: 4.940A pdb=" N ASP D 353 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP D 354 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 380 removed outlier: 3.547A pdb=" N ILE D 373 " --> pdb=" O SER D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 Processing helix chain 'D' and resid 388 through 418 removed outlier: 3.640A pdb=" N VAL D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS D 417 " --> pdb=" O ARG D 413 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 88 Processing helix chain 'E' and resid 89 through 101 Processing helix chain 'E' and resid 110 through 118 Processing helix chain 'E' and resid 121 through 129 removed outlier: 3.551A pdb=" N LEU E 127 " --> pdb=" O HIS E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 139 Processing helix chain 'E' and resid 139 through 162 Processing helix chain 'E' and resid 176 through 226 Proline residue: E 184 - end of helix Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 231 through 254 Proline residue: E 246 - end of helix Processing helix chain 'E' and resid 258 through 263 Processing helix chain 'E' and resid 268 through 277 removed outlier: 3.880A pdb=" N VAL E 274 " --> pdb=" O ASP E 270 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL E 275 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 Processing helix chain 'E' and resid 299 through 308 Processing helix chain 'E' and resid 310 through 326 removed outlier: 3.513A pdb=" N ILE E 324 " --> pdb=" O CYS E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 356 removed outlier: 3.759A pdb=" N THR E 336 " --> pdb=" O TYR E 332 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) Proline residue: E 348 - end of helix removed outlier: 4.940A pdb=" N ASP E 353 " --> pdb=" O ILE E 349 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP E 354 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 380 removed outlier: 3.547A pdb=" N ILE E 373 " --> pdb=" O SER E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 Processing helix chain 'E' and resid 388 through 418 removed outlier: 3.639A pdb=" N VAL E 396 " --> pdb=" O LEU E 392 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS E 408 " --> pdb=" O LEU E 404 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU E 409 " --> pdb=" O ALA E 405 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS E 417 " --> pdb=" O ARG E 413 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY E 418 " --> pdb=" O LEU E 414 " (cutoff:3.500A) 1015 hydrogen bonds defined for protein. 3015 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.64 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2110 1.29 - 1.42: 3527 1.42 - 1.55: 8102 1.55 - 1.68: 16 1.68 - 1.81: 75 Bond restraints: 13830 Sorted by residual: bond pdb=" C GLN B 401 " pdb=" O GLN B 401 " ideal model delta sigma weight residual 1.236 1.345 -0.109 1.15e-02 7.56e+03 8.93e+01 bond pdb=" C GLN D 401 " pdb=" O GLN D 401 " ideal model delta sigma weight residual 1.236 1.345 -0.109 1.15e-02 7.56e+03 8.93e+01 bond pdb=" C GLN E 401 " pdb=" O GLN E 401 " ideal model delta sigma weight residual 1.236 1.345 -0.109 1.15e-02 7.56e+03 8.92e+01 bond pdb=" C GLN A 401 " pdb=" O GLN A 401 " ideal model delta sigma weight residual 1.236 1.345 -0.108 1.15e-02 7.56e+03 8.89e+01 bond pdb=" C GLN C 401 " pdb=" O GLN C 401 " ideal model delta sigma weight residual 1.236 1.345 -0.108 1.15e-02 7.56e+03 8.83e+01 ... (remaining 13825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 14836 2.17 - 4.34: 3654 4.34 - 6.51: 285 6.51 - 8.69: 27 8.69 - 10.86: 8 Bond angle restraints: 18810 Sorted by residual: angle pdb=" C GLU A 382 " pdb=" CA GLU A 382 " pdb=" CB GLU A 382 " ideal model delta sigma weight residual 110.33 118.26 -7.93 1.02e+00 9.61e-01 6.04e+01 angle pdb=" C GLU B 382 " pdb=" CA GLU B 382 " pdb=" CB GLU B 382 " ideal model delta sigma weight residual 110.33 118.26 -7.93 1.02e+00 9.61e-01 6.04e+01 angle pdb=" C GLU E 382 " pdb=" CA GLU E 382 " pdb=" CB GLU E 382 " ideal model delta sigma weight residual 110.33 118.26 -7.93 1.02e+00 9.61e-01 6.04e+01 angle pdb=" C GLU D 382 " pdb=" CA GLU D 382 " pdb=" CB GLU D 382 " ideal model delta sigma weight residual 110.33 118.26 -7.93 1.02e+00 9.61e-01 6.04e+01 angle pdb=" C GLU C 382 " pdb=" CA GLU C 382 " pdb=" CB GLU C 382 " ideal model delta sigma weight residual 110.33 118.23 -7.90 1.02e+00 9.61e-01 5.99e+01 ... (remaining 18805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 7550 16.77 - 33.54: 645 33.54 - 50.31: 160 50.31 - 67.07: 20 67.07 - 83.84: 15 Dihedral angle restraints: 8390 sinusoidal: 3360 harmonic: 5030 Sorted by residual: dihedral pdb=" CA GLU B 382 " pdb=" C GLU B 382 " pdb=" N PRO B 383 " pdb=" CA PRO B 383 " ideal model delta harmonic sigma weight residual 180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA GLU C 382 " pdb=" C GLU C 382 " pdb=" N PRO C 383 " pdb=" CA PRO C 383 " ideal model delta harmonic sigma weight residual -180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA GLU D 382 " pdb=" C GLU D 382 " pdb=" N PRO D 383 " pdb=" CA PRO D 383 " ideal model delta harmonic sigma weight residual -180.00 -159.75 -20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 8387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1068 0.058 - 0.116: 774 0.116 - 0.175: 358 0.175 - 0.233: 35 0.233 - 0.291: 10 Chirality restraints: 2245 Sorted by residual: chirality pdb=" CB VAL E 378 " pdb=" CA VAL E 378 " pdb=" CG1 VAL E 378 " pdb=" CG2 VAL E 378 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB VAL C 378 " pdb=" CA VAL C 378 " pdb=" CG1 VAL C 378 " pdb=" CG2 VAL C 378 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB VAL A 378 " pdb=" CA VAL A 378 " pdb=" CG1 VAL A 378 " pdb=" CG2 VAL A 378 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 2242 not shown) Planarity restraints: 2345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 343 " 0.034 2.00e-02 2.50e+03 1.58e-02 6.26e+00 pdb=" CG TRP B 343 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP B 343 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 343 " -0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP B 343 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 343 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 343 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 343 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 343 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 343 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 343 " 0.033 2.00e-02 2.50e+03 1.58e-02 6.26e+00 pdb=" CG TRP C 343 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP C 343 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 343 " -0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP C 343 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 343 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 343 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 343 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 343 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 343 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 343 " 0.033 2.00e-02 2.50e+03 1.58e-02 6.25e+00 pdb=" CG TRP A 343 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP A 343 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 343 " -0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP A 343 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 343 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 343 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 343 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 343 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 343 " 0.016 2.00e-02 2.50e+03 ... (remaining 2342 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1360 2.77 - 3.31: 14132 3.31 - 3.84: 22770 3.84 - 4.37: 28598 4.37 - 4.90: 47163 Nonbonded interactions: 114023 Sorted by model distance: nonbonded pdb=" OH TYR C 179 " pdb=" OG1 THR C 346 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR D 179 " pdb=" OG1 THR D 346 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR A 179 " pdb=" OG1 THR A 346 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR B 179 " pdb=" OG1 THR B 346 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR E 179 " pdb=" OG1 THR E 346 " model vdw 2.245 3.040 ... (remaining 114018 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.080 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 27.200 Find NCS groups from input model: 0.390 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:10.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.109 13830 Z= 1.125 Angle : 1.769 10.857 18810 Z= 1.322 Chirality : 0.083 0.291 2245 Planarity : 0.005 0.019 2345 Dihedral : 13.886 83.843 5100 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.99 % Allowed : 3.63 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.19), residues: 1695 helix: 0.27 (0.13), residues: 1385 sheet: None (None), residues: 0 loop : -0.70 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.006 TRP B 343 HIS 0.009 0.003 HIS B 126 PHE 0.022 0.004 PHE E 192 TYR 0.014 0.005 TYR B 179 ARG 0.011 0.001 ARG D 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 240 time to evaluate : 1.464 Fit side-chains REVERT: A 88 ARG cc_start: 0.6747 (ttm-80) cc_final: 0.6392 (ttm110) REVERT: A 100 ARG cc_start: 0.7434 (ttp-110) cc_final: 0.7143 (ttm110) REVERT: A 103 ARG cc_start: 0.7337 (mtp85) cc_final: 0.7091 (mmm-85) REVERT: A 104 GLN cc_start: 0.7018 (mm110) cc_final: 0.6223 (pt0) REVERT: A 148 LEU cc_start: 0.8085 (mp) cc_final: 0.7877 (mt) REVERT: A 206 LYS cc_start: 0.8608 (mttp) cc_final: 0.8172 (mttp) REVERT: A 233 GLN cc_start: 0.7230 (mm-40) cc_final: 0.7008 (tp40) REVERT: A 332 TYR cc_start: 0.8763 (t80) cc_final: 0.8440 (t80) REVERT: A 354 ASP cc_start: 0.7033 (m-30) cc_final: 0.6431 (p0) REVERT: A 397 ARG cc_start: 0.8240 (ttp80) cc_final: 0.8022 (ttm170) REVERT: A 402 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6178 (mt-10) REVERT: B 104 GLN cc_start: 0.6832 (mm110) cc_final: 0.5923 (pt0) REVERT: B 206 LYS cc_start: 0.8356 (mttp) cc_final: 0.8094 (mmtp) REVERT: B 233 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6981 (mm110) REVERT: B 264 GLN cc_start: 0.8535 (tt0) cc_final: 0.8261 (tt0) REVERT: B 265 ASN cc_start: 0.8407 (m-40) cc_final: 0.8170 (m-40) REVERT: B 300 GLU cc_start: 0.8080 (tp30) cc_final: 0.7744 (mm-30) REVERT: B 397 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7674 (ttp80) REVERT: B 402 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6130 (mt-10) REVERT: C 92 ASP cc_start: 0.7190 (m-30) cc_final: 0.6810 (m-30) REVERT: C 103 ARG cc_start: 0.7385 (mtp85) cc_final: 0.7173 (mmm-85) REVERT: C 206 LYS cc_start: 0.8335 (mttp) cc_final: 0.7689 (mttp) REVERT: C 217 ASP cc_start: 0.8729 (t70) cc_final: 0.8518 (t70) REVERT: C 233 GLN cc_start: 0.7384 (mm-40) cc_final: 0.7152 (mm-40) REVERT: C 264 GLN cc_start: 0.8148 (tt0) cc_final: 0.7834 (tt0) REVERT: C 297 LYS cc_start: 0.8575 (mmtp) cc_final: 0.8080 (mmtm) REVERT: C 315 GLU cc_start: 0.8224 (tt0) cc_final: 0.7582 (mt-10) REVERT: C 354 ASP cc_start: 0.7717 (m-30) cc_final: 0.7098 (p0) REVERT: C 391 ASP cc_start: 0.7968 (m-30) cc_final: 0.7450 (m-30) REVERT: C 401 GLN cc_start: 0.7959 (mt0) cc_final: 0.7701 (mt0) REVERT: C 402 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6144 (mt-10) REVERT: D 104 GLN cc_start: 0.7569 (mm110) cc_final: 0.7294 (mm110) REVERT: D 106 ARG cc_start: 0.7458 (mtt-85) cc_final: 0.7202 (mtp85) REVERT: D 206 LYS cc_start: 0.8400 (mttp) cc_final: 0.7927 (mttp) REVERT: D 210 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7896 (mt-10) REVERT: D 264 GLN cc_start: 0.8599 (tt0) cc_final: 0.8365 (tt0) REVERT: D 299 GLU cc_start: 0.8020 (tt0) cc_final: 0.7810 (tt0) REVERT: D 315 GLU cc_start: 0.8312 (tt0) cc_final: 0.7584 (mt-10) REVERT: D 397 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7770 (ttp80) REVERT: D 401 GLN cc_start: 0.7997 (mt0) cc_final: 0.7754 (mt0) REVERT: D 402 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6704 (mt-10) REVERT: E 163 ASP cc_start: 0.6698 (m-30) cc_final: 0.6432 (t0) REVERT: E 206 LYS cc_start: 0.8219 (mttp) cc_final: 0.7702 (mttp) REVERT: E 264 GLN cc_start: 0.8315 (tt0) cc_final: 0.8081 (tt0) REVERT: E 265 ASN cc_start: 0.8248 (m-40) cc_final: 0.7805 (m110) REVERT: E 397 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7925 (ttp80) REVERT: E 402 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6092 (mt-10) outliers start: 15 outliers final: 0 residues processed: 251 average time/residue: 1.7995 time to fit residues: 481.2116 Evaluate side-chains 184 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 179 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS A 401 GLN B 98 GLN B 123 HIS C 123 HIS D 98 GLN D 394 ASN E 123 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13830 Z= 0.229 Angle : 0.578 6.874 18810 Z= 0.299 Chirality : 0.040 0.152 2245 Planarity : 0.006 0.070 2345 Dihedral : 5.658 48.242 1875 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.71 % Allowed : 7.92 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.20), residues: 1695 helix: 1.46 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -0.29 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 352 HIS 0.005 0.001 HIS A 344 PHE 0.014 0.002 PHE D 245 TYR 0.013 0.001 TYR B 241 ARG 0.009 0.001 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 189 time to evaluate : 1.546 Fit side-chains REVERT: A 88 ARG cc_start: 0.6359 (ttm-80) cc_final: 0.5793 (ttm110) REVERT: A 100 ARG cc_start: 0.7681 (ttp-110) cc_final: 0.7441 (ttm110) REVERT: A 104 GLN cc_start: 0.6919 (mm110) cc_final: 0.6189 (pt0) REVERT: A 156 TYR cc_start: 0.7695 (t80) cc_final: 0.7452 (t80) REVERT: A 162 LEU cc_start: 0.6596 (mt) cc_final: 0.6371 (mt) REVERT: A 164 LEU cc_start: 0.6644 (mp) cc_final: 0.6407 (mp) REVERT: A 206 LYS cc_start: 0.8586 (mttp) cc_final: 0.8228 (mttp) REVERT: A 233 GLN cc_start: 0.7064 (mm-40) cc_final: 0.6775 (mm110) REVERT: A 354 ASP cc_start: 0.7324 (m-30) cc_final: 0.6583 (p0) REVERT: A 390 ASP cc_start: 0.7977 (m-30) cc_final: 0.7596 (m-30) REVERT: A 397 ARG cc_start: 0.7718 (ttp80) cc_final: 0.7512 (ttm110) REVERT: B 104 GLN cc_start: 0.6778 (mm110) cc_final: 0.5954 (pt0) REVERT: B 115 MET cc_start: 0.7653 (mtm) cc_final: 0.7419 (ttm) REVERT: B 206 LYS cc_start: 0.8158 (mttp) cc_final: 0.7820 (mttp) REVERT: B 233 GLN cc_start: 0.7041 (mm-40) cc_final: 0.6769 (mm110) REVERT: B 264 GLN cc_start: 0.8493 (tt0) cc_final: 0.8216 (tt0) REVERT: B 297 LYS cc_start: 0.7987 (mmtp) cc_final: 0.7647 (mmtm) REVERT: B 390 ASP cc_start: 0.7705 (m-30) cc_final: 0.7471 (m-30) REVERT: B 397 ARG cc_start: 0.7318 (ttp80) cc_final: 0.7087 (ttp80) REVERT: C 116 HIS cc_start: 0.7672 (t-90) cc_final: 0.7237 (t70) REVERT: C 206 LYS cc_start: 0.8310 (mttp) cc_final: 0.7751 (mttp) REVERT: C 264 GLN cc_start: 0.8031 (tt0) cc_final: 0.7713 (tt0) REVERT: C 297 LYS cc_start: 0.8359 (mmtp) cc_final: 0.8120 (tppt) REVERT: C 315 GLU cc_start: 0.8186 (tt0) cc_final: 0.7596 (mt-10) REVERT: C 354 ASP cc_start: 0.7524 (m-30) cc_final: 0.6739 (p0) REVERT: C 390 ASP cc_start: 0.7832 (m-30) cc_final: 0.7425 (m-30) REVERT: C 391 ASP cc_start: 0.7797 (m-30) cc_final: 0.7296 (m-30) REVERT: C 402 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6091 (mt-10) REVERT: D 104 GLN cc_start: 0.7393 (mm110) cc_final: 0.7139 (mm110) REVERT: D 206 LYS cc_start: 0.8296 (mttp) cc_final: 0.7845 (mttp) REVERT: D 264 GLN cc_start: 0.8567 (tt0) cc_final: 0.8331 (tt0) REVERT: D 300 GLU cc_start: 0.7885 (tp30) cc_final: 0.7626 (mm-30) REVERT: D 315 GLU cc_start: 0.8295 (tt0) cc_final: 0.7610 (mt-10) REVERT: D 390 ASP cc_start: 0.8349 (m-30) cc_final: 0.8002 (m-30) REVERT: E 106 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6745 (mtt-85) REVERT: E 163 ASP cc_start: 0.6780 (m-30) cc_final: 0.6516 (t0) REVERT: E 206 LYS cc_start: 0.8247 (mttp) cc_final: 0.7742 (mttp) REVERT: E 264 GLN cc_start: 0.8432 (tt0) cc_final: 0.8169 (tt0) REVERT: E 265 ASN cc_start: 0.8270 (m-40) cc_final: 0.7825 (m110) REVERT: E 390 ASP cc_start: 0.8038 (m-30) cc_final: 0.7807 (m-30) REVERT: E 397 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7692 (ttm110) REVERT: E 417 LYS cc_start: 0.6720 (OUTLIER) cc_final: 0.4386 (mptt) outliers start: 41 outliers final: 13 residues processed: 218 average time/residue: 1.6784 time to fit residues: 391.6797 Evaluate side-chains 183 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 417 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 128 optimal weight: 0.0470 chunk 105 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 154 optimal weight: 0.0000 chunk 167 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 overall best weight: 1.0088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN D 98 GLN D 123 HIS D 401 GLN E 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13830 Z= 0.156 Angle : 0.490 6.942 18810 Z= 0.249 Chirality : 0.037 0.152 2245 Planarity : 0.005 0.046 2345 Dihedral : 5.176 49.041 1875 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.84 % Allowed : 9.17 % Favored : 87.99 % 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: 2.53 (0.21), residues: 1695 helix: 2.04 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -0.23 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 343 HIS 0.002 0.001 HIS A 344 PHE 0.010 0.002 PHE D 245 TYR 0.012 0.001 TYR E 156 ARG 0.006 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 232 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 189 time to evaluate : 1.475 Fit side-chains REVERT: A 88 ARG cc_start: 0.6292 (ttm-80) cc_final: 0.5870 (ttm110) REVERT: A 100 ARG cc_start: 0.7726 (ttp-110) cc_final: 0.7342 (ttm110) REVERT: A 104 GLN cc_start: 0.6925 (mm110) cc_final: 0.6187 (pt0) REVERT: A 162 LEU cc_start: 0.6447 (mt) cc_final: 0.6224 (mt) REVERT: A 164 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6544 (mp) REVERT: A 206 LYS cc_start: 0.8499 (mttp) cc_final: 0.8105 (mttp) REVERT: A 233 GLN cc_start: 0.7092 (mm-40) cc_final: 0.6781 (mm110) REVERT: A 390 ASP cc_start: 0.7912 (m-30) cc_final: 0.7572 (m-30) REVERT: A 402 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.5992 (mt-10) REVERT: B 104 GLN cc_start: 0.6728 (mm110) cc_final: 0.5925 (pt0) REVERT: B 206 LYS cc_start: 0.8137 (mttp) cc_final: 0.7778 (mttp) REVERT: B 233 GLN cc_start: 0.7089 (mm-40) cc_final: 0.6801 (mm110) REVERT: B 264 GLN cc_start: 0.8572 (tt0) cc_final: 0.8323 (tt0) REVERT: B 297 LYS cc_start: 0.7795 (mmtp) cc_final: 0.7477 (mmtm) REVERT: B 390 ASP cc_start: 0.7888 (m-30) cc_final: 0.7501 (m-30) REVERT: B 397 ARG cc_start: 0.7124 (ttp80) cc_final: 0.6924 (ttp80) REVERT: B 402 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.5942 (mt-10) REVERT: C 104 GLN cc_start: 0.6976 (mm110) cc_final: 0.6097 (pt0) REVERT: C 116 HIS cc_start: 0.7635 (t-90) cc_final: 0.7249 (t70) REVERT: C 206 LYS cc_start: 0.8329 (mttp) cc_final: 0.7611 (mttp) REVERT: C 264 GLN cc_start: 0.8024 (tt0) cc_final: 0.7717 (tt0) REVERT: C 315 GLU cc_start: 0.7993 (tt0) cc_final: 0.7351 (mt-10) REVERT: C 390 ASP cc_start: 0.7749 (m-30) cc_final: 0.7409 (m-30) REVERT: C 402 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.5977 (mt-10) REVERT: D 206 LYS cc_start: 0.8272 (mttp) cc_final: 0.7886 (mttp) REVERT: D 235 LYS cc_start: 0.7506 (tttt) cc_final: 0.7257 (ttmt) REVERT: D 264 GLN cc_start: 0.8568 (tt0) cc_final: 0.8313 (tt0) REVERT: D 300 GLU cc_start: 0.7930 (tp30) cc_final: 0.7693 (mm-30) REVERT: D 315 GLU cc_start: 0.8350 (tt0) cc_final: 0.7592 (mt-10) REVERT: D 390 ASP cc_start: 0.8176 (m-30) cc_final: 0.7857 (m-30) REVERT: E 99 GLU cc_start: 0.6660 (mm-30) cc_final: 0.6002 (mm-30) REVERT: E 106 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6711 (mtt-85) REVERT: E 163 ASP cc_start: 0.6745 (m-30) cc_final: 0.6499 (t0) REVERT: E 206 LYS cc_start: 0.8256 (mttp) cc_final: 0.7695 (mttp) REVERT: E 217 ASP cc_start: 0.8210 (t70) cc_final: 0.7675 (t0) REVERT: E 264 GLN cc_start: 0.8418 (tt0) cc_final: 0.8151 (tt0) REVERT: E 265 ASN cc_start: 0.8280 (m-40) cc_final: 0.7910 (m110) REVERT: E 300 GLU cc_start: 0.8068 (tp30) cc_final: 0.7784 (mm-30) REVERT: E 390 ASP cc_start: 0.8026 (m-30) cc_final: 0.7748 (m-30) REVERT: E 397 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7731 (ttm110) REVERT: E 402 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.5822 (mt-10) outliers start: 43 outliers final: 13 residues processed: 218 average time/residue: 1.6799 time to fit residues: 392.5549 Evaluate side-chains 197 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 178 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 279 LYS Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 0.0050 chunk 164 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 147 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN D 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13830 Z= 0.159 Angle : 0.484 6.933 18810 Z= 0.245 Chirality : 0.037 0.155 2245 Planarity : 0.005 0.050 2345 Dihedral : 5.054 48.841 1875 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.64 % Allowed : 10.30 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.83 (0.21), residues: 1695 helix: 2.24 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -0.08 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 208 HIS 0.003 0.001 HIS D 344 PHE 0.010 0.002 PHE A 146 TYR 0.011 0.001 TYR C 156 ARG 0.007 0.000 ARG D 397 *********************** 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 220 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 180 time to evaluate : 1.713 Fit side-chains REVERT: A 100 ARG cc_start: 0.7760 (ttp-110) cc_final: 0.7371 (ttm110) REVERT: A 104 GLN cc_start: 0.7000 (mm110) cc_final: 0.6305 (pt0) REVERT: A 156 TYR cc_start: 0.7830 (t80) cc_final: 0.7570 (t80) REVERT: A 162 LEU cc_start: 0.6427 (mt) cc_final: 0.6224 (mt) REVERT: A 164 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6448 (mp) REVERT: A 206 LYS cc_start: 0.8496 (mttp) cc_final: 0.8101 (mttp) REVERT: A 233 GLN cc_start: 0.7027 (mm-40) cc_final: 0.6696 (mm110) REVERT: A 390 ASP cc_start: 0.7887 (m-30) cc_final: 0.7549 (m-30) REVERT: A 402 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.5941 (mt-10) REVERT: B 104 GLN cc_start: 0.6746 (mm110) cc_final: 0.5850 (pt0) REVERT: B 156 TYR cc_start: 0.8159 (t80) cc_final: 0.7886 (t80) REVERT: B 206 LYS cc_start: 0.8137 (mttp) cc_final: 0.7761 (mttp) REVERT: B 233 GLN cc_start: 0.7027 (mm-40) cc_final: 0.6706 (mm110) REVERT: B 264 GLN cc_start: 0.8583 (tt0) cc_final: 0.8329 (tt0) REVERT: B 297 LYS cc_start: 0.7774 (mmtp) cc_final: 0.7446 (mmtm) REVERT: B 390 ASP cc_start: 0.7890 (m-30) cc_final: 0.7503 (m-30) REVERT: B 402 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.5896 (mt-10) REVERT: C 104 GLN cc_start: 0.6789 (mm110) cc_final: 0.5711 (pt0) REVERT: C 132 SER cc_start: 0.8470 (p) cc_final: 0.8201 (m) REVERT: C 206 LYS cc_start: 0.8331 (mttp) cc_final: 0.7603 (mttp) REVERT: C 264 GLN cc_start: 0.8045 (tt0) cc_final: 0.7746 (tt0) REVERT: C 315 GLU cc_start: 0.7986 (tt0) cc_final: 0.7380 (mt-10) REVERT: C 390 ASP cc_start: 0.7745 (m-30) cc_final: 0.7416 (m-30) REVERT: C 402 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6018 (mt-10) REVERT: D 104 GLN cc_start: 0.7089 (mm110) cc_final: 0.6203 (pt0) REVERT: D 206 LYS cc_start: 0.8286 (mttp) cc_final: 0.7845 (mttp) REVERT: D 235 LYS cc_start: 0.7465 (tttt) cc_final: 0.7234 (ttmt) REVERT: D 264 GLN cc_start: 0.8559 (tt0) cc_final: 0.8295 (tt0) REVERT: D 300 GLU cc_start: 0.7915 (tp30) cc_final: 0.7690 (mm-30) REVERT: D 315 GLU cc_start: 0.8421 (tt0) cc_final: 0.7619 (mt-10) REVERT: D 390 ASP cc_start: 0.8166 (m-30) cc_final: 0.7852 (m-30) REVERT: D 402 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6379 (mt-10) REVERT: E 99 GLU cc_start: 0.6619 (mm-30) cc_final: 0.5993 (mm-30) REVERT: E 104 GLN cc_start: 0.7000 (mm110) cc_final: 0.6503 (mt0) REVERT: E 106 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6720 (mtt-85) REVERT: E 206 LYS cc_start: 0.8088 (mttp) cc_final: 0.7654 (mttp) REVERT: E 217 ASP cc_start: 0.8222 (t70) cc_final: 0.7659 (t0) REVERT: E 264 GLN cc_start: 0.8423 (tt0) cc_final: 0.8170 (tt0) REVERT: E 300 GLU cc_start: 0.8009 (tp30) cc_final: 0.7781 (mm-30) REVERT: E 390 ASP cc_start: 0.7916 (m-30) cc_final: 0.7645 (m-30) REVERT: E 397 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7713 (ttm110) REVERT: E 402 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.5798 (mt-10) outliers start: 40 outliers final: 14 residues processed: 206 average time/residue: 1.6366 time to fit residues: 362.0124 Evaluate side-chains 195 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 174 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 279 LYS Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 40.0000 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 122 optimal weight: 0.0010 chunk 67 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 83 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 overall best weight: 3.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13830 Z= 0.286 Angle : 0.563 7.132 18810 Z= 0.288 Chirality : 0.041 0.158 2245 Planarity : 0.006 0.066 2345 Dihedral : 5.391 50.091 1875 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.51 % Allowed : 10.69 % Favored : 86.80 % 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 (0.20), residues: 1695 helix: 1.87 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -0.31 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 343 HIS 0.005 0.002 HIS D 117 PHE 0.018 0.003 PHE B 146 TYR 0.011 0.002 TYR A 109 ARG 0.007 0.001 ARG D 397 *********************** 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 224 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 186 time to evaluate : 1.584 Fit side-chains REVERT: A 88 ARG cc_start: 0.6331 (ttm-80) cc_final: 0.5973 (ttm110) REVERT: A 100 ARG cc_start: 0.7738 (ttp-110) cc_final: 0.7349 (ttm110) REVERT: A 104 GLN cc_start: 0.7014 (mm110) cc_final: 0.6334 (pt0) REVERT: A 156 TYR cc_start: 0.8020 (t80) cc_final: 0.7788 (t80) REVERT: A 164 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6316 (mp) REVERT: A 206 LYS cc_start: 0.8466 (mttp) cc_final: 0.8070 (mttp) REVERT: A 233 GLN cc_start: 0.7065 (mm-40) cc_final: 0.6769 (mm110) REVERT: A 390 ASP cc_start: 0.7980 (m-30) cc_final: 0.7544 (m-30) REVERT: A 402 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.5789 (mt-10) REVERT: B 104 GLN cc_start: 0.6744 (mm110) cc_final: 0.5848 (pt0) REVERT: B 206 LYS cc_start: 0.8148 (mttp) cc_final: 0.7809 (mttp) REVERT: B 233 GLN cc_start: 0.7109 (mm-40) cc_final: 0.6785 (mm110) REVERT: B 264 GLN cc_start: 0.8532 (tt0) cc_final: 0.8285 (tt0) REVERT: B 297 LYS cc_start: 0.7997 (mmtp) cc_final: 0.7628 (mmtm) REVERT: B 390 ASP cc_start: 0.7896 (m-30) cc_final: 0.7490 (m-30) REVERT: B 402 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6168 (mt-10) REVERT: C 104 GLN cc_start: 0.6852 (mm110) cc_final: 0.5704 (pt0) REVERT: C 116 HIS cc_start: 0.7711 (t-90) cc_final: 0.7380 (t70) REVERT: C 132 SER cc_start: 0.8512 (p) cc_final: 0.8233 (m) REVERT: C 206 LYS cc_start: 0.8317 (mttp) cc_final: 0.7741 (mttp) REVERT: C 264 GLN cc_start: 0.8079 (tt0) cc_final: 0.7758 (tt0) REVERT: C 315 GLU cc_start: 0.8297 (tt0) cc_final: 0.7533 (mt-10) REVERT: C 390 ASP cc_start: 0.7805 (m-30) cc_final: 0.7403 (m-30) REVERT: C 402 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6050 (mt-10) REVERT: D 88 ARG cc_start: 0.6523 (ttm-80) cc_final: 0.6260 (ttm110) REVERT: D 104 GLN cc_start: 0.7192 (mm110) cc_final: 0.6317 (pt0) REVERT: D 206 LYS cc_start: 0.8278 (mttp) cc_final: 0.7858 (mttp) REVERT: D 235 LYS cc_start: 0.7547 (tttt) cc_final: 0.7308 (ttmt) REVERT: D 264 GLN cc_start: 0.8569 (tt0) cc_final: 0.8307 (tt0) REVERT: D 300 GLU cc_start: 0.7950 (tp30) cc_final: 0.7705 (mm-30) REVERT: D 390 ASP cc_start: 0.8285 (m-30) cc_final: 0.7895 (m-30) REVERT: E 99 GLU cc_start: 0.6625 (mm-30) cc_final: 0.5981 (mm-30) REVERT: E 106 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6771 (mtt-85) REVERT: E 206 LYS cc_start: 0.8154 (mttp) cc_final: 0.7666 (mttp) REVERT: E 264 GLN cc_start: 0.8465 (tt0) cc_final: 0.8217 (tt0) REVERT: E 300 GLU cc_start: 0.8026 (tp30) cc_final: 0.7781 (mm-30) REVERT: E 390 ASP cc_start: 0.8018 (m-30) cc_final: 0.7707 (m-30) REVERT: E 397 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7806 (ttm110) REVERT: E 402 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.5779 (mt-10) outliers start: 38 outliers final: 21 residues processed: 211 average time/residue: 1.6741 time to fit residues: 378.2481 Evaluate side-chains 203 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 176 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 40.0000 chunk 76 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN D 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13830 Z= 0.156 Angle : 0.480 6.951 18810 Z= 0.244 Chirality : 0.037 0.154 2245 Planarity : 0.005 0.043 2345 Dihedral : 5.113 50.207 1875 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.38 % Allowed : 11.42 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.21), residues: 1695 helix: 2.20 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -0.10 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 343 HIS 0.003 0.001 HIS D 344 PHE 0.010 0.002 PHE A 146 TYR 0.007 0.001 TYR C 241 ARG 0.009 0.000 ARG D 397 *********************** 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 219 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 1.651 Fit side-chains REVERT: A 88 ARG cc_start: 0.6461 (ttm-80) cc_final: 0.6102 (ttm110) REVERT: A 100 ARG cc_start: 0.7761 (ttp-110) cc_final: 0.7407 (ttm110) REVERT: A 104 GLN cc_start: 0.7003 (mm110) cc_final: 0.6339 (pt0) REVERT: A 156 TYR cc_start: 0.7845 (t80) cc_final: 0.7616 (t80) REVERT: A 162 LEU cc_start: 0.6457 (mt) cc_final: 0.6128 (mt) REVERT: A 164 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7171 (mp) REVERT: A 206 LYS cc_start: 0.8509 (mttp) cc_final: 0.8109 (mttp) REVERT: A 233 GLN cc_start: 0.7045 (mm-40) cc_final: 0.6781 (mm110) REVERT: A 382 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7232 (tm-30) REVERT: A 390 ASP cc_start: 0.7899 (m-30) cc_final: 0.7487 (m-30) REVERT: A 402 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.5770 (mt-10) REVERT: B 104 GLN cc_start: 0.6741 (mm110) cc_final: 0.5852 (pt0) REVERT: B 156 TYR cc_start: 0.8238 (t80) cc_final: 0.7949 (t80) REVERT: B 206 LYS cc_start: 0.8145 (mttp) cc_final: 0.7796 (mttp) REVERT: B 233 GLN cc_start: 0.7020 (mm-40) cc_final: 0.6755 (mm110) REVERT: B 264 GLN cc_start: 0.8611 (tt0) cc_final: 0.8368 (tt0) REVERT: B 390 ASP cc_start: 0.7807 (m-30) cc_final: 0.7438 (m-30) REVERT: B 402 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6036 (mt-10) REVERT: C 104 GLN cc_start: 0.6872 (mm110) cc_final: 0.5741 (pt0) REVERT: C 132 SER cc_start: 0.8448 (p) cc_final: 0.8206 (m) REVERT: C 206 LYS cc_start: 0.8341 (mttp) cc_final: 0.7613 (mttp) REVERT: C 264 GLN cc_start: 0.8044 (tt0) cc_final: 0.7676 (tt0) REVERT: C 315 GLU cc_start: 0.8163 (tt0) cc_final: 0.7364 (mt-10) REVERT: C 390 ASP cc_start: 0.7744 (m-30) cc_final: 0.7369 (m-30) REVERT: C 402 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.5965 (mt-10) REVERT: D 104 GLN cc_start: 0.7204 (mm110) cc_final: 0.6359 (pt0) REVERT: D 206 LYS cc_start: 0.8285 (mttp) cc_final: 0.7845 (mttp) REVERT: D 235 LYS cc_start: 0.7479 (tttt) cc_final: 0.7247 (ttmt) REVERT: D 264 GLN cc_start: 0.8566 (tt0) cc_final: 0.8301 (tt0) REVERT: D 300 GLU cc_start: 0.7887 (tp30) cc_final: 0.7666 (mm-30) REVERT: D 390 ASP cc_start: 0.8192 (m-30) cc_final: 0.7890 (m-30) REVERT: D 402 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6321 (mt-10) REVERT: D 408 LYS cc_start: 0.7142 (tttm) cc_final: 0.6869 (ttmm) REVERT: E 99 GLU cc_start: 0.6637 (mm-30) cc_final: 0.5993 (mm-30) REVERT: E 206 LYS cc_start: 0.8093 (mttp) cc_final: 0.7645 (mttp) REVERT: E 264 GLN cc_start: 0.8444 (tt0) cc_final: 0.8186 (tt0) REVERT: E 300 GLU cc_start: 0.7990 (tp30) cc_final: 0.7750 (mm-30) REVERT: E 390 ASP cc_start: 0.7954 (m-30) cc_final: 0.7655 (m-30) REVERT: E 397 ARG cc_start: 0.8023 (ttp80) cc_final: 0.7768 (ttm110) REVERT: E 402 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.5776 (mt-10) outliers start: 36 outliers final: 14 residues processed: 206 average time/residue: 1.6008 time to fit residues: 354.5320 Evaluate side-chains 200 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 179 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 102 optimal weight: 40.0000 chunk 99 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13830 Z= 0.273 Angle : 0.557 7.106 18810 Z= 0.284 Chirality : 0.040 0.158 2245 Planarity : 0.005 0.062 2345 Dihedral : 5.377 50.025 1875 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.44 % Allowed : 11.49 % Favored : 86.07 % 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: 2.31 (0.20), residues: 1695 helix: 1.89 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -0.27 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 343 HIS 0.005 0.001 HIS D 344 PHE 0.018 0.003 PHE B 146 TYR 0.008 0.002 TYR A 109 ARG 0.008 0.001 ARG D 397 *********************** 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 226 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 189 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: A 88 ARG cc_start: 0.6385 (ttm-80) cc_final: 0.6014 (ttm110) REVERT: A 100 ARG cc_start: 0.7772 (ttp-110) cc_final: 0.7401 (ttm110) REVERT: A 104 GLN cc_start: 0.7095 (mm110) cc_final: 0.6369 (pt0) REVERT: A 156 TYR cc_start: 0.8043 (t80) cc_final: 0.7797 (t80) REVERT: A 162 LEU cc_start: 0.6405 (mt) cc_final: 0.6080 (mt) REVERT: A 164 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6319 (mp) REVERT: A 206 LYS cc_start: 0.8467 (mttp) cc_final: 0.8072 (mttp) REVERT: A 233 GLN cc_start: 0.7016 (mm-40) cc_final: 0.6724 (mm110) REVERT: A 382 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7243 (tm-30) REVERT: A 390 ASP cc_start: 0.7972 (m-30) cc_final: 0.7518 (m-30) REVERT: B 104 GLN cc_start: 0.6715 (mm110) cc_final: 0.5845 (pt0) REVERT: B 206 LYS cc_start: 0.8157 (mttp) cc_final: 0.7817 (mttp) REVERT: B 233 GLN cc_start: 0.7041 (mm-40) cc_final: 0.6772 (mm110) REVERT: B 264 GLN cc_start: 0.8534 (tt0) cc_final: 0.8286 (tt0) REVERT: B 297 LYS cc_start: 0.7982 (mmtp) cc_final: 0.7622 (mmtm) REVERT: B 390 ASP cc_start: 0.7709 (m-30) cc_final: 0.7452 (m-30) REVERT: B 402 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6167 (mt-10) REVERT: C 88 ARG cc_start: 0.5916 (ttm-80) cc_final: 0.5361 (ttm110) REVERT: C 104 GLN cc_start: 0.6843 (mm110) cc_final: 0.5688 (pt0) REVERT: C 116 HIS cc_start: 0.7800 (t-90) cc_final: 0.7478 (t70) REVERT: C 132 SER cc_start: 0.8471 (p) cc_final: 0.8221 (m) REVERT: C 206 LYS cc_start: 0.8321 (mttp) cc_final: 0.7748 (mttp) REVERT: C 264 GLN cc_start: 0.8085 (tt0) cc_final: 0.7757 (tt0) REVERT: C 315 GLU cc_start: 0.8289 (tt0) cc_final: 0.7574 (mt-10) REVERT: C 390 ASP cc_start: 0.7790 (m-30) cc_final: 0.7378 (m-30) REVERT: C 402 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6046 (mt-10) REVERT: D 88 ARG cc_start: 0.6572 (ttm-80) cc_final: 0.6303 (ttm110) REVERT: D 104 GLN cc_start: 0.7278 (mm110) cc_final: 0.6396 (pt0) REVERT: D 206 LYS cc_start: 0.8282 (mttp) cc_final: 0.7862 (mttp) REVERT: D 235 LYS cc_start: 0.7540 (tttt) cc_final: 0.7300 (ttmt) REVERT: D 264 GLN cc_start: 0.8620 (tt0) cc_final: 0.8335 (tt0) REVERT: D 300 GLU cc_start: 0.7931 (tp30) cc_final: 0.7686 (mm-30) REVERT: D 390 ASP cc_start: 0.8320 (m-30) cc_final: 0.7898 (m-30) REVERT: D 397 ARG cc_start: 0.7755 (ttp80) cc_final: 0.7533 (ttp80) REVERT: D 408 LYS cc_start: 0.7191 (tttm) cc_final: 0.6907 (ttmm) REVERT: E 99 GLU cc_start: 0.6635 (mm-30) cc_final: 0.5916 (mm-30) REVERT: E 106 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6728 (mtt-85) REVERT: E 206 LYS cc_start: 0.8093 (mttp) cc_final: 0.7649 (mttp) REVERT: E 264 GLN cc_start: 0.8470 (tt0) cc_final: 0.8233 (tt0) REVERT: E 299 GLU cc_start: 0.8046 (tt0) cc_final: 0.7443 (tt0) REVERT: E 300 GLU cc_start: 0.8053 (tp30) cc_final: 0.7766 (mm-30) REVERT: E 390 ASP cc_start: 0.8026 (m-30) cc_final: 0.7709 (m-30) REVERT: E 402 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.5777 (mt-10) outliers start: 37 outliers final: 18 residues processed: 215 average time/residue: 1.6578 time to fit residues: 381.7871 Evaluate side-chains 207 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 183 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 104 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 0.0010 chunk 128 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13830 Z= 0.195 Angle : 0.506 7.203 18810 Z= 0.257 Chirality : 0.038 0.154 2245 Planarity : 0.005 0.052 2345 Dihedral : 5.261 49.945 1875 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.38 % Allowed : 11.95 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.21), residues: 1695 helix: 2.06 (0.14), residues: 1430 sheet: None (None), residues: 0 loop : -0.24 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 343 HIS 0.004 0.001 HIS D 344 PHE 0.012 0.002 PHE D 245 TYR 0.007 0.001 TYR E 156 ARG 0.007 0.000 ARG D 397 *********************** 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 227 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 191 time to evaluate : 1.666 Fit side-chains revert: symmetry clash REVERT: A 88 ARG cc_start: 0.6406 (ttm-80) cc_final: 0.6027 (ttm110) REVERT: A 100 ARG cc_start: 0.7745 (ttp-110) cc_final: 0.7400 (ttm110) REVERT: A 104 GLN cc_start: 0.7083 (mm110) cc_final: 0.6371 (pt0) REVERT: A 162 LEU cc_start: 0.6392 (mt) cc_final: 0.6069 (mt) REVERT: A 164 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7159 (mp) REVERT: A 206 LYS cc_start: 0.8487 (mttp) cc_final: 0.8087 (mttp) REVERT: A 233 GLN cc_start: 0.6966 (mm-40) cc_final: 0.6721 (mm110) REVERT: A 382 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: A 390 ASP cc_start: 0.7928 (m-30) cc_final: 0.7478 (m-30) REVERT: B 100 ARG cc_start: 0.7377 (ttm-80) cc_final: 0.7173 (ttp-110) REVERT: B 104 GLN cc_start: 0.6797 (mm110) cc_final: 0.5955 (pt0) REVERT: B 206 LYS cc_start: 0.8152 (mttp) cc_final: 0.7802 (mttp) REVERT: B 233 GLN cc_start: 0.6981 (mm-40) cc_final: 0.6717 (mm110) REVERT: B 264 GLN cc_start: 0.8534 (tt0) cc_final: 0.8313 (tt0) REVERT: B 390 ASP cc_start: 0.7675 (m-30) cc_final: 0.7439 (m-30) REVERT: B 402 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6100 (mt-10) REVERT: C 88 ARG cc_start: 0.6025 (ttm-80) cc_final: 0.5496 (ttm110) REVERT: C 104 GLN cc_start: 0.6837 (mm110) cc_final: 0.5688 (pt0) REVERT: C 116 HIS cc_start: 0.7744 (t-90) cc_final: 0.7396 (t70) REVERT: C 132 SER cc_start: 0.8484 (p) cc_final: 0.8237 (m) REVERT: C 206 LYS cc_start: 0.8338 (mttp) cc_final: 0.7760 (mttp) REVERT: C 264 GLN cc_start: 0.8073 (tt0) cc_final: 0.7749 (tt0) REVERT: C 315 GLU cc_start: 0.8289 (tt0) cc_final: 0.7559 (mt-10) REVERT: C 390 ASP cc_start: 0.7767 (m-30) cc_final: 0.7353 (m-30) REVERT: C 402 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6022 (mt-10) REVERT: D 88 ARG cc_start: 0.6577 (ttm-80) cc_final: 0.6228 (ttm110) REVERT: D 104 GLN cc_start: 0.7274 (mm110) cc_final: 0.6397 (pt0) REVERT: D 206 LYS cc_start: 0.8253 (mttp) cc_final: 0.7818 (mttp) REVERT: D 235 LYS cc_start: 0.7500 (tttt) cc_final: 0.7262 (ttmt) REVERT: D 264 GLN cc_start: 0.8575 (tt0) cc_final: 0.8308 (tt0) REVERT: D 300 GLU cc_start: 0.7897 (tp30) cc_final: 0.7650 (mm-30) REVERT: D 390 ASP cc_start: 0.8270 (m-30) cc_final: 0.7885 (m-30) REVERT: D 397 ARG cc_start: 0.7721 (ttp80) cc_final: 0.7476 (ttp80) REVERT: D 408 LYS cc_start: 0.7181 (tttm) cc_final: 0.6896 (ttmm) REVERT: E 99 GLU cc_start: 0.6636 (mm-30) cc_final: 0.5997 (mm-30) REVERT: E 106 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6754 (mtt-85) REVERT: E 206 LYS cc_start: 0.8095 (mttp) cc_final: 0.7642 (mttp) REVERT: E 264 GLN cc_start: 0.8460 (tt0) cc_final: 0.8200 (tt0) REVERT: E 299 GLU cc_start: 0.7972 (tt0) cc_final: 0.7383 (tt0) REVERT: E 300 GLU cc_start: 0.8023 (tp30) cc_final: 0.7738 (mm-30) REVERT: E 390 ASP cc_start: 0.7985 (m-30) cc_final: 0.7666 (m-30) REVERT: E 402 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.5786 (mt-10) outliers start: 36 outliers final: 18 residues processed: 218 average time/residue: 1.6785 time to fit residues: 392.0210 Evaluate side-chains 208 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 66 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13830 Z= 0.203 Angle : 0.516 7.494 18810 Z= 0.262 Chirality : 0.038 0.154 2245 Planarity : 0.005 0.053 2345 Dihedral : 5.274 49.737 1875 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.31 % Allowed : 12.01 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.21), residues: 1695 helix: 2.06 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -0.20 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 343 HIS 0.005 0.001 HIS A 344 PHE 0.012 0.002 PHE B 146 TYR 0.009 0.001 TYR E 156 ARG 0.008 0.000 ARG E 100 *********************** 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 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 192 time to evaluate : 1.572 Fit side-chains revert: symmetry clash REVERT: A 88 ARG cc_start: 0.6417 (ttm-80) cc_final: 0.6037 (ttm110) REVERT: A 100 ARG cc_start: 0.7744 (ttp-110) cc_final: 0.7401 (ttm110) REVERT: A 104 GLN cc_start: 0.7079 (mm110) cc_final: 0.6369 (pt0) REVERT: A 155 SER cc_start: 0.8099 (m) cc_final: 0.7796 (m) REVERT: A 162 LEU cc_start: 0.6406 (mt) cc_final: 0.6060 (mt) REVERT: A 164 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6310 (mp) REVERT: A 206 LYS cc_start: 0.8482 (mttp) cc_final: 0.8080 (mttp) REVERT: A 233 GLN cc_start: 0.6967 (mm-40) cc_final: 0.6724 (mm110) REVERT: A 382 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7285 (tm-30) REVERT: A 390 ASP cc_start: 0.7903 (m-30) cc_final: 0.7460 (m-30) REVERT: B 100 ARG cc_start: 0.7409 (ttm-80) cc_final: 0.7179 (ttp-110) REVERT: B 104 GLN cc_start: 0.6791 (mm110) cc_final: 0.5938 (pt0) REVERT: B 206 LYS cc_start: 0.8157 (mttp) cc_final: 0.7803 (mttp) REVERT: B 233 GLN cc_start: 0.6978 (mm-40) cc_final: 0.6774 (mm110) REVERT: B 264 GLN cc_start: 0.8623 (tt0) cc_final: 0.8381 (tt0) REVERT: B 390 ASP cc_start: 0.7852 (m-30) cc_final: 0.7456 (m-30) REVERT: B 402 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6098 (mt-10) REVERT: C 88 ARG cc_start: 0.6029 (ttm-80) cc_final: 0.5502 (ttm110) REVERT: C 104 GLN cc_start: 0.6831 (mm110) cc_final: 0.5676 (pt0) REVERT: C 116 HIS cc_start: 0.7747 (t-90) cc_final: 0.7429 (t70) REVERT: C 132 SER cc_start: 0.8518 (p) cc_final: 0.8271 (m) REVERT: C 206 LYS cc_start: 0.8332 (mttp) cc_final: 0.7755 (mttp) REVERT: C 264 GLN cc_start: 0.8069 (tt0) cc_final: 0.7751 (tt0) REVERT: C 315 GLU cc_start: 0.8154 (tt0) cc_final: 0.7392 (mt-10) REVERT: C 390 ASP cc_start: 0.7773 (m-30) cc_final: 0.7360 (m-30) REVERT: C 402 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6027 (mt-10) REVERT: D 88 ARG cc_start: 0.6475 (ttm-80) cc_final: 0.6098 (ttm110) REVERT: D 104 GLN cc_start: 0.7281 (mm110) cc_final: 0.6404 (pt0) REVERT: D 206 LYS cc_start: 0.8250 (mttp) cc_final: 0.7816 (mttp) REVERT: D 235 LYS cc_start: 0.7504 (tttt) cc_final: 0.7262 (ttmt) REVERT: D 264 GLN cc_start: 0.8614 (tt0) cc_final: 0.8326 (tt0) REVERT: D 300 GLU cc_start: 0.7891 (tp30) cc_final: 0.7642 (mm-30) REVERT: D 390 ASP cc_start: 0.8276 (m-30) cc_final: 0.7902 (m-30) REVERT: D 408 LYS cc_start: 0.7161 (tttm) cc_final: 0.6876 (ttmm) REVERT: E 99 GLU cc_start: 0.6639 (mm-30) cc_final: 0.6002 (mm-30) REVERT: E 106 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6745 (mtt-85) REVERT: E 206 LYS cc_start: 0.8097 (mttp) cc_final: 0.7642 (mttp) REVERT: E 264 GLN cc_start: 0.8463 (tt0) cc_final: 0.8194 (tt0) REVERT: E 299 GLU cc_start: 0.7955 (tt0) cc_final: 0.7376 (tt0) REVERT: E 300 GLU cc_start: 0.8019 (tp30) cc_final: 0.7729 (mm-30) REVERT: E 390 ASP cc_start: 0.7999 (m-30) cc_final: 0.7680 (m-30) REVERT: E 402 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.5789 (mt-10) outliers start: 35 outliers final: 19 residues processed: 219 average time/residue: 1.5933 time to fit residues: 374.6173 Evaluate side-chains 211 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 GLN D 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13830 Z= 0.285 Angle : 0.570 7.726 18810 Z= 0.291 Chirality : 0.041 0.163 2245 Planarity : 0.005 0.061 2345 Dihedral : 5.494 49.589 1875 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.85 % Allowed : 12.81 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.17 (0.20), residues: 1695 helix: 1.82 (0.14), residues: 1415 sheet: None (None), residues: 0 loop : -0.38 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 352 HIS 0.005 0.002 HIS D 344 PHE 0.018 0.003 PHE B 146 TYR 0.014 0.002 TYR E 156 ARG 0.008 0.001 ARG E 100 ********************** 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 218 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 1.516 Fit side-chains REVERT: A 88 ARG cc_start: 0.6461 (ttm-80) cc_final: 0.6068 (ttm110) REVERT: A 100 ARG cc_start: 0.7775 (ttp-110) cc_final: 0.7418 (ttm110) REVERT: A 104 GLN cc_start: 0.7086 (mm110) cc_final: 0.6369 (pt0) REVERT: A 155 SER cc_start: 0.8085 (m) cc_final: 0.7774 (m) REVERT: A 162 LEU cc_start: 0.6453 (mt) cc_final: 0.6126 (mt) REVERT: A 164 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6308 (mp) REVERT: A 206 LYS cc_start: 0.8465 (mttp) cc_final: 0.8069 (mttp) REVERT: A 233 GLN cc_start: 0.6900 (mm-40) cc_final: 0.6637 (mm110) REVERT: A 382 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: A 390 ASP cc_start: 0.7987 (m-30) cc_final: 0.7507 (m-30) REVERT: B 100 ARG cc_start: 0.7275 (ttm-80) cc_final: 0.7032 (ttp-110) REVERT: B 104 GLN cc_start: 0.6726 (mm110) cc_final: 0.5898 (pt0) REVERT: B 206 LYS cc_start: 0.8161 (mttp) cc_final: 0.7809 (mttp) REVERT: B 233 GLN cc_start: 0.7027 (mm-40) cc_final: 0.6754 (mm110) REVERT: B 264 GLN cc_start: 0.8605 (tt0) cc_final: 0.8364 (tt0) REVERT: B 297 LYS cc_start: 0.8016 (mmtp) cc_final: 0.7655 (mmtm) REVERT: B 390 ASP cc_start: 0.7703 (m-30) cc_final: 0.7433 (m-30) REVERT: B 402 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6177 (mt-10) REVERT: C 88 ARG cc_start: 0.5954 (ttm-80) cc_final: 0.5505 (ttm110) REVERT: C 104 GLN cc_start: 0.6694 (mm110) cc_final: 0.5632 (pt0) REVERT: C 116 HIS cc_start: 0.7811 (t-90) cc_final: 0.7482 (t70) REVERT: C 132 SER cc_start: 0.8487 (p) cc_final: 0.8252 (m) REVERT: C 206 LYS cc_start: 0.8322 (mttp) cc_final: 0.7745 (mttp) REVERT: C 264 GLN cc_start: 0.8088 (tt0) cc_final: 0.7764 (tt0) REVERT: C 315 GLU cc_start: 0.8328 (tt0) cc_final: 0.7606 (mt-10) REVERT: C 390 ASP cc_start: 0.7794 (m-30) cc_final: 0.7354 (m-30) REVERT: C 402 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6046 (mt-10) REVERT: D 88 ARG cc_start: 0.6464 (ttm-80) cc_final: 0.6140 (ttm110) REVERT: D 104 GLN cc_start: 0.7287 (mm110) cc_final: 0.6404 (pt0) REVERT: D 206 LYS cc_start: 0.8278 (mttp) cc_final: 0.7862 (mttp) REVERT: D 235 LYS cc_start: 0.7547 (tttt) cc_final: 0.7200 (tttp) REVERT: D 264 GLN cc_start: 0.8624 (tt0) cc_final: 0.8341 (tt0) REVERT: D 300 GLU cc_start: 0.7933 (tp30) cc_final: 0.7689 (mm-30) REVERT: D 390 ASP cc_start: 0.8330 (m-30) cc_final: 0.7888 (m-30) REVERT: D 408 LYS cc_start: 0.7200 (tttm) cc_final: 0.6912 (ttmm) REVERT: E 99 GLU cc_start: 0.6631 (mm-30) cc_final: 0.5904 (mm-30) REVERT: E 106 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6724 (mtt-85) REVERT: E 206 LYS cc_start: 0.8093 (mttp) cc_final: 0.7644 (mttp) REVERT: E 264 GLN cc_start: 0.8478 (tt0) cc_final: 0.8212 (tt0) REVERT: E 299 GLU cc_start: 0.8051 (tt0) cc_final: 0.7436 (tt0) REVERT: E 300 GLU cc_start: 0.8038 (tp30) cc_final: 0.7784 (mm-30) REVERT: E 390 ASP cc_start: 0.8032 (m-30) cc_final: 0.7706 (m-30) REVERT: E 397 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7816 (ttm110) REVERT: E 402 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.5653 (mt-10) outliers start: 28 outliers final: 19 residues processed: 211 average time/residue: 1.6527 time to fit residues: 373.8919 Evaluate side-chains 213 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 188 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 HIS D 98 GLN D 180 GLN D 394 ASN E 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.117596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.093281 restraints weight = 14932.967| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.35 r_work: 0.2718 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 13830 Z= 0.439 Angle : 0.673 7.815 18810 Z= 0.345 Chirality : 0.045 0.174 2245 Planarity : 0.006 0.069 2345 Dihedral : 5.853 52.620 1875 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.05 % Allowed : 12.94 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.20), residues: 1695 helix: 1.33 (0.14), residues: 1415 sheet: None (None), residues: 0 loop : -0.65 (0.32), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 352 HIS 0.008 0.002 HIS E 117 PHE 0.026 0.004 PHE B 146 TYR 0.018 0.003 TYR E 156 ARG 0.009 0.001 ARG D 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5768.63 seconds wall clock time: 100 minutes 59.71 seconds (6059.71 seconds total)