Starting phenix.real_space_refine on Tue Aug 4 12:46:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28lj_56597/08_2026/28lj_56597.cif Found real_map, /net/cci-nas-00/data/ceres_data/28lj_56597/08_2026/28lj_56597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/28lj_56597/08_2026/28lj_56597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28lj_56597/08_2026/28lj_56597.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/28lj_56597/08_2026/28lj_56597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28lj_56597/08_2026/28lj_56597.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 4 5.16 5 C 1848 2.51 5 N 552 2.21 5 O 544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2948 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 737 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Restraints were copied for chains: B, C, D Time building chain proxies: 0.61, per 1000 atoms: 0.21 Number of scatterers: 2948 At special positions: 0 Unit cell: (111.24, 84.872, 42.024, 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 4 16.00 O 544 8.00 N 552 7.00 C 1848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.20 Conformation dependent library (CDL) restraints added in 118.1 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 672 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 81.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 254 through 260 removed outlier: 6.535A pdb=" N ASN A 255 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER B 258 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS A 257 " --> pdb=" O SER B 258 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ILE B 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS A 259 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.671A pdb=" N THR A 263 " --> pdb=" O GLU C 264 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LEU C 266 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASN A 265 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N HIS C 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS A 267 " --> pdb=" O HIS C 268 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR C 263 " --> pdb=" O GLU D 264 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LEU D 266 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN C 265 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N HIS D 268 " --> pdb=" O ASN C 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS C 267 " --> pdb=" O HIS D 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 274 through 310 removed outlier: 6.316A pdb=" N LYS A 274 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE B 308 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.898A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 317 through 320 removed outlier: 6.255A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N SER B 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR A 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.155A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE C 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 336 through 351 removed outlier: 6.963A pdb=" N VAL A 337 " --> pdb=" O GLN B 336 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU B 338 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A 339 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS B 340 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER A 341 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU B 342 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N GLN A 336 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N VAL C 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N GLU A 338 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N SER C 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N LYS A 340 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N LYS C 343 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU A 342 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ASP C 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU A 344 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LYS C 347 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE A 346 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ARG C 349 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASP A 348 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N GLN C 351 " --> pdb=" O ASP A 348 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N GLN C 336 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N VAL D 339 " --> pdb=" O GLN C 336 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N GLU C 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N SER D 341 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N LYS C 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N LYS D 343 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU C 342 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ASP D 345 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU C 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LYS D 347 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE C 346 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ARG D 349 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASP C 348 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N GLN D 351 " --> pdb=" O ASP C 348 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL C 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.322A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 369 through 378 removed outlier: 5.832A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS A 370 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS C 370 " --> pdb=" O LYS D 369 " (cutoff:3.500A) 66 hydrogen bonds defined for protein. 198 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: 0.24 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 611 1.33 - 1.45: 607 1.45 - 1.57: 1770 1.57 - 1.69: 0 1.69 - 1.81: 4 Bond restraints: 2992 Sorted by residual: bond pdb=" C ILE B 308 " pdb=" O ILE B 308 " ideal model delta sigma weight residual 1.236 1.206 0.029 1.01e-02 9.80e+03 8.52e+00 bond pdb=" C ILE C 308 " pdb=" O ILE C 308 " ideal model delta sigma weight residual 1.236 1.206 0.029 1.01e-02 9.80e+03 8.51e+00 bond pdb=" C ILE D 308 " pdb=" O ILE D 308 " ideal model delta sigma weight residual 1.236 1.206 0.029 1.01e-02 9.80e+03 8.50e+00 bond pdb=" C ILE A 308 " pdb=" O ILE A 308 " ideal model delta sigma weight residual 1.236 1.206 0.029 1.01e-02 9.80e+03 8.46e+00 bond pdb=" CG HIS B 362 " pdb=" CD2 HIS B 362 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.34e+00 ... (remaining 2987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 3377 2.51 - 5.02: 483 5.02 - 7.52: 100 7.52 - 10.03: 28 10.03 - 12.54: 8 Bond angle restraints: 3996 Sorted by residual: angle pdb=" C ASN D 359 " pdb=" CA ASN D 359 " pdb=" CB ASN D 359 " ideal model delta sigma weight residual 110.78 98.24 12.54 1.60e+00 3.91e-01 6.14e+01 angle pdb=" C ASN A 359 " pdb=" CA ASN A 359 " pdb=" CB ASN A 359 " ideal model delta sigma weight residual 110.78 98.26 12.52 1.60e+00 3.91e-01 6.12e+01 angle pdb=" C ASN B 359 " pdb=" CA ASN B 359 " pdb=" CB ASN B 359 " ideal model delta sigma weight residual 110.78 98.26 12.52 1.60e+00 3.91e-01 6.12e+01 angle pdb=" C ASN C 359 " pdb=" CA ASN C 359 " pdb=" CB ASN C 359 " ideal model delta sigma weight residual 110.78 98.28 12.50 1.60e+00 3.91e-01 6.11e+01 angle pdb=" C LYS C 340 " pdb=" CA LYS C 340 " pdb=" CB LYS C 340 " ideal model delta sigma weight residual 109.38 121.92 -12.54 2.09e+00 2.29e-01 3.60e+01 ... (remaining 3991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.88: 1484 10.88 - 21.75: 260 21.75 - 32.63: 60 32.63 - 43.50: 24 43.50 - 54.38: 8 Dihedral angle restraints: 1836 sinusoidal: 776 harmonic: 1060 Sorted by residual: dihedral pdb=" C ASN B 359 " pdb=" N ASN B 359 " pdb=" CA ASN B 359 " pdb=" CB ASN B 359 " ideal model delta harmonic sigma weight residual -122.60 -107.40 -15.20 0 2.50e+00 1.60e-01 3.70e+01 dihedral pdb=" C ASN D 359 " pdb=" N ASN D 359 " pdb=" CA ASN D 359 " pdb=" CB ASN D 359 " ideal model delta harmonic sigma weight residual -122.60 -107.40 -15.20 0 2.50e+00 1.60e-01 3.69e+01 dihedral pdb=" C ASN A 359 " pdb=" N ASN A 359 " pdb=" CA ASN A 359 " pdb=" CB ASN A 359 " ideal model delta harmonic sigma weight residual -122.60 -107.41 -15.19 0 2.50e+00 1.60e-01 3.69e+01 ... (remaining 1833 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.077: 232 0.077 - 0.153: 136 0.153 - 0.229: 60 0.229 - 0.305: 12 0.305 - 0.381: 8 Chirality restraints: 448 Sorted by residual: chirality pdb=" CA GLU C 372 " pdb=" N GLU C 372 " pdb=" C GLU C 372 " pdb=" CB GLU C 372 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA GLU B 372 " pdb=" N GLU B 372 " pdb=" C GLU B 372 " pdb=" CB GLU B 372 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CA GLU D 372 " pdb=" N GLU D 372 " pdb=" C GLU D 372 " pdb=" CB GLU D 372 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 445 not shown) Planarity restraints: 508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 310 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C TYR A 310 " 0.037 2.00e-02 2.50e+03 pdb=" O TYR A 310 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS A 311 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 310 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C TYR D 310 " 0.037 2.00e-02 2.50e+03 pdb=" O TYR D 310 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS D 311 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 310 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.59e+00 pdb=" C TYR C 310 " 0.037 2.00e-02 2.50e+03 pdb=" O TYR C 310 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS C 311 " -0.013 2.00e-02 2.50e+03 ... (remaining 505 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.02: 1534 3.02 - 3.49: 2651 3.49 - 3.96: 4258 3.96 - 4.43: 4746 4.43 - 4.90: 10107 Nonbonded interactions: 23296 Sorted by model distance: nonbonded pdb=" O ASN D 359 " pdb=" CB ASN D 359 " model vdw 2.544 2.752 nonbonded pdb=" O ASN A 359 " pdb=" CB ASN A 359 " model vdw 2.544 2.752 nonbonded pdb=" O ASN B 359 " pdb=" CB ASN B 359 " model vdw 2.544 2.752 nonbonded pdb=" O ASN C 359 " pdb=" CB ASN C 359 " model vdw 2.545 2.752 nonbonded pdb=" O ASN A 359 " pdb=" O ASP B 358 " model vdw 2.570 3.040 ... (remaining 23291 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.430 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:5.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 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 : 0.011 0.049 2992 Z= 0.719 Angle : 2.062 12.541 3996 Z= 1.279 Chirality : 0.116 0.381 448 Planarity : 0.009 0.024 508 Dihedral : 12.844 54.377 1164 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.57 % Allowed : 11.90 % Favored : 84.52 % Cbeta Deviations : 3.57 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.26), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.20), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.002 ARG B 379 TYR 0.024 0.012 TYR C 310 PHE 0.014 0.005 PHE C 346 HIS 0.008 0.004 HIS D 329 Details of bonding type rmsd/Z covalent geometry : bond 0.01131 / 0.72 ( 2992) covalent geometry : angle 2.06158 / 1.28 ( 3996) hydrogen bonds : bond 0.14727 / 9.56 ( 66) hydrogen bonds : angle 7.28506 / 5.05 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.073 Fit side-chains REVERT: A 379 ARG cc_start: 0.7536 (mtt90) cc_final: 0.6712 (tpm170) REVERT: B 379 ARG cc_start: 0.7978 (mtt90) cc_final: 0.7137 (tpm170) REVERT: C 331 LYS cc_start: 0.8714 (mttt) cc_final: 0.8236 (ttpt) REVERT: C 379 ARG cc_start: 0.7302 (mtt90) cc_final: 0.6564 (tpm170) REVERT: D 331 LYS cc_start: 0.8721 (mttt) cc_final: 0.8255 (ttpt) REVERT: D 379 ARG cc_start: 0.7635 (mtt90) cc_final: 0.6881 (tpm170) outliers start: 12 outliers final: 2 residues processed: 67 average time/residue: 0.5141 time to fit residues: 35.1081 Evaluate side-chains 44 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain D residue 341 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.0870 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN A 359 ASN A 374 HIS B 336 GLN B 359 ASN B 374 HIS C 336 GLN C 359 ASN C 374 HIS D 359 ASN D 374 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.116270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.097560 restraints weight = 3560.441| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.62 r_work: 0.3753 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2992 Z= 0.131 Angle : 0.715 6.313 3996 Z= 0.354 Chirality : 0.053 0.149 448 Planarity : 0.003 0.017 508 Dihedral : 5.980 44.612 399 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.57 % Allowed : 12.80 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 349 TYR 0.003 0.001 TYR A 310 PHE 0.005 0.001 PHE B 346 HIS 0.002 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 2992) covalent geometry : angle 0.71483 / 0.35 ( 3996) hydrogen bonds : bond 0.02784 / 1.86 ( 66) hydrogen bonds : angle 5.25801 / 3.60 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.150 Fit side-chains REVERT: A 379 ARG cc_start: 0.6804 (mtt90) cc_final: 0.6601 (tpm170) REVERT: B 379 ARG cc_start: 0.7312 (mtt90) cc_final: 0.6919 (tpm170) REVERT: C 325 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7185 (tt) REVERT: C 331 LYS cc_start: 0.8247 (mttt) cc_final: 0.8036 (mtpm) REVERT: D 325 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7465 (tt) REVERT: D 331 LYS cc_start: 0.8151 (mttt) cc_final: 0.7594 (ttpt) REVERT: D 379 ARG cc_start: 0.7009 (mtt90) cc_final: 0.6692 (tpm170) outliers start: 12 outliers final: 2 residues processed: 51 average time/residue: 0.7015 time to fit residues: 36.4116 Evaluate side-chains 40 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 6.9990 chunk 17 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 GLN C 336 GLN D 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.119062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.099134 restraints weight = 3554.405| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.63 r_work: 0.3802 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2992 Z= 0.164 Angle : 0.684 6.435 3996 Z= 0.333 Chirality : 0.052 0.149 448 Planarity : 0.002 0.016 508 Dihedral : 5.450 43.171 398 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.17 % Allowed : 16.07 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.34), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 379 TYR 0.005 0.001 TYR A 310 PHE 0.013 0.002 PHE C 378 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 ( 2992) covalent geometry : angle 0.68369 / 0.33 ( 3996) hydrogen bonds : bond 0.02519 / 1.62 ( 66) hydrogen bonds : angle 4.97237 / 3.45 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.115 Fit side-chains REVERT: A 325 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7454 (tt) REVERT: A 379 ARG cc_start: 0.6721 (mtt90) cc_final: 0.6477 (tpm170) REVERT: C 325 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7092 (tt) REVERT: D 264 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7802 (mt-10) REVERT: D 325 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7400 (tt) REVERT: D 379 ARG cc_start: 0.7036 (mtt90) cc_final: 0.6681 (tpm170) outliers start: 14 outliers final: 4 residues processed: 49 average time/residue: 0.5671 time to fit residues: 28.4150 Evaluate side-chains 41 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 336 GLN D 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.117226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.097405 restraints weight = 3580.935| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.62 r_work: 0.3817 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2992 Z= 0.181 Angle : 0.673 6.691 3996 Z= 0.325 Chirality : 0.052 0.147 448 Planarity : 0.003 0.017 508 Dihedral : 4.848 14.132 396 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.27 % Allowed : 19.05 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.36), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.27), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 379 TYR 0.012 0.002 TYR A 310 PHE 0.008 0.002 PHE B 378 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 2992) covalent geometry : angle 0.67316 / 0.33 ( 3996) hydrogen bonds : bond 0.02245 / 1.43 ( 66) hydrogen bonds : angle 4.78672 / 3.31 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.074 Fit side-chains REVERT: A 325 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7355 (tt) REVERT: A 379 ARG cc_start: 0.6778 (mtt90) cc_final: 0.6506 (tpm170) REVERT: B 379 ARG cc_start: 0.7310 (tmm160) cc_final: 0.6179 (tmm160) REVERT: C 325 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7154 (tt) REVERT: D 325 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7348 (tt) REVERT: D 379 ARG cc_start: 0.7100 (mtt90) cc_final: 0.6682 (tpm170) outliers start: 11 outliers final: 5 residues processed: 41 average time/residue: 0.4583 time to fit residues: 19.4091 Evaluate side-chains 41 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 336 GLN D 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.115788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.096533 restraints weight = 3419.664| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.54 r_work: 0.3731 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2992 Z= 0.155 Angle : 0.617 6.544 3996 Z= 0.298 Chirality : 0.050 0.146 448 Planarity : 0.002 0.015 508 Dihedral : 4.713 13.742 396 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.87 % Allowed : 18.15 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.37), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 379 TYR 0.005 0.001 TYR B 310 PHE 0.005 0.001 PHE D 378 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 ( 2992) covalent geometry : angle 0.61744 / 0.30 ( 3996) hydrogen bonds : bond 0.02051 / 1.31 ( 66) hydrogen bonds : angle 4.65909 / 3.22 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.070 Fit side-chains REVERT: A 325 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7372 (tt) REVERT: A 379 ARG cc_start: 0.6815 (mtt90) cc_final: 0.6466 (tpm170) REVERT: C 325 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7160 (tt) REVERT: D 325 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7260 (tt) REVERT: D 379 ARG cc_start: 0.7025 (mtt90) cc_final: 0.6531 (tpm170) outliers start: 13 outliers final: 6 residues processed: 43 average time/residue: 0.5072 time to fit residues: 22.3964 Evaluate side-chains 41 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.108974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.089310 restraints weight = 3587.137| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.51 r_work: 0.3644 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.053 2992 Z= 0.363 Angle : 0.820 8.049 3996 Z= 0.407 Chirality : 0.057 0.157 448 Planarity : 0.003 0.020 508 Dihedral : 5.199 16.046 396 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.65 % Allowed : 16.67 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.36), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 379 TYR 0.009 0.004 TYR A 310 PHE 0.012 0.003 PHE D 378 HIS 0.008 0.002 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00854 / 0.36 ( 2992) covalent geometry : angle 0.82017 / 0.41 ( 3996) hydrogen bonds : bond 0.02957 / 1.89 ( 66) hydrogen bonds : angle 4.85838 / 3.37 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 31 time to evaluate : 0.135 Fit side-chains REVERT: A 325 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7516 (tt) REVERT: A 379 ARG cc_start: 0.6862 (mtt90) cc_final: 0.6504 (tpm170) REVERT: B 325 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7636 (tt) REVERT: D 325 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7435 (tt) REVERT: D 379 ARG cc_start: 0.7029 (mtt90) cc_final: 0.6546 (tpm170) outliers start: 19 outliers final: 9 residues processed: 43 average time/residue: 0.4573 time to fit residues: 20.2756 Evaluate side-chains 42 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.113603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.093932 restraints weight = 3571.634| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.58 r_work: 0.3690 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2992 Z= 0.179 Angle : 0.671 6.810 3996 Z= 0.321 Chirality : 0.051 0.145 448 Planarity : 0.002 0.021 508 Dihedral : 4.904 15.090 396 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.76 % Allowed : 17.26 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.37), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.007 0.002 TYR A 310 PHE 0.005 0.001 PHE C 378 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 ( 2992) covalent geometry : angle 0.67093 / 0.32 ( 3996) hydrogen bonds : bond 0.02268 / 1.48 ( 66) hydrogen bonds : angle 4.72029 / 3.26 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.114 Fit side-chains REVERT: A 325 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7377 (tt) REVERT: A 379 ARG cc_start: 0.6886 (mtt90) cc_final: 0.6479 (tpm170) REVERT: B 325 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7556 (tt) REVERT: D 325 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7280 (tt) REVERT: D 372 GLU cc_start: 0.8127 (pm20) cc_final: 0.7821 (mp0) REVERT: D 379 ARG cc_start: 0.6942 (mtt90) cc_final: 0.6499 (tpm170) outliers start: 16 outliers final: 9 residues processed: 41 average time/residue: 0.3871 time to fit residues: 16.3687 Evaluate side-chains 44 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.115874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.095632 restraints weight = 3646.874| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.77 r_work: 0.3763 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2992 Z= 0.106 Angle : 0.587 5.941 3996 Z= 0.279 Chirality : 0.049 0.137 448 Planarity : 0.002 0.020 508 Dihedral : 4.570 13.635 396 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.98 % Allowed : 19.35 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.37), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.010 0.002 TYR D 310 PHE 0.003 0.001 PHE B 378 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 2992) covalent geometry : angle 0.58707 / 0.28 ( 3996) hydrogen bonds : bond 0.01727 / 1.14 ( 66) hydrogen bonds : angle 4.45648 / 3.06 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.086 Fit side-chains REVERT: A 325 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7278 (tt) REVERT: A 379 ARG cc_start: 0.6814 (mtt90) cc_final: 0.6462 (tpm170) REVERT: B 325 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7447 (tt) REVERT: D 264 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7703 (mt-10) REVERT: D 325 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7166 (tt) REVERT: D 372 GLU cc_start: 0.8155 (pm20) cc_final: 0.7770 (mp0) REVERT: D 379 ARG cc_start: 0.6901 (mtt90) cc_final: 0.6461 (tpm170) outliers start: 10 outliers final: 2 residues processed: 42 average time/residue: 0.6944 time to fit residues: 29.8230 Evaluate side-chains 38 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.115610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.095445 restraints weight = 3607.271| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.70 r_work: 0.3797 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2992 Z= 0.121 Angle : 0.626 6.833 3996 Z= 0.295 Chirality : 0.049 0.141 448 Planarity : 0.002 0.020 508 Dihedral : 4.495 13.490 396 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.38 % Allowed : 20.54 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.38), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.006 0.001 TYR B 310 PHE 0.014 0.001 PHE B 378 HIS 0.002 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 ( 2992) covalent geometry : angle 0.62638 / 0.29 ( 3996) hydrogen bonds : bond 0.01700 / 1.13 ( 66) hydrogen bonds : angle 4.39927 / 3.02 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.080 Fit side-chains REVERT: A 325 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7237 (tt) REVERT: A 379 ARG cc_start: 0.6824 (mtt90) cc_final: 0.6452 (tpm170) REVERT: B 325 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7396 (tt) REVERT: D 264 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7707 (mt-10) REVERT: D 325 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7136 (tt) REVERT: D 379 ARG cc_start: 0.6924 (mtt90) cc_final: 0.6434 (tpm170) outliers start: 8 outliers final: 2 residues processed: 38 average time/residue: 0.6749 time to fit residues: 26.2337 Evaluate side-chains 37 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 0.0470 chunk 35 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.114274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.094190 restraints weight = 3660.529| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.66 r_work: 0.3777 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2992 Z= 0.159 Angle : 0.666 7.477 3996 Z= 0.315 Chirality : 0.050 0.145 448 Planarity : 0.002 0.021 508 Dihedral : 4.589 14.389 396 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.68 % Allowed : 20.24 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.38), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.011 0.003 TYR D 310 PHE 0.013 0.002 PHE C 378 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 2992) covalent geometry : angle 0.66572 / 0.31 ( 3996) hydrogen bonds : bond 0.01923 / 1.27 ( 66) hydrogen bonds : angle 4.45413 / 3.06 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.072 Fit side-chains REVERT: A 325 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7363 (tt) REVERT: A 379 ARG cc_start: 0.6899 (mtt90) cc_final: 0.6509 (tpm170) REVERT: B 325 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7514 (tt) REVERT: D 325 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7206 (tt) REVERT: D 372 GLU cc_start: 0.8037 (pm20) cc_final: 0.7679 (mp0) REVERT: D 379 ARG cc_start: 0.6979 (mtt90) cc_final: 0.6478 (tpm170) outliers start: 9 outliers final: 5 residues processed: 34 average time/residue: 0.5122 time to fit residues: 17.8350 Evaluate side-chains 37 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.112306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.092326 restraints weight = 3653.120| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.63 r_work: 0.3740 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2992 Z= 0.219 Angle : 0.719 8.055 3996 Z= 0.343 Chirality : 0.051 0.146 448 Planarity : 0.003 0.020 508 Dihedral : 4.763 15.371 396 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.68 % Allowed : 20.24 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.38), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.009 0.002 TYR B 310 PHE 0.012 0.002 PHE C 378 HIS 0.005 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 ( 2992) covalent geometry : angle 0.71938 / 0.34 ( 3996) hydrogen bonds : bond 0.02235 / 1.47 ( 66) hydrogen bonds : angle 4.56338 / 3.13 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1320.52 seconds wall clock time: 23 minutes 12.93 seconds (1392.93 seconds total)