Starting phenix.real_space_refine on Fri Aug 22 13:42:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7f_18215/08_2025/8q7f_18215.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7f_18215/08_2025/8q7f_18215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q7f_18215/08_2025/8q7f_18215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7f_18215/08_2025/8q7f_18215.map" model { file = "/net/cci-nas-00/data/ceres_data/8q7f_18215/08_2025/8q7f_18215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7f_18215/08_2025/8q7f_18215.cif" } resolution = 3.72 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= 0.003 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 6 5.16 5 C 2136 2.51 5 N 618 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3402 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "A" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 1.06, per 1000 atoms: 0.31 Number of scatterers: 3402 At special positions: 0 Unit cell: (106.142, 107.596, 37.804, 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 6 16.00 O 642 8.00 N 618 7.00 C 2136 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 80.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 53.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 305 through 310 removed outlier: 6.581A pdb=" N SER B 305 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE D 308 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.992A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.326A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.448A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.652A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER B 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.687A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE B 346 " --> pdb=" O ASP F 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.612A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.715A pdb=" N LEU B 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ILE F 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASN B 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N HIS F 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 368 through 377 removed outlier: 6.555A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 305 through 310 removed outlier: 6.581A pdb=" N SER A 305 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE C 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.991A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.326A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER C 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY A 323 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.448A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.653A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.823A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.381A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.732A pdb=" N LEU A 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ILE E 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASN A 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N HIS E 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 368 through 377 88 hydrogen bonds defined for protein. 264 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: 0.29 Time building geometry restraints manager: 0.29 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: 708 1.33 - 1.45: 664 1.45 - 1.57: 2078 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3456 Sorted by residual: bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.72e+00 bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.51e+00 bond pdb=" CA ASP F 345 " pdb=" C ASP F 345 " ideal model delta sigma weight residual 1.521 1.552 -0.031 1.20e-02 6.94e+03 6.76e+00 bond pdb=" CZ ARG B 349 " pdb=" NH2 ARG B 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.73e+00 ... (remaining 3451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 2859 1.59 - 3.17: 1338 3.17 - 4.76: 361 4.76 - 6.35: 62 6.35 - 7.93: 6 Bond angle restraints: 4626 Sorted by residual: angle pdb=" CA PHE F 346 " pdb=" CB PHE F 346 " pdb=" CG PHE F 346 " ideal model delta sigma weight residual 113.80 121.73 -7.93 1.00e+00 1.00e+00 6.29e+01 angle pdb=" CA ASP F 358 " pdb=" CB ASP F 358 " pdb=" CG ASP F 358 " ideal model delta sigma weight residual 112.60 118.20 -5.60 1.00e+00 1.00e+00 3.14e+01 angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 119.13 -5.33 1.00e+00 1.00e+00 2.84e+01 angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 117.89 -5.29 1.00e+00 1.00e+00 2.79e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 117.82 -5.22 1.00e+00 1.00e+00 2.72e+01 ... (remaining 4621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 1972 17.23 - 34.47: 82 34.47 - 51.70: 28 51.70 - 68.93: 4 68.93 - 86.17: 8 Dihedral angle restraints: 2094 sinusoidal: 864 harmonic: 1230 Sorted by residual: dihedral pdb=" CA SER E 356 " pdb=" C SER E 356 " pdb=" N LEU E 357 " pdb=" CA LEU E 357 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA LYS C 347 " pdb=" C LYS C 347 " pdb=" N ASP C 348 " pdb=" CA ASP C 348 " ideal model delta harmonic sigma weight residual -180.00 -151.73 -28.27 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LYS D 347 " pdb=" C LYS D 347 " pdb=" N ASP D 348 " pdb=" CA ASP D 348 " ideal model delta harmonic sigma weight residual -180.00 -151.77 -28.23 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 2091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 362 0.088 - 0.175: 129 0.175 - 0.263: 17 0.263 - 0.350: 11 0.350 - 0.437: 3 Chirality restraints: 522 Sorted by residual: chirality pdb=" CA LYS E 343 " pdb=" N LYS E 343 " pdb=" C LYS E 343 " pdb=" CB LYS E 343 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA LYS F 343 " pdb=" N LYS F 343 " pdb=" C LYS F 343 " pdb=" CB LYS F 343 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" CA PHE F 346 " pdb=" N PHE F 346 " pdb=" C PHE F 346 " pdb=" CB PHE F 346 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 519 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.129 2.00e-02 2.50e+03 7.14e-02 1.02e+02 pdb=" CG TYR A 310 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " -0.117 2.00e-02 2.50e+03 6.38e-02 8.15e+01 pdb=" CG TYR B 310 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " -0.110 2.00e-02 2.50e+03 6.25e-02 7.81e+01 pdb=" CG TYR F 310 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " -0.102 2.00e-02 2.50e+03 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1477 2.97 - 3.46: 2642 3.46 - 3.94: 5446 3.94 - 4.42: 5403 4.42 - 4.90: 10518 Nonbonded interactions: 25486 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.492 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.504 3.040 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.508 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.508 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.567 3.040 ... (remaining 25481 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' selection = chain 'F' } 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 group one per residue 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: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.740 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 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 0.044 3456 Z= 0.708 Angle : 1.876 7.933 4626 Z= 1.252 Chirality : 0.099 0.437 522 Planarity : 0.011 0.071 588 Dihedral : 12.868 86.167 1314 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.51 % 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 aren not related in a simple way. whole: -1.74 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG C 349 TYR 0.129 0.046 TYR A 310 PHE 0.063 0.013 PHE E 346 HIS 0.006 0.002 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.01121 ( 3456) covalent geometry : angle 1.87618 ( 4626) hydrogen bonds : bond 0.10371 ( 88) hydrogen bonds : angle 7.62140 ( 264) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.089 Fit side-chains REVERT: B 325 LEU cc_start: 0.7851 (mp) cc_final: 0.7613 (mt) REVERT: B 337 VAL cc_start: 0.8207 (t) cc_final: 0.7963 (p) REVERT: B 338 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7149 (tm-30) REVERT: B 340 LYS cc_start: 0.7414 (tttt) cc_final: 0.7091 (mttm) REVERT: B 345 ASP cc_start: 0.7560 (t0) cc_final: 0.6947 (t70) REVERT: B 347 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7402 (mmtt) REVERT: B 375 LYS cc_start: 0.7749 (tttt) cc_final: 0.7047 (tttm) REVERT: D 311 LYS cc_start: 0.8160 (mttt) cc_final: 0.7846 (mttp) REVERT: D 331 LYS cc_start: 0.8258 (mttt) cc_final: 0.7683 (mtpt) REVERT: D 340 LYS cc_start: 0.7824 (tttt) cc_final: 0.7336 (mtpt) REVERT: D 375 LYS cc_start: 0.8314 (tttt) cc_final: 0.7801 (tttp) REVERT: F 311 LYS cc_start: 0.7389 (mttt) cc_final: 0.6788 (tppt) REVERT: F 331 LYS cc_start: 0.8102 (mttt) cc_final: 0.7335 (mtpp) REVERT: F 338 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6972 (tt0) REVERT: F 340 LYS cc_start: 0.7464 (tttt) cc_final: 0.6987 (mttm) REVERT: F 349 ARG cc_start: 0.6727 (mmt90) cc_final: 0.5364 (mmp-170) REVERT: F 362 HIS cc_start: 0.7671 (t-170) cc_final: 0.7449 (m-70) REVERT: F 375 LYS cc_start: 0.7625 (tttt) cc_final: 0.7056 (tttm) REVERT: A 331 LYS cc_start: 0.8133 (mttt) cc_final: 0.7763 (mttp) REVERT: A 349 ARG cc_start: 0.7415 (mmt90) cc_final: 0.6465 (mmm160) REVERT: A 351 GLN cc_start: 0.6186 (mp10) cc_final: 0.5765 (mt0) REVERT: A 369 LYS cc_start: 0.7461 (tttt) cc_final: 0.6668 (ttmm) REVERT: C 311 LYS cc_start: 0.8106 (mttt) cc_final: 0.7794 (mtpp) REVERT: C 316 SER cc_start: 0.8199 (p) cc_final: 0.7999 (p) REVERT: C 349 ARG cc_start: 0.7078 (mmt90) cc_final: 0.6402 (mtm180) REVERT: C 361 THR cc_start: 0.8773 (m) cc_final: 0.8568 (m) REVERT: C 369 LYS cc_start: 0.7628 (tttt) cc_final: 0.6976 (ttmm) REVERT: C 375 LYS cc_start: 0.7418 (tttt) cc_final: 0.6951 (tttm) REVERT: E 311 LYS cc_start: 0.7634 (mttt) cc_final: 0.6977 (mmtt) REVERT: E 342 GLU cc_start: 0.7776 (pt0) cc_final: 0.6898 (mm-30) REVERT: E 369 LYS cc_start: 0.7369 (tttt) cc_final: 0.6375 (mtpt) REVERT: E 375 LYS cc_start: 0.6512 (tttt) cc_final: 0.6206 (tttm) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.0974 time to fit residues: 16.1624 Evaluate side-chains 107 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.0980 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS D 327 ASN F 329 HIS C 327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.152029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.141599 restraints weight = 4817.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.143907 restraints weight = 2425.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.145459 restraints weight = 1494.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.146492 restraints weight = 1042.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.147179 restraints weight = 793.934| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3456 Z= 0.168 Angle : 0.676 4.753 4626 Z= 0.355 Chirality : 0.053 0.133 522 Planarity : 0.004 0.047 588 Dihedral : 6.060 21.815 456 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.03 % Allowed : 7.44 % Favored : 91.54 % 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 aren not related in a simple way. whole: -1.13 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.85 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 349 TYR 0.011 0.003 TYR A 310 PHE 0.018 0.002 PHE F 346 HIS 0.006 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 3456) covalent geometry : angle 0.67614 ( 4626) hydrogen bonds : bond 0.02768 ( 88) hydrogen bonds : angle 6.07286 ( 264) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: B 345 ASP cc_start: 0.8102 (t0) cc_final: 0.7508 (t70) REVERT: B 375 LYS cc_start: 0.8401 (tttt) cc_final: 0.7848 (tttm) REVERT: D 315 LEU cc_start: 0.8581 (mp) cc_final: 0.8234 (mt) REVERT: D 331 LYS cc_start: 0.8271 (mttt) cc_final: 0.7948 (mttm) REVERT: D 347 LYS cc_start: 0.7601 (mmtt) cc_final: 0.6623 (mtmm) REVERT: D 375 LYS cc_start: 0.8352 (tttt) cc_final: 0.8098 (tttp) REVERT: F 331 LYS cc_start: 0.8130 (mttt) cc_final: 0.7538 (mtpp) REVERT: F 337 VAL cc_start: 0.8257 (t) cc_final: 0.8032 (m) REVERT: F 349 ARG cc_start: 0.7084 (mmt90) cc_final: 0.6312 (mmp-170) REVERT: A 316 SER cc_start: 0.8917 (p) cc_final: 0.8701 (p) REVERT: A 348 ASP cc_start: 0.7353 (t0) cc_final: 0.7143 (t0) REVERT: A 369 LYS cc_start: 0.7704 (tttt) cc_final: 0.6984 (ttmm) REVERT: C 369 LYS cc_start: 0.7568 (tttt) cc_final: 0.6986 (ttmm) REVERT: E 311 LYS cc_start: 0.7779 (mttt) cc_final: 0.7275 (mmmt) REVERT: E 369 LYS cc_start: 0.7808 (tttt) cc_final: 0.7147 (mtpt) outliers start: 4 outliers final: 4 residues processed: 117 average time/residue: 0.0716 time to fit residues: 9.8774 Evaluate side-chains 112 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain F residue 353 LYS Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 378 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.0470 chunk 31 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.144986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.134187 restraints weight = 4859.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.136252 restraints weight = 2501.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.137717 restraints weight = 1594.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.138506 restraints weight = 1149.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.139244 restraints weight = 937.711| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3456 Z= 0.183 Angle : 0.660 4.582 4626 Z= 0.344 Chirality : 0.052 0.153 522 Planarity : 0.003 0.028 588 Dihedral : 5.612 19.574 456 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.54 % Allowed : 12.31 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.88 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 349 TYR 0.018 0.004 TYR A 310 PHE 0.019 0.002 PHE F 346 HIS 0.005 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 3456) covalent geometry : angle 0.65976 ( 4626) hydrogen bonds : bond 0.02531 ( 88) hydrogen bonds : angle 5.67768 ( 264) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.139 Fit side-chains REVERT: B 315 LEU cc_start: 0.8579 (mp) cc_final: 0.8157 (mt) REVERT: B 345 ASP cc_start: 0.8133 (t0) cc_final: 0.7633 (t70) REVERT: B 375 LYS cc_start: 0.8425 (tttt) cc_final: 0.7973 (tttm) REVERT: D 315 LEU cc_start: 0.8696 (mp) cc_final: 0.8359 (mt) REVERT: D 331 LYS cc_start: 0.8304 (mttt) cc_final: 0.8059 (mttm) REVERT: D 347 LYS cc_start: 0.7954 (mmtt) cc_final: 0.6780 (mtmm) REVERT: D 349 ARG cc_start: 0.7672 (mmt90) cc_final: 0.7235 (mtt90) REVERT: D 375 LYS cc_start: 0.8378 (tttt) cc_final: 0.8105 (tttp) REVERT: F 337 VAL cc_start: 0.8244 (t) cc_final: 0.8015 (m) REVERT: F 349 ARG cc_start: 0.7264 (mmt90) cc_final: 0.6380 (mmp-170) REVERT: F 362 HIS cc_start: 0.7614 (OUTLIER) cc_final: 0.6815 (m90) REVERT: F 375 LYS cc_start: 0.8514 (tttt) cc_final: 0.8209 (tttm) REVERT: A 316 SER cc_start: 0.9030 (p) cc_final: 0.8813 (p) REVERT: A 369 LYS cc_start: 0.7895 (tttt) cc_final: 0.7218 (ttmm) REVERT: C 369 LYS cc_start: 0.7821 (tttt) cc_final: 0.7300 (mtpt) REVERT: E 349 ARG cc_start: 0.6621 (mmt90) cc_final: 0.5248 (mmp-170) REVERT: E 369 LYS cc_start: 0.7886 (tttt) cc_final: 0.7289 (mtpt) outliers start: 6 outliers final: 5 residues processed: 107 average time/residue: 0.0833 time to fit residues: 10.4419 Evaluate side-chains 106 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain F residue 362 HIS Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 378 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 30 optimal weight: 0.0030 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.146260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.135541 restraints weight = 4817.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.137629 restraints weight = 2524.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.139018 restraints weight = 1619.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.139847 restraints weight = 1181.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.140466 restraints weight = 962.252| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3456 Z= 0.186 Angle : 0.656 6.206 4626 Z= 0.339 Chirality : 0.051 0.150 522 Planarity : 0.003 0.035 588 Dihedral : 5.445 17.792 456 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 3.08 % Allowed : 11.79 % Favored : 85.13 % 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 aren not related in a simple way. whole: -1.31 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.018 0.003 TYR A 310 PHE 0.014 0.001 PHE F 346 HIS 0.005 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 3456) covalent geometry : angle 0.65643 ( 4626) hydrogen bonds : bond 0.02353 ( 88) hydrogen bonds : angle 5.53300 ( 264) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.138 Fit side-chains REVERT: B 315 LEU cc_start: 0.8623 (mp) cc_final: 0.8178 (mt) REVERT: B 345 ASP cc_start: 0.8131 (t0) cc_final: 0.7681 (t70) REVERT: B 375 LYS cc_start: 0.8416 (tttt) cc_final: 0.8002 (tttm) REVERT: D 315 LEU cc_start: 0.8689 (mp) cc_final: 0.8352 (mt) REVERT: D 331 LYS cc_start: 0.8339 (mttt) cc_final: 0.8095 (mttm) REVERT: D 347 LYS cc_start: 0.7972 (mmtt) cc_final: 0.6825 (mtmm) REVERT: D 375 LYS cc_start: 0.8381 (tttt) cc_final: 0.8123 (tttp) REVERT: F 331 LYS cc_start: 0.8071 (mttt) cc_final: 0.7516 (mtpp) REVERT: F 337 VAL cc_start: 0.8255 (t) cc_final: 0.8047 (m) REVERT: F 349 ARG cc_start: 0.7286 (mmt90) cc_final: 0.6351 (mmp-170) REVERT: F 375 LYS cc_start: 0.8518 (tttt) cc_final: 0.8230 (tttm) REVERT: A 369 LYS cc_start: 0.7898 (tttt) cc_final: 0.7201 (ttmm) REVERT: C 369 LYS cc_start: 0.7796 (tttt) cc_final: 0.7285 (mtpt) REVERT: E 342 GLU cc_start: 0.4408 (mm-30) cc_final: 0.4196 (pt0) REVERT: E 349 ARG cc_start: 0.6653 (mmt90) cc_final: 0.5284 (mmp-170) REVERT: E 369 LYS cc_start: 0.7919 (tttt) cc_final: 0.7277 (mtpt) REVERT: E 375 LYS cc_start: 0.8604 (tttt) cc_final: 0.8381 (tttt) outliers start: 12 outliers final: 10 residues processed: 104 average time/residue: 0.0883 time to fit residues: 10.6929 Evaluate side-chains 108 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain F residue 362 HIS Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain E residue 378 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 0.1980 chunk 9 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.147355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.136331 restraints weight = 4812.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.138553 restraints weight = 2484.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.140011 restraints weight = 1568.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.140909 restraints weight = 1137.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.141575 restraints weight = 920.795| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3456 Z= 0.144 Angle : 0.607 6.628 4626 Z= 0.309 Chirality : 0.051 0.145 522 Planarity : 0.003 0.045 588 Dihedral : 5.138 14.960 456 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 2.56 % Allowed : 13.59 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.015 0.002 TYR A 310 PHE 0.011 0.001 PHE F 346 HIS 0.004 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3456) covalent geometry : angle 0.60689 ( 4626) hydrogen bonds : bond 0.02206 ( 88) hydrogen bonds : angle 5.35667 ( 264) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.106 Fit side-chains REVERT: B 331 LYS cc_start: 0.8237 (mttt) cc_final: 0.7882 (mttm) REVERT: B 345 ASP cc_start: 0.8109 (t0) cc_final: 0.7707 (t70) REVERT: B 375 LYS cc_start: 0.8395 (tttt) cc_final: 0.7990 (tttm) REVERT: D 315 LEU cc_start: 0.8616 (mp) cc_final: 0.8291 (mt) REVERT: D 331 LYS cc_start: 0.8303 (mttt) cc_final: 0.8093 (mttm) REVERT: D 347 LYS cc_start: 0.7916 (mmtt) cc_final: 0.6695 (mtmm) REVERT: D 349 ARG cc_start: 0.7564 (mtt90) cc_final: 0.7058 (mtt90) REVERT: D 375 LYS cc_start: 0.8372 (tttt) cc_final: 0.8105 (tttp) REVERT: F 331 LYS cc_start: 0.8074 (mttt) cc_final: 0.7506 (mtpp) REVERT: F 349 ARG cc_start: 0.7342 (mmt90) cc_final: 0.6359 (mmp-170) REVERT: F 375 LYS cc_start: 0.8542 (tttt) cc_final: 0.8286 (tttm) REVERT: A 369 LYS cc_start: 0.7875 (tttt) cc_final: 0.7127 (ttmm) REVERT: C 369 LYS cc_start: 0.7732 (tttt) cc_final: 0.7093 (ttmm) REVERT: E 342 GLU cc_start: 0.4304 (mm-30) cc_final: 0.3836 (pt0) REVERT: E 349 ARG cc_start: 0.6547 (mmt90) cc_final: 0.5537 (mmp-170) REVERT: E 369 LYS cc_start: 0.7911 (tttt) cc_final: 0.7270 (mtpt) outliers start: 10 outliers final: 7 residues processed: 106 average time/residue: 0.0814 time to fit residues: 9.9670 Evaluate side-chains 104 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain E residue 378 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 23 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS C 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.149148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.138202 restraints weight = 4695.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.140286 restraints weight = 2426.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.141829 restraints weight = 1541.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.142648 restraints weight = 1109.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.143340 restraints weight = 902.591| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3456 Z= 0.111 Angle : 0.599 6.551 4626 Z= 0.301 Chirality : 0.050 0.138 522 Planarity : 0.003 0.051 588 Dihedral : 4.829 14.210 456 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.54 % Allowed : 14.10 % Favored : 84.36 % 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 aren not related in a simple way. whole: -1.46 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.022 0.003 TYR B 310 PHE 0.009 0.001 PHE F 346 HIS 0.004 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 3456) covalent geometry : angle 0.59910 ( 4626) hydrogen bonds : bond 0.02026 ( 88) hydrogen bonds : angle 5.22168 ( 264) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.085 Fit side-chains REVERT: B 315 LEU cc_start: 0.8569 (mp) cc_final: 0.8287 (mt) REVERT: B 331 LYS cc_start: 0.8193 (mttt) cc_final: 0.7868 (mttm) REVERT: B 345 ASP cc_start: 0.8061 (t0) cc_final: 0.7679 (t70) REVERT: B 375 LYS cc_start: 0.8372 (tttt) cc_final: 0.8125 (tttp) REVERT: D 315 LEU cc_start: 0.8589 (mp) cc_final: 0.8310 (mt) REVERT: D 331 LYS cc_start: 0.8266 (mttt) cc_final: 0.8064 (mttm) REVERT: D 340 LYS cc_start: 0.8296 (mtpt) cc_final: 0.8009 (mttm) REVERT: D 347 LYS cc_start: 0.7767 (mmtt) cc_final: 0.6585 (mtmm) REVERT: D 375 LYS cc_start: 0.8308 (tttt) cc_final: 0.8049 (tttp) REVERT: F 331 LYS cc_start: 0.8046 (mttt) cc_final: 0.7445 (mtpp) REVERT: F 349 ARG cc_start: 0.7305 (mmt90) cc_final: 0.6315 (mmp-170) REVERT: F 375 LYS cc_start: 0.8544 (tttt) cc_final: 0.8298 (tttm) REVERT: A 369 LYS cc_start: 0.7711 (tttt) cc_final: 0.7105 (ttmm) REVERT: C 369 LYS cc_start: 0.7720 (tttt) cc_final: 0.7072 (ttmm) REVERT: E 342 GLU cc_start: 0.4224 (mm-30) cc_final: 0.3792 (pt0) REVERT: E 349 ARG cc_start: 0.6341 (mmt90) cc_final: 0.5070 (mmp-170) REVERT: E 369 LYS cc_start: 0.7891 (tttt) cc_final: 0.7259 (mtpt) REVERT: E 375 LYS cc_start: 0.8603 (tttt) cc_final: 0.8046 (tmtt) outliers start: 6 outliers final: 5 residues processed: 103 average time/residue: 0.0843 time to fit residues: 10.0231 Evaluate side-chains 104 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain E residue 378 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 0.0070 chunk 8 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN C 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.146097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.135350 restraints weight = 4953.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.137462 restraints weight = 2574.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.138895 restraints weight = 1634.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.139815 restraints weight = 1184.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.140341 restraints weight = 943.338| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3456 Z= 0.170 Angle : 0.626 6.363 4626 Z= 0.322 Chirality : 0.051 0.153 522 Planarity : 0.003 0.052 588 Dihedral : 5.054 15.230 456 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 2.82 % Allowed : 14.36 % Favored : 82.82 % 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 aren not related in a simple way. whole: -1.53 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.015 0.003 TYR A 310 PHE 0.012 0.001 PHE F 346 HIS 0.004 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 3456) covalent geometry : angle 0.62609 ( 4626) hydrogen bonds : bond 0.02202 ( 88) hydrogen bonds : angle 5.25156 ( 264) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: B 315 LEU cc_start: 0.8703 (mp) cc_final: 0.8282 (mt) REVERT: B 331 LYS cc_start: 0.8244 (mttt) cc_final: 0.7897 (mttm) REVERT: B 345 ASP cc_start: 0.8038 (t0) cc_final: 0.7656 (t70) REVERT: D 315 LEU cc_start: 0.8711 (mp) cc_final: 0.8367 (mt) REVERT: D 331 LYS cc_start: 0.8318 (mttt) cc_final: 0.8111 (mttm) REVERT: D 336 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.6817 (pt0) REVERT: D 340 LYS cc_start: 0.8313 (mtpt) cc_final: 0.7995 (mttm) REVERT: D 347 LYS cc_start: 0.7981 (mmtt) cc_final: 0.6731 (mtmm) REVERT: D 375 LYS cc_start: 0.8334 (tttt) cc_final: 0.8049 (tttp) REVERT: F 331 LYS cc_start: 0.8162 (mttt) cc_final: 0.7602 (mttm) REVERT: F 349 ARG cc_start: 0.7397 (mmt90) cc_final: 0.6155 (mmm160) REVERT: F 375 LYS cc_start: 0.8551 (tttt) cc_final: 0.8270 (tttm) REVERT: A 369 LYS cc_start: 0.7805 (tttt) cc_final: 0.7158 (ttmm) REVERT: C 369 LYS cc_start: 0.7756 (tttt) cc_final: 0.7102 (ttmm) REVERT: E 342 GLU cc_start: 0.4427 (mm-30) cc_final: 0.3566 (pm20) REVERT: E 349 ARG cc_start: 0.6419 (mmt90) cc_final: 0.5001 (mmp-170) REVERT: E 369 LYS cc_start: 0.7895 (tttt) cc_final: 0.7302 (mtpt) REVERT: E 375 LYS cc_start: 0.8652 (tttt) cc_final: 0.8135 (tmtt) outliers start: 11 outliers final: 9 residues processed: 106 average time/residue: 0.0906 time to fit residues: 11.0680 Evaluate side-chains 111 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain E residue 378 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN C 359 ASN E 329 HIS E 359 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.144575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.133794 restraints weight = 4996.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.135879 restraints weight = 2604.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.137324 restraints weight = 1669.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.138265 restraints weight = 1205.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.138801 restraints weight = 957.983| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3456 Z= 0.197 Angle : 0.648 6.105 4626 Z= 0.334 Chirality : 0.051 0.147 522 Planarity : 0.004 0.058 588 Dihedral : 5.173 16.562 456 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 2.56 % Allowed : 15.38 % Favored : 82.05 % 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 aren not related in a simple way. whole: -1.60 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 349 TYR 0.016 0.003 TYR A 310 PHE 0.011 0.002 PHE F 346 HIS 0.004 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 3456) covalent geometry : angle 0.64790 ( 4626) hydrogen bonds : bond 0.02285 ( 88) hydrogen bonds : angle 5.30537 ( 264) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.149 Fit side-chains REVERT: B 315 LEU cc_start: 0.8691 (mp) cc_final: 0.8286 (mt) REVERT: B 331 LYS cc_start: 0.8289 (mttt) cc_final: 0.7971 (mttm) REVERT: B 336 GLN cc_start: 0.8331 (mm110) cc_final: 0.8017 (mm110) REVERT: B 345 ASP cc_start: 0.7993 (t0) cc_final: 0.7692 (t70) REVERT: B 375 LYS cc_start: 0.8396 (tttt) cc_final: 0.8012 (tttm) REVERT: D 315 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8410 (mt) REVERT: D 331 LYS cc_start: 0.8320 (mttt) cc_final: 0.8116 (mttm) REVERT: D 336 GLN cc_start: 0.7442 (mm110) cc_final: 0.6806 (pt0) REVERT: D 347 LYS cc_start: 0.8074 (mmtt) cc_final: 0.6762 (mtmm) REVERT: D 375 LYS cc_start: 0.8342 (tttt) cc_final: 0.8053 (tttp) REVERT: F 331 LYS cc_start: 0.8136 (mttt) cc_final: 0.7643 (mttm) REVERT: F 347 LYS cc_start: 0.7420 (mmtm) cc_final: 0.7109 (mmtt) REVERT: F 349 ARG cc_start: 0.7465 (mmt90) cc_final: 0.6191 (mmm160) REVERT: F 375 LYS cc_start: 0.8541 (tttt) cc_final: 0.8292 (tttm) REVERT: A 369 LYS cc_start: 0.7840 (tttt) cc_final: 0.7179 (ttmm) REVERT: C 369 LYS cc_start: 0.7789 (tttt) cc_final: 0.7128 (ttmm) REVERT: E 342 GLU cc_start: 0.4606 (mm-30) cc_final: 0.3469 (pm20) REVERT: E 349 ARG cc_start: 0.6423 (mmt90) cc_final: 0.5088 (mmp-170) REVERT: E 369 LYS cc_start: 0.7905 (tttt) cc_final: 0.7313 (mtpt) REVERT: E 375 LYS cc_start: 0.8654 (tttt) cc_final: 0.8135 (tmtt) outliers start: 10 outliers final: 9 residues processed: 104 average time/residue: 0.0932 time to fit residues: 11.2145 Evaluate side-chains 111 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain E residue 378 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 329 HIS C 359 ASN E 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.143439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.132503 restraints weight = 4835.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.134649 restraints weight = 2527.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.136047 restraints weight = 1614.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.136983 restraints weight = 1174.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.137560 restraints weight = 940.873| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3456 Z= 0.215 Angle : 0.668 5.988 4626 Z= 0.346 Chirality : 0.052 0.151 522 Planarity : 0.004 0.059 588 Dihedral : 5.327 16.397 456 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 2.31 % Allowed : 16.41 % Favored : 81.28 % 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 aren not related in a simple way. whole: -1.70 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 349 TYR 0.017 0.003 TYR A 310 PHE 0.012 0.002 PHE F 346 HIS 0.004 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 3456) covalent geometry : angle 0.66813 ( 4626) hydrogen bonds : bond 0.02367 ( 88) hydrogen bonds : angle 5.36766 ( 264) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: B 315 LEU cc_start: 0.8691 (mp) cc_final: 0.8302 (mt) REVERT: B 336 GLN cc_start: 0.8373 (mm110) cc_final: 0.8025 (mm110) REVERT: B 345 ASP cc_start: 0.7974 (t0) cc_final: 0.7740 (t70) REVERT: B 375 LYS cc_start: 0.8400 (tttt) cc_final: 0.7987 (tttm) REVERT: D 331 LYS cc_start: 0.8386 (mttt) cc_final: 0.8176 (mttm) REVERT: D 336 GLN cc_start: 0.7586 (mm110) cc_final: 0.6811 (pt0) REVERT: D 347 LYS cc_start: 0.8275 (mmtt) cc_final: 0.7048 (mtmt) REVERT: D 375 LYS cc_start: 0.8322 (tttt) cc_final: 0.8019 (tttp) REVERT: F 331 LYS cc_start: 0.8152 (mttt) cc_final: 0.7694 (mttm) REVERT: F 347 LYS cc_start: 0.7424 (mmtm) cc_final: 0.7137 (mmtt) REVERT: F 349 ARG cc_start: 0.7535 (mmt90) cc_final: 0.6190 (mmm160) REVERT: A 369 LYS cc_start: 0.7835 (tttt) cc_final: 0.7292 (ttmm) REVERT: C 369 LYS cc_start: 0.7812 (tttt) cc_final: 0.7133 (ttmm) REVERT: E 349 ARG cc_start: 0.6530 (mmt90) cc_final: 0.5076 (mmp-170) REVERT: E 369 LYS cc_start: 0.7907 (tttt) cc_final: 0.7274 (ttmm) REVERT: E 375 LYS cc_start: 0.8676 (tttt) cc_final: 0.8150 (tmtt) outliers start: 9 outliers final: 8 residues processed: 104 average time/residue: 0.0980 time to fit residues: 11.7231 Evaluate side-chains 107 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain E residue 378 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 13 optimal weight: 0.0570 chunk 9 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 ASN E 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.146342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.135454 restraints weight = 4819.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.137638 restraints weight = 2488.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.139052 restraints weight = 1569.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.139988 restraints weight = 1131.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.140562 restraints weight = 902.574| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3456 Z= 0.140 Angle : 0.618 5.795 4626 Z= 0.313 Chirality : 0.051 0.145 522 Planarity : 0.003 0.060 588 Dihedral : 5.023 15.167 456 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.79 % Allowed : 16.67 % Favored : 81.54 % 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 aren not related in a simple way. whole: -1.68 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.013 0.002 TYR A 310 PHE 0.009 0.001 PHE F 346 HIS 0.003 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3456) covalent geometry : angle 0.61837 ( 4626) hydrogen bonds : bond 0.02102 ( 88) hydrogen bonds : angle 5.22820 ( 264) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: B 315 LEU cc_start: 0.8711 (mp) cc_final: 0.8232 (mt) REVERT: B 331 LYS cc_start: 0.8271 (mttt) cc_final: 0.7905 (mttm) REVERT: B 336 GLN cc_start: 0.8407 (mm110) cc_final: 0.8128 (mm110) REVERT: B 345 ASP cc_start: 0.7970 (t0) cc_final: 0.7727 (t70) REVERT: D 315 LEU cc_start: 0.8662 (mp) cc_final: 0.8338 (mt) REVERT: D 331 LYS cc_start: 0.8357 (mttt) cc_final: 0.8153 (mttm) REVERT: D 336 GLN cc_start: 0.7444 (mm110) cc_final: 0.6700 (pt0) REVERT: D 340 LYS cc_start: 0.8296 (mtpt) cc_final: 0.7992 (mttm) REVERT: D 347 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7022 (mtmt) REVERT: D 375 LYS cc_start: 0.8239 (tttt) cc_final: 0.7984 (tttp) REVERT: F 331 LYS cc_start: 0.8120 (mttt) cc_final: 0.7637 (mttm) REVERT: F 347 LYS cc_start: 0.7178 (mmtm) cc_final: 0.6913 (mmtt) REVERT: F 349 ARG cc_start: 0.7499 (mmt90) cc_final: 0.6168 (mmm160) REVERT: F 375 LYS cc_start: 0.8533 (tttt) cc_final: 0.8254 (tttm) REVERT: A 331 LYS cc_start: 0.8127 (mttt) cc_final: 0.7638 (mttp) REVERT: A 369 LYS cc_start: 0.7812 (tttt) cc_final: 0.7198 (ttmm) REVERT: C 369 LYS cc_start: 0.7759 (tttt) cc_final: 0.7082 (ttmm) REVERT: E 349 ARG cc_start: 0.6513 (mmt90) cc_final: 0.5053 (mmp-170) REVERT: E 369 LYS cc_start: 0.7888 (tttt) cc_final: 0.7266 (mtpt) REVERT: E 375 LYS cc_start: 0.8643 (tttt) cc_final: 0.8140 (tmtt) outliers start: 7 outliers final: 7 residues processed: 102 average time/residue: 0.0981 time to fit residues: 11.4622 Evaluate side-chains 107 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain E residue 378 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.0870 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 ASN E 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.143593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.132596 restraints weight = 4879.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.134743 restraints weight = 2558.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.136186 restraints weight = 1623.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.137129 restraints weight = 1172.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.137740 restraints weight = 932.722| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3456 Z= 0.210 Angle : 0.671 6.188 4626 Z= 0.345 Chirality : 0.052 0.151 522 Planarity : 0.004 0.062 588 Dihedral : 5.256 15.718 456 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.31 % Allowed : 17.69 % Favored : 80.00 % 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 aren not related in a simple way. whole: -1.74 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 349 TYR 0.017 0.003 TYR A 310 PHE 0.011 0.002 PHE F 346 HIS 0.004 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 3456) covalent geometry : angle 0.67074 ( 4626) hydrogen bonds : bond 0.02311 ( 88) hydrogen bonds : angle 5.31853 ( 264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 776.77 seconds wall clock time: 14 minutes 9.42 seconds (849.42 seconds total)