Starting phenix.real_space_refine on Tue Feb 11 00:58:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7f_18215/02_2025/8q7f_18215.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7f_18215/02_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_18215/02_2025/8q7f_18215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7f_18215/02_2025/8q7f_18215.map" model { file = "/net/cci-nas-00/data/ceres_data/8q7f_18215/02_2025/8q7f_18215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7f_18215/02_2025/8q7f_18215.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.66, per 1000 atoms: 1.08 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: 0.77 Conformation dependent library (CDL) restraints added in 414.0 milliseconds 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: 0.56 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: 0.81 Time building geometry restraints manager: 0.92 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: 0.01 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.800 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.670 ------------------------------------------------------------------------------- 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= 0.765 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.32), 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 HIS 0.006 0.002 HIS D 362 PHE 0.063 0.013 PHE E 346 TYR 0.129 0.046 TYR A 310 ARG 0.009 0.002 ARG C 349 *********************** 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 : 0.414 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: 0.7450 (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: 0.6527 (mmm160) REVERT: A 351 GLN cc_start: 0.6186 (mp10) cc_final: 0.5762 (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 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: 0.6205 (tttm) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2375 time to fit residues: 39.5550 Evaluate side-chains 108 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS F 329 HIS C 327 ASN E 329 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.152691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.141996 restraints weight = 4613.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.144370 restraints weight = 2334.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.145916 restraints weight = 1432.804| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3456 Z= 0.201 Angle : 0.651 5.255 4626 Z= 0.339 Chirality : 0.052 0.135 522 Planarity : 0.003 0.028 588 Dihedral : 5.930 20.572 456 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.77 % Allowed : 7.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.90 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 362 PHE 0.015 0.001 PHE F 346 TYR 0.013 0.003 TYR A 310 ARG 0.002 0.000 ARG B 349 *********************** 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 121 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 0.390 Fit side-chains REVERT: B 345 ASP cc_start: 0.8074 (t0) cc_final: 0.7584 (t70) REVERT: B 375 LYS cc_start: 0.8403 (tttt) cc_final: 0.7864 (tttm) REVERT: D 315 LEU cc_start: 0.8508 (mp) cc_final: 0.8171 (mt) REVERT: D 331 LYS cc_start: 0.8254 (mttt) cc_final: 0.7911 (mttm) REVERT: D 345 ASP cc_start: 0.8199 (t0) cc_final: 0.7974 (t70) REVERT: D 347 LYS cc_start: 0.7547 (mmtt) cc_final: 0.6574 (mtmm) REVERT: D 375 LYS cc_start: 0.8297 (tttt) cc_final: 0.8066 (tttp) REVERT: F 331 LYS cc_start: 0.8117 (mttt) cc_final: 0.7509 (mtpp) REVERT: F 337 VAL cc_start: 0.8225 (t) cc_final: 0.7967 (m) REVERT: F 349 ARG cc_start: 0.6971 (mmt90) cc_final: 0.6301 (mmp-170) REVERT: F 375 LYS cc_start: 0.8432 (tttt) cc_final: 0.8126 (tttm) REVERT: A 316 SER cc_start: 0.8781 (p) cc_final: 0.8572 (p) REVERT: A 369 LYS cc_start: 0.7552 (tttt) cc_final: 0.6910 (ttmm) REVERT: C 369 LYS cc_start: 0.7237 (tttt) cc_final: 0.6757 (ttmm) REVERT: C 375 LYS cc_start: 0.8150 (tttt) cc_final: 0.7581 (tmtt) REVERT: E 311 LYS cc_start: 0.7621 (mttt) cc_final: 0.7402 (mmtt) REVERT: E 349 ARG cc_start: 0.6056 (mmt90) cc_final: 0.5339 (mmp-170) REVERT: E 369 LYS cc_start: 0.7717 (tttt) cc_final: 0.7135 (mtpt) outliers start: 3 outliers final: 2 residues processed: 120 average time/residue: 0.2013 time to fit residues: 28.0119 Evaluate side-chains 109 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 353 LYS Chi-restraints excluded: chain A residue 378 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.144290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.133734 restraints weight = 4743.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.135794 restraints weight = 2498.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.137208 restraints weight = 1600.614| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3456 Z= 0.373 Angle : 0.708 4.793 4626 Z= 0.372 Chirality : 0.054 0.171 522 Planarity : 0.004 0.035 588 Dihedral : 5.801 20.212 456 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.54 % Allowed : 11.03 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.89 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 362 PHE 0.020 0.002 PHE F 346 TYR 0.023 0.004 TYR A 310 ARG 0.003 0.001 ARG A 349 *********************** 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 109 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.438 Fit side-chains REVERT: B 345 ASP cc_start: 0.8159 (t0) cc_final: 0.7695 (t70) REVERT: B 375 LYS cc_start: 0.8429 (tttt) cc_final: 0.8001 (tttm) REVERT: D 315 LEU cc_start: 0.8782 (mp) cc_final: 0.8447 (mt) REVERT: D 331 LYS cc_start: 0.8306 (mttt) cc_final: 0.8057 (mttm) REVERT: D 340 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7632 (mtmt) REVERT: D 347 LYS cc_start: 0.7786 (mmtt) cc_final: 0.6872 (mtmm) REVERT: D 349 ARG cc_start: 0.7774 (mmt90) cc_final: 0.7362 (mtt90) REVERT: D 375 LYS cc_start: 0.8386 (tttt) cc_final: 0.8094 (tttp) REVERT: F 337 VAL cc_start: 0.8274 (t) cc_final: 0.8067 (m) REVERT: F 349 ARG cc_start: 0.7263 (mmt90) cc_final: 0.6363 (mmp-170) REVERT: F 375 LYS cc_start: 0.8535 (tttt) cc_final: 0.8237 (tttm) REVERT: A 316 SER cc_start: 0.8993 (p) cc_final: 0.8731 (p) REVERT: A 349 ARG cc_start: 0.7652 (mmt180) cc_final: 0.7230 (mmt180) REVERT: A 369 LYS cc_start: 0.7916 (tttt) cc_final: 0.7210 (ttmm) REVERT: C 342 GLU cc_start: 0.8057 (pm20) cc_final: 0.7718 (mt-10) REVERT: C 369 LYS cc_start: 0.7817 (tttt) cc_final: 0.7276 (mtpt) REVERT: E 311 LYS cc_start: 0.7812 (mttt) cc_final: 0.7534 (mmmt) REVERT: E 348 ASP cc_start: 0.7570 (t0) cc_final: 0.7332 (t0) REVERT: E 349 ARG cc_start: 0.6572 (mmt90) cc_final: 0.5412 (mmp-170) REVERT: E 369 LYS cc_start: 0.7903 (tttt) cc_final: 0.7282 (mtpt) outliers start: 6 outliers final: 6 residues processed: 105 average time/residue: 0.1965 time to fit residues: 24.1483 Evaluate side-chains 104 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS D 327 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 = 0.4071 r_free = 0.4071 target = 0.147312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.136613 restraints weight = 4742.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.138755 restraints weight = 2467.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.140204 restraints weight = 1558.526| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4130 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= 0.211 Angle : 0.599 4.746 4626 Z= 0.304 Chirality : 0.051 0.152 522 Planarity : 0.003 0.040 588 Dihedral : 5.244 16.122 456 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 2.05 % Allowed : 12.56 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.011 0.001 PHE F 346 TYR 0.015 0.003 TYR A 310 ARG 0.002 0.000 ARG A 349 *********************** 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: 8 poor density : 105 time to evaluate : 0.371 Fit side-chains REVERT: B 345 ASP cc_start: 0.8124 (t0) cc_final: 0.7681 (t70) REVERT: B 349 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7641 (mtm-85) REVERT: B 375 LYS cc_start: 0.8424 (tttt) cc_final: 0.7976 (tttm) REVERT: D 315 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8380 (mt) REVERT: D 331 LYS cc_start: 0.8310 (mttt) cc_final: 0.8080 (mttm) REVERT: D 340 LYS cc_start: 0.8117 (mtpt) cc_final: 0.7638 (mtmt) REVERT: D 347 LYS cc_start: 0.7790 (mmtt) cc_final: 0.6715 (mtmm) REVERT: D 349 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7022 (mtt90) REVERT: D 375 LYS cc_start: 0.8365 (tttt) cc_final: 0.8129 (tttp) REVERT: F 331 LYS cc_start: 0.8029 (mttt) cc_final: 0.7481 (mtpp) REVERT: F 337 VAL cc_start: 0.8190 (t) cc_final: 0.7980 (m) REVERT: F 349 ARG cc_start: 0.7209 (mmt90) cc_final: 0.6318 (mmp-170) REVERT: F 375 LYS cc_start: 0.8534 (tttt) cc_final: 0.8253 (tttm) REVERT: A 316 SER cc_start: 0.9005 (p) cc_final: 0.8803 (p) REVERT: A 349 ARG cc_start: 0.7677 (mmt180) cc_final: 0.7195 (mmt180) REVERT: A 369 LYS cc_start: 0.7852 (tttt) cc_final: 0.7190 (ttmm) REVERT: C 311 LYS cc_start: 0.8226 (mmmt) cc_final: 0.7963 (mtpp) REVERT: C 342 GLU cc_start: 0.7910 (pm20) cc_final: 0.7637 (mt-10) REVERT: C 369 LYS cc_start: 0.7748 (tttt) cc_final: 0.7252 (mtpt) REVERT: E 349 ARG cc_start: 0.6437 (mmt90) cc_final: 0.5323 (mmp-170) REVERT: E 369 LYS cc_start: 0.7867 (tttt) cc_final: 0.7249 (mtpt) outliers start: 8 outliers final: 5 residues processed: 106 average time/residue: 0.2081 time to fit residues: 25.5449 Evaluate side-chains 109 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 349 ARG 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.143289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.132773 restraints weight = 5000.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.134783 restraints weight = 2577.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.136195 restraints weight = 1647.710| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3456 Z= 0.338 Angle : 0.684 5.813 4626 Z= 0.355 Chirality : 0.052 0.153 522 Planarity : 0.004 0.048 588 Dihedral : 5.455 17.996 456 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 2.82 % Allowed : 13.59 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 362 PHE 0.016 0.002 PHE F 346 TYR 0.018 0.004 TYR A 310 ARG 0.002 0.000 ARG E 349 *********************** 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 112 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.391 Fit side-chains REVERT: B 315 LEU cc_start: 0.8664 (mp) cc_final: 0.8387 (mt) REVERT: B 331 LYS cc_start: 0.8258 (mttt) cc_final: 0.7907 (mttm) REVERT: B 345 ASP cc_start: 0.8094 (t0) cc_final: 0.7734 (t70) REVERT: B 375 LYS cc_start: 0.8401 (tttt) cc_final: 0.8020 (tttm) REVERT: D 340 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7692 (mtmt) REVERT: D 347 LYS cc_start: 0.8038 (mmtt) cc_final: 0.6765 (mtmm) REVERT: D 375 LYS cc_start: 0.8355 (tttt) cc_final: 0.8066 (tttp) REVERT: F 331 LYS cc_start: 0.8107 (mttt) cc_final: 0.7531 (mtpp) REVERT: F 337 VAL cc_start: 0.8251 (t) cc_final: 0.8034 (m) REVERT: F 349 ARG cc_start: 0.7418 (mmt90) cc_final: 0.6134 (mmm160) REVERT: F 375 LYS cc_start: 0.8505 (tttt) cc_final: 0.8232 (tttm) REVERT: A 369 LYS cc_start: 0.7926 (tttt) cc_final: 0.7177 (ttmm) REVERT: C 342 GLU cc_start: 0.7898 (pm20) cc_final: 0.7674 (mt-10) REVERT: C 369 LYS cc_start: 0.7782 (tttt) cc_final: 0.7143 (ttmm) REVERT: E 336 GLN cc_start: 0.7702 (mp10) cc_final: 0.7073 (mp10) REVERT: E 349 ARG cc_start: 0.6610 (mmt90) cc_final: 0.5315 (mmp-170) REVERT: E 369 LYS cc_start: 0.7924 (tttt) cc_final: 0.7308 (mtpt) outliers start: 11 outliers final: 7 residues processed: 104 average time/residue: 0.2026 time to fit residues: 24.5374 Evaluate side-chains 103 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 4.9990 chunk 29 optimal weight: 0.0770 chunk 33 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 0.0670 chunk 32 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 overall best weight: 2.2280 ------------------------------------------------------------------------------- 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 E 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.146536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.136075 restraints weight = 4939.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.138175 restraints weight = 2541.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.139592 restraints weight = 1597.291| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3456 Z= 0.213 Angle : 0.621 7.027 4626 Z= 0.313 Chirality : 0.051 0.144 522 Planarity : 0.003 0.052 588 Dihedral : 5.062 15.025 456 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.05 % Allowed : 15.38 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.010 0.001 PHE F 346 TYR 0.021 0.003 TYR B 310 ARG 0.001 0.000 ARG D 349 *********************** 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 109 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.479 Fit side-chains REVERT: B 315 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8354 (mt) REVERT: B 331 LYS cc_start: 0.8199 (mttt) cc_final: 0.7843 (mttm) REVERT: B 345 ASP cc_start: 0.8039 (t0) cc_final: 0.7686 (t70) REVERT: B 375 LYS cc_start: 0.8403 (tttt) cc_final: 0.8006 (tttm) REVERT: D 347 LYS cc_start: 0.7827 (mmtt) cc_final: 0.6649 (mtmm) REVERT: D 349 ARG cc_start: 0.7542 (mtt90) cc_final: 0.7046 (mtt90) REVERT: D 375 LYS cc_start: 0.8313 (tttt) cc_final: 0.8023 (tttp) REVERT: F 331 LYS cc_start: 0.8125 (mttt) cc_final: 0.7535 (mtpp) REVERT: F 337 VAL cc_start: 0.8201 (t) cc_final: 0.7992 (m) REVERT: F 349 ARG cc_start: 0.7352 (mmt90) cc_final: 0.6098 (mmm160) REVERT: F 375 LYS cc_start: 0.8547 (tttt) cc_final: 0.8302 (tttm) REVERT: A 369 LYS cc_start: 0.7771 (tttt) cc_final: 0.7189 (ttmm) REVERT: C 369 LYS cc_start: 0.7748 (tttt) cc_final: 0.7097 (ttmm) REVERT: E 336 GLN cc_start: 0.7704 (mp10) cc_final: 0.7285 (mp10) REVERT: E 349 ARG cc_start: 0.6542 (mmt90) cc_final: 0.5287 (mmp-170) REVERT: E 369 LYS cc_start: 0.7875 (tttt) cc_final: 0.7246 (mtpt) REVERT: E 375 LYS cc_start: 0.8620 (tttt) cc_final: 0.8149 (tttm) outliers start: 8 outliers final: 6 residues processed: 103 average time/residue: 0.1918 time to fit residues: 23.1600 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 : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.0970 chunk 15 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 0.0470 chunk 0 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 overall best weight: 4.4282 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.142385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.131817 restraints weight = 4872.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.134010 restraints weight = 2499.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.135389 restraints weight = 1568.100| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3456 Z= 0.345 Angle : 0.684 8.532 4626 Z= 0.350 Chirality : 0.052 0.141 522 Planarity : 0.004 0.054 588 Dihedral : 5.392 16.338 456 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.56 % Allowed : 15.13 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 362 PHE 0.012 0.002 PHE F 346 TYR 0.017 0.004 TYR A 310 ARG 0.002 0.000 ARG D 349 *********************** 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 111 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: B 315 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8324 (mt) REVERT: B 331 LYS cc_start: 0.8302 (mttt) cc_final: 0.7961 (mttm) REVERT: B 345 ASP cc_start: 0.8009 (t0) cc_final: 0.7694 (t70) REVERT: B 375 LYS cc_start: 0.8425 (tttt) cc_final: 0.8032 (tttm) REVERT: D 315 LEU cc_start: 0.8700 (mp) cc_final: 0.8283 (mt) REVERT: D 347 LYS cc_start: 0.8010 (mmtt) cc_final: 0.6937 (mtmt) REVERT: D 375 LYS cc_start: 0.8310 (tttt) cc_final: 0.8017 (tttp) REVERT: F 331 LYS cc_start: 0.8147 (mttt) cc_final: 0.7678 (mttm) REVERT: F 337 VAL cc_start: 0.8106 (t) cc_final: 0.7897 (m) REVERT: F 349 ARG cc_start: 0.7520 (mmt90) cc_final: 0.6195 (mmm160) REVERT: A 369 LYS cc_start: 0.7874 (tttt) cc_final: 0.7267 (ttmm) REVERT: C 369 LYS cc_start: 0.7836 (tttt) cc_final: 0.7158 (ttmm) REVERT: E 336 GLN cc_start: 0.7647 (mp10) cc_final: 0.7316 (mp10) REVERT: E 349 ARG cc_start: 0.6544 (mmt90) cc_final: 0.5471 (mmp-170) REVERT: E 369 LYS cc_start: 0.7896 (tttt) cc_final: 0.7304 (ttmm) REVERT: E 375 LYS cc_start: 0.8679 (tttt) cc_final: 0.8152 (tmtt) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.1983 time to fit residues: 23.8569 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 : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B 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 8 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.145384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.134784 restraints weight = 4809.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.136996 restraints weight = 2467.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.138460 restraints weight = 1540.515| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3456 Z= 0.222 Angle : 0.633 8.395 4626 Z= 0.321 Chirality : 0.051 0.146 522 Planarity : 0.003 0.058 588 Dihedral : 5.182 16.558 456 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.56 % Allowed : 14.87 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 362 PHE 0.010 0.001 PHE F 346 TYR 0.015 0.002 TYR A 310 ARG 0.001 0.000 ARG E 349 *********************** 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 114 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.316 Fit side-chains REVERT: B 315 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8273 (mt) REVERT: B 331 LYS cc_start: 0.8260 (mttt) cc_final: 0.7930 (mttm) REVERT: B 345 ASP cc_start: 0.7982 (t0) cc_final: 0.7672 (t70) REVERT: B 375 LYS cc_start: 0.8402 (tttt) cc_final: 0.8000 (tttm) REVERT: D 315 LEU cc_start: 0.8645 (mp) cc_final: 0.8261 (mt) REVERT: D 347 LYS cc_start: 0.8005 (mmtt) cc_final: 0.6713 (mtmm) REVERT: D 375 LYS cc_start: 0.8255 (tttt) cc_final: 0.7982 (tttp) REVERT: F 331 LYS cc_start: 0.8119 (mttt) cc_final: 0.7631 (mttm) REVERT: F 337 VAL cc_start: 0.8090 (t) cc_final: 0.7875 (m) REVERT: F 349 ARG cc_start: 0.7477 (mmt90) cc_final: 0.6145 (mmm160) REVERT: F 375 LYS cc_start: 0.8533 (tttt) cc_final: 0.8280 (tttm) REVERT: A 331 LYS cc_start: 0.8131 (mttt) cc_final: 0.7639 (mttp) REVERT: A 369 LYS cc_start: 0.7829 (tttt) cc_final: 0.7209 (ttmm) REVERT: C 369 LYS cc_start: 0.7768 (tttt) cc_final: 0.7097 (ttmm) REVERT: E 336 GLN cc_start: 0.7565 (mp10) cc_final: 0.7229 (mp10) REVERT: E 349 ARG cc_start: 0.6458 (mmt90) cc_final: 0.5072 (mmp-170) REVERT: E 369 LYS cc_start: 0.7881 (tttt) cc_final: 0.7278 (mtpt) REVERT: E 375 LYS cc_start: 0.8650 (tttt) cc_final: 0.8152 (tmtt) outliers start: 10 outliers final: 9 residues processed: 106 average time/residue: 0.2080 time to fit residues: 25.3493 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 : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 GLU 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 28 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4037 r_free = 0.4037 target = 0.144205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.133501 restraints weight = 4799.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.135705 restraints weight = 2493.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.137138 restraints weight = 1573.802| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3456 Z= 0.290 Angle : 0.667 8.316 4626 Z= 0.341 Chirality : 0.051 0.151 522 Planarity : 0.004 0.058 588 Dihedral : 5.234 16.101 456 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.56 % Allowed : 15.64 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 362 PHE 0.008 0.001 PHE C 346 TYR 0.017 0.003 TYR A 310 ARG 0.001 0.000 ARG D 349 *********************** 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 112 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.428 Fit side-chains REVERT: B 315 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8294 (mt) REVERT: B 345 ASP cc_start: 0.7925 (t0) cc_final: 0.7722 (t70) REVERT: B 375 LYS cc_start: 0.8390 (tttt) cc_final: 0.7999 (tttm) REVERT: D 315 LEU cc_start: 0.8694 (mp) cc_final: 0.8340 (mt) REVERT: D 336 GLN cc_start: 0.7008 (mm-40) cc_final: 0.5122 (pm20) REVERT: D 347 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7018 (mtmt) REVERT: D 375 LYS cc_start: 0.8304 (tttt) cc_final: 0.8019 (tttp) REVERT: F 331 LYS cc_start: 0.8129 (mttt) cc_final: 0.7675 (mttm) REVERT: F 337 VAL cc_start: 0.8112 (t) cc_final: 0.7896 (m) REVERT: F 347 LYS cc_start: 0.7207 (mmtm) cc_final: 0.6996 (mmtt) REVERT: F 349 ARG cc_start: 0.7530 (mmt90) cc_final: 0.6180 (mmm160) REVERT: F 375 LYS cc_start: 0.8546 (tttt) cc_final: 0.8287 (tttm) REVERT: A 369 LYS cc_start: 0.7839 (tttt) cc_final: 0.7273 (ttmm) REVERT: C 369 LYS cc_start: 0.7811 (tttt) cc_final: 0.7113 (ttmm) REVERT: E 336 GLN cc_start: 0.7585 (mp10) cc_final: 0.7298 (mp10) REVERT: E 349 ARG cc_start: 0.6596 (mmt90) cc_final: 0.5162 (mmp-170) REVERT: E 369 LYS cc_start: 0.7873 (tttt) cc_final: 0.7251 (ttmm) REVERT: E 375 LYS cc_start: 0.8657 (tttt) cc_final: 0.8138 (tmtt) outliers start: 10 outliers final: 9 residues processed: 104 average time/residue: 0.1941 time to fit residues: 23.4879 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 : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 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 = 0.4002 r_free = 0.4002 target = 0.141442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.131072 restraints weight = 5053.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.133140 restraints weight = 2637.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.134518 restraints weight = 1675.993| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 3456 Z= 0.453 Angle : 0.752 8.333 4626 Z= 0.393 Chirality : 0.054 0.156 522 Planarity : 0.004 0.060 588 Dihedral : 5.595 16.700 456 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.08 % Allowed : 15.90 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 362 PHE 0.013 0.002 PHE C 346 TYR 0.019 0.004 TYR A 310 ARG 0.004 0.001 ARG E 349 ********************** 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 111 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 345 ASP cc_start: 0.7928 (t0) cc_final: 0.7543 (t70) REVERT: B 347 LYS cc_start: 0.8476 (mmtt) cc_final: 0.7826 (mmtt) REVERT: D 315 LEU cc_start: 0.8765 (mp) cc_final: 0.8424 (mt) REVERT: D 336 GLN cc_start: 0.7167 (mm-40) cc_final: 0.5297 (pm20) REVERT: D 343 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.7048 (pptt) REVERT: D 375 LYS cc_start: 0.8313 (tttt) cc_final: 0.7977 (tttp) REVERT: D 376 LEU cc_start: 0.8891 (tp) cc_final: 0.8600 (tt) REVERT: F 331 LYS cc_start: 0.8177 (mttt) cc_final: 0.7723 (mtpp) REVERT: F 349 ARG cc_start: 0.7594 (mmt90) cc_final: 0.6200 (mmm160) REVERT: A 369 LYS cc_start: 0.7878 (tttt) cc_final: 0.7247 (ttmm) REVERT: C 369 LYS cc_start: 0.7845 (tttt) cc_final: 0.7181 (ttmm) REVERT: E 336 GLN cc_start: 0.7632 (mp10) cc_final: 0.7344 (mp10) REVERT: E 349 ARG cc_start: 0.6699 (mmt90) cc_final: 0.5151 (mmp-170) REVERT: E 369 LYS cc_start: 0.7907 (tttt) cc_final: 0.7337 (ttmm) REVERT: E 375 LYS cc_start: 0.8681 (tttt) cc_final: 0.8136 (tmtt) outliers start: 12 outliers final: 9 residues processed: 103 average time/residue: 0.2019 time to fit residues: 24.1631 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 : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 343 LYS 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 28 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.142537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.132161 restraints weight = 5012.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.134243 restraints weight = 2609.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.135655 restraints weight = 1642.068| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3456 Z= 0.373 Angle : 0.719 8.207 4626 Z= 0.370 Chirality : 0.053 0.151 522 Planarity : 0.004 0.061 588 Dihedral : 5.549 17.040 456 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.56 % Allowed : 16.92 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 362 PHE 0.011 0.002 PHE C 346 TYR 0.017 0.003 TYR A 310 ARG 0.002 0.000 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1490.22 seconds wall clock time: 27 minutes 44.00 seconds (1664.00 seconds total)