Starting phenix.real_space_refine on Sun Mar 10 17:08:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7f_18215/03_2024/8q7f_18215.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7f_18215/03_2024/8q7f_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7f_18215/03_2024/8q7f_18215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7f_18215/03_2024/8q7f_18215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7f_18215/03_2024/8q7f_18215.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7f_18215/03_2024/8q7f_18215.pdb" } 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 Residue "B GLU 342": "OE1" <-> "OE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "E GLU 342": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.19, per 1000 atoms: 0.64 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 - 3.50 Amino acid : False - 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: 1.11 Conformation dependent library (CDL) restraints added in 629.8 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: 0.48 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: 0.80 Time building geometry restraints manager: 1.23 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: 101.97 - 107.52: 235 107.52 - 113.07: 1706 113.07 - 118.61: 847 118.61 - 124.16: 1584 124.16 - 129.70: 254 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 2.440 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.504 2.440 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.508 2.440 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.508 2.440 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.567 2.440 ... (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 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.600 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.520 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.423 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: 0.2323 time to fit residues: 38.7153 Evaluate side-chains 108 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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: 0.7980 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN F 329 HIS C 327 ASN E 329 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3456 Z= 0.189 Angle : 0.634 4.694 4626 Z= 0.329 Chirality : 0.052 0.134 522 Planarity : 0.003 0.024 588 Dihedral : 5.790 19.939 456 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.03 % Allowed : 7.69 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.11 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.84 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 362 PHE 0.013 0.001 PHE F 346 TYR 0.011 0.002 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 fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 0.410 Fit side-chains REVERT: B 338 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6921 (tt0) REVERT: B 340 LYS cc_start: 0.7555 (tttt) cc_final: 0.6992 (mttm) REVERT: B 345 ASP cc_start: 0.7520 (t0) cc_final: 0.6627 (t70) REVERT: B 375 LYS cc_start: 0.8011 (tttt) cc_final: 0.7166 (tttm) REVERT: D 311 LYS cc_start: 0.8102 (mttt) cc_final: 0.7853 (mttp) REVERT: D 315 LEU cc_start: 0.8329 (mp) cc_final: 0.8077 (mt) REVERT: D 319 THR cc_start: 0.7901 (m) cc_final: 0.7635 (t) REVERT: D 331 LYS cc_start: 0.8146 (mttt) cc_final: 0.7638 (mttm) REVERT: D 340 LYS cc_start: 0.8011 (tttt) cc_final: 0.7430 (mtpt) REVERT: D 347 LYS cc_start: 0.7713 (mmtt) cc_final: 0.6586 (mtmm) REVERT: D 375 LYS cc_start: 0.8421 (tttt) cc_final: 0.7963 (tttp) REVERT: F 311 LYS cc_start: 0.7468 (mttt) cc_final: 0.6918 (tppt) REVERT: F 331 LYS cc_start: 0.8029 (mttt) cc_final: 0.7279 (mtpp) REVERT: F 338 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6967 (pt0) REVERT: F 340 LYS cc_start: 0.7538 (tttt) cc_final: 0.6964 (mttm) REVERT: F 349 ARG cc_start: 0.6623 (mmt90) cc_final: 0.5412 (mmp-170) REVERT: F 356 SER cc_start: 0.8709 (m) cc_final: 0.8397 (p) REVERT: F 362 HIS cc_start: 0.7707 (t-170) cc_final: 0.7407 (m170) REVERT: F 375 LYS cc_start: 0.7889 (tttt) cc_final: 0.7294 (tttm) REVERT: A 348 ASP cc_start: 0.6512 (t0) cc_final: 0.6305 (t0) REVERT: A 349 ARG cc_start: 0.7299 (mmt90) cc_final: 0.6526 (mmt180) REVERT: A 369 LYS cc_start: 0.7559 (tttt) cc_final: 0.6742 (ttmm) REVERT: C 311 LYS cc_start: 0.8124 (mttt) cc_final: 0.7724 (mtpp) REVERT: C 342 GLU cc_start: 0.8162 (pm20) cc_final: 0.7580 (pm20) REVERT: C 369 LYS cc_start: 0.7453 (tttt) cc_final: 0.6808 (ttmm) REVERT: C 375 LYS cc_start: 0.7839 (tttt) cc_final: 0.7045 (tmtt) REVERT: E 311 LYS cc_start: 0.7661 (mttt) cc_final: 0.6900 (mmtt) REVERT: E 342 GLU cc_start: 0.7811 (pt0) cc_final: 0.6720 (mm-30) REVERT: E 348 ASP cc_start: 0.6815 (t0) cc_final: 0.6380 (t0) REVERT: E 369 LYS cc_start: 0.7543 (tttt) cc_final: 0.6500 (mtpt) outliers start: 4 outliers final: 3 residues processed: 119 average time/residue: 0.1911 time to fit residues: 26.4863 Evaluate side-chains 112 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS B 368 ASN A 327 ASN E 327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 3456 Z= 0.455 Angle : 0.770 8.611 4626 Z= 0.401 Chirality : 0.056 0.168 522 Planarity : 0.004 0.032 588 Dihedral : 6.088 23.129 456 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.79 % Allowed : 11.54 % Favored : 86.67 % 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: -1.21 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.91 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 362 PHE 0.024 0.002 PHE F 346 TYR 0.021 0.005 TYR A 310 ARG 0.002 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 116 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.396 Fit side-chains REVERT: B 338 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7199 (tm-30) REVERT: B 345 ASP cc_start: 0.7634 (t0) cc_final: 0.6916 (t70) REVERT: B 375 LYS cc_start: 0.8145 (tttt) cc_final: 0.7383 (tttm) REVERT: D 311 LYS cc_start: 0.8090 (mttt) cc_final: 0.7608 (mtmt) REVERT: D 331 LYS cc_start: 0.8196 (mttt) cc_final: 0.7857 (mttm) REVERT: D 337 VAL cc_start: 0.8547 (p) cc_final: 0.8262 (m) REVERT: D 340 LYS cc_start: 0.8034 (tttt) cc_final: 0.7477 (mtpt) REVERT: D 347 LYS cc_start: 0.8053 (mmtt) cc_final: 0.6707 (mtmm) REVERT: D 375 LYS cc_start: 0.8354 (tttt) cc_final: 0.7847 (tttp) REVERT: F 311 LYS cc_start: 0.7605 (mttt) cc_final: 0.6918 (tppt) REVERT: F 315 LEU cc_start: 0.7878 (mt) cc_final: 0.7541 (mt) REVERT: F 338 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7052 (tm-30) REVERT: F 349 ARG cc_start: 0.7057 (mmt90) cc_final: 0.5452 (mmm160) REVERT: F 362 HIS cc_start: 0.7619 (t-170) cc_final: 0.7322 (m170) REVERT: F 375 LYS cc_start: 0.7947 (tttt) cc_final: 0.7395 (tttm) REVERT: A 316 SER cc_start: 0.8905 (p) cc_final: 0.8550 (p) REVERT: A 349 ARG cc_start: 0.7279 (mmt90) cc_final: 0.6248 (mmt180) REVERT: A 369 LYS cc_start: 0.7837 (tttt) cc_final: 0.6909 (ttmm) REVERT: C 349 ARG cc_start: 0.6957 (mmt90) cc_final: 0.6523 (mtm180) REVERT: C 369 LYS cc_start: 0.7976 (tttt) cc_final: 0.7209 (ttmm) REVERT: E 311 LYS cc_start: 0.7811 (mttt) cc_final: 0.7125 (mmtt) REVERT: E 316 SER cc_start: 0.8724 (p) cc_final: 0.8485 (p) REVERT: E 342 GLU cc_start: 0.7803 (pt0) cc_final: 0.6864 (mm-30) REVERT: E 348 ASP cc_start: 0.6681 (t0) cc_final: 0.6215 (t0) REVERT: E 369 LYS cc_start: 0.7826 (tttt) cc_final: 0.6777 (mtpt) outliers start: 7 outliers final: 7 residues processed: 111 average time/residue: 0.2146 time to fit residues: 27.3346 Evaluate side-chains 108 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain F residue 353 LYS 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 4 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS A 329 HIS E 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4190 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= 0.314 Angle : 0.655 6.122 4626 Z= 0.332 Chirality : 0.052 0.154 522 Planarity : 0.003 0.039 588 Dihedral : 5.567 17.252 456 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 2.31 % Allowed : 12.56 % 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 (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: -1.39 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.014 0.002 PHE F 346 TYR 0.018 0.003 TYR A 310 ARG 0.002 0.000 ARG D 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 114 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 0.424 Fit side-chains REVERT: B 331 LYS cc_start: 0.7938 (mttt) cc_final: 0.7469 (mttm) REVERT: B 345 ASP cc_start: 0.7648 (t0) cc_final: 0.7096 (t70) REVERT: B 375 LYS cc_start: 0.8169 (tttt) cc_final: 0.7425 (tttm) REVERT: D 311 LYS cc_start: 0.8066 (mttt) cc_final: 0.7684 (mttm) REVERT: D 331 LYS cc_start: 0.8162 (mttt) cc_final: 0.7911 (mttm) REVERT: D 337 VAL cc_start: 0.8525 (p) cc_final: 0.8228 (m) REVERT: D 340 LYS cc_start: 0.8028 (tttt) cc_final: 0.7469 (mtpt) REVERT: D 347 LYS cc_start: 0.8164 (mmtt) cc_final: 0.6686 (mtmm) REVERT: D 375 LYS cc_start: 0.8391 (tttt) cc_final: 0.7871 (tttp) REVERT: F 311 LYS cc_start: 0.7669 (mttt) cc_final: 0.7051 (tppt) REVERT: F 338 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7143 (tm-30) REVERT: F 349 ARG cc_start: 0.7177 (mmt90) cc_final: 0.5502 (mmm160) REVERT: F 356 SER cc_start: 0.8885 (m) cc_final: 0.8417 (p) REVERT: F 362 HIS cc_start: 0.7635 (t-170) cc_final: 0.7315 (m170) REVERT: F 375 LYS cc_start: 0.8022 (tttt) cc_final: 0.7473 (tttm) REVERT: A 316 SER cc_start: 0.8928 (p) cc_final: 0.8620 (p) REVERT: A 349 ARG cc_start: 0.7322 (mmt90) cc_final: 0.6557 (mmt180) REVERT: A 369 LYS cc_start: 0.7813 (tttt) cc_final: 0.6835 (ttmm) REVERT: C 311 LYS cc_start: 0.8353 (mtpp) cc_final: 0.8090 (mtpp) REVERT: C 369 LYS cc_start: 0.7889 (tttt) cc_final: 0.7083 (ttmm) REVERT: E 311 LYS cc_start: 0.7808 (mttt) cc_final: 0.7072 (mmtt) REVERT: E 316 SER cc_start: 0.8800 (p) cc_final: 0.8582 (p) REVERT: E 342 GLU cc_start: 0.7812 (pt0) cc_final: 0.6934 (mm-30) REVERT: E 349 ARG cc_start: 0.5972 (mmt90) cc_final: 0.4295 (mmp-170) REVERT: E 369 LYS cc_start: 0.7748 (tttt) cc_final: 0.6686 (mtpt) outliers start: 9 outliers final: 7 residues processed: 108 average time/residue: 0.1974 time to fit residues: 24.7681 Evaluate side-chains 107 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 316 SER 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 30 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3456 Z= 0.294 Angle : 0.647 7.103 4626 Z= 0.326 Chirality : 0.051 0.155 522 Planarity : 0.003 0.046 588 Dihedral : 5.394 15.895 456 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.31 % Allowed : 14.10 % 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: -1.47 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.28), 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 0.024 0.004 TYR B 310 ARG 0.002 0.000 ARG A 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 fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 0.407 Fit side-chains REVERT: B 310 TYR cc_start: 0.8851 (t80) cc_final: 0.8531 (t80) REVERT: B 315 LEU cc_start: 0.7834 (mp) cc_final: 0.7614 (mt) REVERT: B 331 LYS cc_start: 0.7924 (mttt) cc_final: 0.7499 (mttm) REVERT: B 345 ASP cc_start: 0.7596 (t0) cc_final: 0.6869 (t70) REVERT: B 375 LYS cc_start: 0.8195 (tttt) cc_final: 0.7437 (tttm) REVERT: D 311 LYS cc_start: 0.8054 (mttt) cc_final: 0.7682 (mttm) REVERT: D 331 LYS cc_start: 0.8220 (mttt) cc_final: 0.7897 (mttm) REVERT: D 337 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8272 (m) REVERT: D 340 LYS cc_start: 0.7990 (tttt) cc_final: 0.7503 (mtpt) REVERT: D 347 LYS cc_start: 0.7980 (mmtt) cc_final: 0.6502 (mtmm) REVERT: D 375 LYS cc_start: 0.8349 (tttt) cc_final: 0.7828 (tttp) REVERT: F 311 LYS cc_start: 0.7706 (mttt) cc_final: 0.6901 (tppt) REVERT: F 338 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7100 (tm-30) REVERT: F 349 ARG cc_start: 0.7193 (mmt90) cc_final: 0.5489 (mmm160) REVERT: F 362 HIS cc_start: 0.7623 (t-170) cc_final: 0.7318 (m170) REVERT: F 375 LYS cc_start: 0.8042 (tttt) cc_final: 0.7502 (tttm) REVERT: A 316 SER cc_start: 0.8889 (p) cc_final: 0.8582 (p) REVERT: A 369 LYS cc_start: 0.7781 (tttt) cc_final: 0.6905 (ttmm) REVERT: C 311 LYS cc_start: 0.8343 (mtpp) cc_final: 0.8123 (mtpp) REVERT: C 369 LYS cc_start: 0.7919 (tttt) cc_final: 0.7108 (ttmm) REVERT: E 311 LYS cc_start: 0.7723 (mttt) cc_final: 0.7006 (mmtt) REVERT: E 316 SER cc_start: 0.8768 (p) cc_final: 0.8553 (p) REVERT: E 342 GLU cc_start: 0.7805 (pt0) cc_final: 0.6865 (mm-30) REVERT: E 349 ARG cc_start: 0.6031 (mmt90) cc_final: 0.4356 (mmp-170) REVERT: E 369 LYS cc_start: 0.7752 (tttt) cc_final: 0.6982 (ttmm) outliers start: 9 outliers final: 8 residues processed: 105 average time/residue: 0.2133 time to fit residues: 25.8084 Evaluate side-chains 109 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 359 ASN 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 10 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3456 Z= 0.409 Angle : 0.707 6.404 4626 Z= 0.359 Chirality : 0.053 0.154 522 Planarity : 0.004 0.052 588 Dihedral : 5.594 16.135 456 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 3.08 % Allowed : 14.36 % 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: -1.58 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 362 PHE 0.012 0.002 PHE F 346 TYR 0.020 0.004 TYR B 310 ARG 0.002 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 112 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.374 Fit side-chains REVERT: B 340 LYS cc_start: 0.7548 (tttt) cc_final: 0.6930 (mttm) REVERT: B 345 ASP cc_start: 0.7508 (t0) cc_final: 0.6724 (t70) REVERT: B 347 LYS cc_start: 0.8190 (mmtt) cc_final: 0.7527 (mmtt) REVERT: B 375 LYS cc_start: 0.8203 (tttt) cc_final: 0.7459 (tttm) REVERT: D 311 LYS cc_start: 0.8087 (mttt) cc_final: 0.7720 (mttm) REVERT: D 315 LEU cc_start: 0.8322 (mp) cc_final: 0.8007 (mt) REVERT: D 337 VAL cc_start: 0.8597 (p) cc_final: 0.8317 (m) REVERT: D 340 LYS cc_start: 0.7975 (tttt) cc_final: 0.7482 (mtpt) REVERT: D 343 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.6697 (pptt) REVERT: D 347 LYS cc_start: 0.8084 (mmtt) cc_final: 0.6614 (mtmm) REVERT: D 375 LYS cc_start: 0.8339 (tttt) cc_final: 0.7818 (tttp) REVERT: F 311 LYS cc_start: 0.7696 (mttt) cc_final: 0.7025 (tppt) REVERT: F 338 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7031 (tm-30) REVERT: F 349 ARG cc_start: 0.7220 (mmt90) cc_final: 0.5471 (mmm160) REVERT: F 362 HIS cc_start: 0.7634 (t-170) cc_final: 0.7234 (m170) REVERT: F 375 LYS cc_start: 0.8025 (tttt) cc_final: 0.7564 (tttp) REVERT: A 316 SER cc_start: 0.8810 (p) cc_final: 0.8483 (p) REVERT: A 369 LYS cc_start: 0.7753 (tttt) cc_final: 0.6850 (ttmm) REVERT: C 311 LYS cc_start: 0.8335 (mtpp) cc_final: 0.8113 (mtpp) REVERT: C 369 LYS cc_start: 0.7934 (tttt) cc_final: 0.7094 (ttmm) REVERT: E 311 LYS cc_start: 0.7686 (mttt) cc_final: 0.7020 (mmtt) REVERT: E 316 SER cc_start: 0.8718 (p) cc_final: 0.8501 (p) REVERT: E 342 GLU cc_start: 0.7708 (pt0) cc_final: 0.6825 (mm-30) REVERT: E 349 ARG cc_start: 0.6107 (mmt90) cc_final: 0.4370 (mmp-170) REVERT: E 369 LYS cc_start: 0.7764 (tttt) cc_final: 0.6993 (ttmm) outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 0.1952 time to fit residues: 23.8286 Evaluate side-chains 108 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 359 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 0.2980 chunk 40 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 overall best weight: 0.9042 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3456 Z= 0.137 Angle : 0.613 7.439 4626 Z= 0.292 Chirality : 0.050 0.143 522 Planarity : 0.003 0.056 588 Dihedral : 4.905 14.292 456 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.79 % Allowed : 16.41 % 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: -1.45 (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 HIS 0.003 0.001 HIS F 362 PHE 0.006 0.001 PHE F 346 TYR 0.025 0.002 TYR B 310 ARG 0.002 0.000 ARG A 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 113 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: B 331 LYS cc_start: 0.7919 (mttt) cc_final: 0.7505 (mttm) REVERT: B 336 GLN cc_start: 0.8116 (mt0) cc_final: 0.7905 (mm-40) REVERT: B 345 ASP cc_start: 0.7566 (t0) cc_final: 0.6820 (t70) REVERT: B 375 LYS cc_start: 0.8170 (tttt) cc_final: 0.7598 (tttp) REVERT: D 331 LYS cc_start: 0.8210 (mttt) cc_final: 0.7942 (mttm) REVERT: D 337 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8275 (m) REVERT: D 340 LYS cc_start: 0.8070 (tttt) cc_final: 0.7543 (mtpt) REVERT: D 347 LYS cc_start: 0.7916 (mmtt) cc_final: 0.6449 (mtmm) REVERT: D 375 LYS cc_start: 0.8366 (tttt) cc_final: 0.7883 (tttp) REVERT: F 311 LYS cc_start: 0.7744 (mttt) cc_final: 0.6978 (tppt) REVERT: F 317 LYS cc_start: 0.7392 (mttt) cc_final: 0.7192 (mtmt) REVERT: F 338 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7122 (tm-30) REVERT: F 340 LYS cc_start: 0.7315 (tttt) cc_final: 0.6898 (mttm) REVERT: F 349 ARG cc_start: 0.7035 (mmt90) cc_final: 0.5351 (mmt-90) REVERT: F 362 HIS cc_start: 0.7571 (t-170) cc_final: 0.7309 (m170) REVERT: F 375 LYS cc_start: 0.8071 (tttt) cc_final: 0.7492 (tttm) REVERT: A 316 SER cc_start: 0.8911 (p) cc_final: 0.8634 (p) REVERT: A 331 LYS cc_start: 0.7868 (mttt) cc_final: 0.7566 (mttp) REVERT: A 336 GLN cc_start: 0.7147 (mp10) cc_final: 0.6751 (mm-40) REVERT: A 369 LYS cc_start: 0.7713 (tttt) cc_final: 0.6831 (ttmm) REVERT: C 369 LYS cc_start: 0.7883 (tttt) cc_final: 0.7055 (ttmm) REVERT: E 311 LYS cc_start: 0.7611 (mttt) cc_final: 0.6907 (mmtt) REVERT: E 340 LYS cc_start: 0.7254 (ttmm) cc_final: 0.6912 (mttm) REVERT: E 349 ARG cc_start: 0.5969 (mmt90) cc_final: 0.4221 (mmp-170) REVERT: E 369 LYS cc_start: 0.7720 (tttt) cc_final: 0.6637 (mtpt) outliers start: 7 outliers final: 4 residues processed: 108 average time/residue: 0.2179 time to fit residues: 27.0025 Evaluate side-chains 107 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain C residue 378 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4820 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= 0.255 Angle : 0.627 8.157 4626 Z= 0.314 Chirality : 0.050 0.150 522 Planarity : 0.004 0.054 588 Dihedral : 5.009 14.382 456 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.79 % Allowed : 17.69 % 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: -1.46 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 362 PHE 0.011 0.001 PHE F 346 TYR 0.025 0.004 TYR B 310 ARG 0.003 0.000 ARG A 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 104 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.354 Fit side-chains REVERT: B 331 LYS cc_start: 0.7888 (mttt) cc_final: 0.7465 (mttm) REVERT: B 345 ASP cc_start: 0.7518 (t0) cc_final: 0.6820 (t70) REVERT: B 375 LYS cc_start: 0.8214 (tttt) cc_final: 0.7465 (tttm) REVERT: D 331 LYS cc_start: 0.8217 (mttt) cc_final: 0.8000 (mttm) REVERT: D 337 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8290 (m) REVERT: D 340 LYS cc_start: 0.8047 (tttt) cc_final: 0.7532 (mtpt) REVERT: D 347 LYS cc_start: 0.8102 (mmtt) cc_final: 0.6610 (mtmm) REVERT: D 375 LYS cc_start: 0.8384 (tttt) cc_final: 0.7903 (tttp) REVERT: F 311 LYS cc_start: 0.7744 (mttt) cc_final: 0.7072 (tppt) REVERT: F 338 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7081 (tm-30) REVERT: F 340 LYS cc_start: 0.7244 (tttt) cc_final: 0.6827 (mttm) REVERT: F 349 ARG cc_start: 0.7166 (mmt90) cc_final: 0.5439 (mmm160) REVERT: F 362 HIS cc_start: 0.7594 (t-170) cc_final: 0.7295 (m170) REVERT: F 375 LYS cc_start: 0.8088 (tttt) cc_final: 0.7554 (tttm) REVERT: A 316 SER cc_start: 0.8779 (p) cc_final: 0.8459 (p) REVERT: A 369 LYS cc_start: 0.7759 (tttt) cc_final: 0.6863 (ttmm) REVERT: C 311 LYS cc_start: 0.8345 (mtpp) cc_final: 0.8110 (mtpp) REVERT: C 369 LYS cc_start: 0.7937 (tttt) cc_final: 0.7084 (ttmm) REVERT: E 311 LYS cc_start: 0.7587 (mttt) cc_final: 0.6858 (mmtt) REVERT: E 369 LYS cc_start: 0.7729 (tttt) cc_final: 0.6962 (ttmm) outliers start: 7 outliers final: 5 residues processed: 100 average time/residue: 0.1994 time to fit residues: 23.1185 Evaluate side-chains 103 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 342 GLU 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 C residue 378 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.4896 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= 0.351 Angle : 0.677 6.664 4626 Z= 0.346 Chirality : 0.052 0.148 522 Planarity : 0.004 0.059 588 Dihedral : 5.326 15.286 456 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.31 % Allowed : 18.21 % Favored : 79.49 % 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: -1.56 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 362 PHE 0.011 0.002 PHE F 346 TYR 0.020 0.004 TYR B 310 ARG 0.003 0.001 ARG A 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 108 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: B 340 LYS cc_start: 0.7526 (tttt) cc_final: 0.6914 (mttm) REVERT: B 345 ASP cc_start: 0.7525 (t0) cc_final: 0.6779 (t70) REVERT: B 347 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7457 (mmtt) REVERT: D 337 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8343 (m) REVERT: D 340 LYS cc_start: 0.8000 (tttt) cc_final: 0.7533 (mtpt) REVERT: D 347 LYS cc_start: 0.8216 (mmtt) cc_final: 0.6672 (mtmm) REVERT: D 375 LYS cc_start: 0.8338 (tttt) cc_final: 0.7823 (tttp) REVERT: F 311 LYS cc_start: 0.7708 (mttt) cc_final: 0.7004 (tppt) REVERT: F 338 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7024 (tm-30) REVERT: F 340 LYS cc_start: 0.7247 (tttt) cc_final: 0.6806 (mttm) REVERT: F 349 ARG cc_start: 0.7157 (mmt90) cc_final: 0.5394 (mmt-90) REVERT: F 362 HIS cc_start: 0.7595 (t-170) cc_final: 0.7221 (m170) REVERT: F 375 LYS cc_start: 0.8030 (tttt) cc_final: 0.7578 (tttp) REVERT: A 316 SER cc_start: 0.8797 (p) cc_final: 0.8467 (p) REVERT: A 336 GLN cc_start: 0.7136 (mp10) cc_final: 0.6680 (mm-40) REVERT: A 369 LYS cc_start: 0.7739 (tttt) cc_final: 0.6842 (ttmm) REVERT: C 311 LYS cc_start: 0.8345 (mtpp) cc_final: 0.8096 (mtpp) REVERT: C 369 LYS cc_start: 0.7927 (tttt) cc_final: 0.7096 (ttmm) REVERT: E 311 LYS cc_start: 0.7528 (mttt) cc_final: 0.6829 (mmtt) REVERT: E 349 ARG cc_start: 0.6058 (mmt90) cc_final: 0.4272 (mmp-170) REVERT: E 369 LYS cc_start: 0.7743 (tttt) cc_final: 0.6982 (ttmm) outliers start: 9 outliers final: 6 residues processed: 102 average time/residue: 0.1925 time to fit residues: 22.9761 Evaluate side-chains 105 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain D residue 337 VAL 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 C residue 378 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.1980 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 0.0020 chunk 33 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3456 Z= 0.137 Angle : 0.589 7.681 4626 Z= 0.289 Chirality : 0.050 0.146 522 Planarity : 0.004 0.059 588 Dihedral : 4.761 13.983 456 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.28 % Allowed : 18.97 % Favored : 79.74 % 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: -1.48 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 362 PHE 0.007 0.001 PHE F 346 TYR 0.027 0.002 TYR B 310 ARG 0.001 0.000 ARG C 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 106 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.419 Fit side-chains REVERT: B 331 LYS cc_start: 0.7927 (mttt) cc_final: 0.7503 (mttm) REVERT: B 336 GLN cc_start: 0.8122 (mt0) cc_final: 0.7911 (mm-40) REVERT: B 345 ASP cc_start: 0.7582 (t0) cc_final: 0.6855 (t70) REVERT: B 375 LYS cc_start: 0.8197 (tttt) cc_final: 0.7630 (tttp) REVERT: D 331 LYS cc_start: 0.8248 (mttt) cc_final: 0.8015 (mttm) REVERT: D 337 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8304 (m) REVERT: D 340 LYS cc_start: 0.8041 (tttt) cc_final: 0.7525 (mtpt) REVERT: D 347 LYS cc_start: 0.8089 (mmtt) cc_final: 0.6621 (mtmm) REVERT: D 375 LYS cc_start: 0.8363 (tttt) cc_final: 0.7909 (tttp) REVERT: F 311 LYS cc_start: 0.7789 (mttt) cc_final: 0.7046 (tppt) REVERT: F 340 LYS cc_start: 0.7280 (tttt) cc_final: 0.6883 (mttm) REVERT: F 349 ARG cc_start: 0.7104 (mmt90) cc_final: 0.5384 (mmt-90) REVERT: F 362 HIS cc_start: 0.7547 (t-170) cc_final: 0.7296 (m170) REVERT: F 375 LYS cc_start: 0.8115 (tttt) cc_final: 0.7533 (tttm) REVERT: A 316 SER cc_start: 0.8871 (p) cc_final: 0.8568 (p) REVERT: A 331 LYS cc_start: 0.7873 (mttt) cc_final: 0.7609 (mttp) REVERT: A 336 GLN cc_start: 0.7138 (mp10) cc_final: 0.6737 (mm-40) REVERT: A 369 LYS cc_start: 0.7712 (tttt) cc_final: 0.6837 (ttmm) REVERT: C 311 LYS cc_start: 0.8304 (mtpp) cc_final: 0.8041 (mtpp) REVERT: C 369 LYS cc_start: 0.7900 (tttt) cc_final: 0.7075 (ttmm) REVERT: E 311 LYS cc_start: 0.7487 (mttt) cc_final: 0.6895 (mmtt) REVERT: E 340 LYS cc_start: 0.7334 (ttmm) cc_final: 0.6934 (mttm) REVERT: E 349 ARG cc_start: 0.5819 (mmt90) cc_final: 0.4177 (mmp-170) REVERT: E 369 LYS cc_start: 0.7714 (tttt) cc_final: 0.6928 (ttmm) outliers start: 5 outliers final: 3 residues processed: 102 average time/residue: 0.2053 time to fit residues: 24.3424 Evaluate side-chains 103 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain C residue 378 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.0970 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.145598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.135262 restraints weight = 4899.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.137412 restraints weight = 2518.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.138788 restraints weight = 1568.391| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3456 Z= 0.204 Angle : 0.619 8.346 4626 Z= 0.304 Chirality : 0.050 0.143 522 Planarity : 0.004 0.059 588 Dihedral : 4.777 13.687 456 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.03 % Allowed : 20.51 % Favored : 78.46 % 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: -1.47 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 362 PHE 0.011 0.001 PHE F 346 TYR 0.026 0.003 TYR B 310 ARG 0.002 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1245.66 seconds wall clock time: 23 minutes 12.47 seconds (1392.47 seconds total)