Starting phenix.real_space_refine on Mon Mar 11 04:35:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9b_18275/03_2024/8q9b_18275.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9b_18275/03_2024/8q9b_18275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9b_18275/03_2024/8q9b_18275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9b_18275/03_2024/8q9b_18275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9b_18275/03_2024/8q9b_18275.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9b_18275/03_2024/8q9b_18275.pdb" } resolution = 3.1 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= 0.002 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 H 3588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 7032 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 3.55, per 1000 atoms: 0.50 Number of scatterers: 7032 At special positions: 0 Unit cell: (96.408, 150.792, 37.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 642 8.00 N 636 7.00 C 2160 6.00 H 3588 1.00 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: 5.03 Conformation dependent library (CDL) restraints added in 692.9 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: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 57.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.585A pdb=" N VAL A 306 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL F 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN E 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR F 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL E 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.743A pdb=" N VAL E 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 325 removed outlier: 6.100A pdb=" N LYS E 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N SER F 320 " --> pdb=" O LYS E 317 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR E 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N CYS F 322 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS E 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N SER F 324 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY E 323 " --> pdb=" O SER F 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.627A pdb=" N ILE E 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 342 Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.517A pdb=" N ASP E 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 362 removed outlier: 6.928A pdb=" N GLN A 351 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER F 352 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS A 353 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE F 354 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLY A 355 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER F 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER F 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU E 357 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP F 358 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN E 359 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE F 360 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR E 361 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N HIS F 362 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 368 through 378 removed outlier: 6.479A pdb=" N LYS E 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLU F 372 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE E 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N HIS F 374 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR E 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU F 376 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS E 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N PHE F 378 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR E 377 " --> pdb=" O PHE F 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.441A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL C 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL D 309 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE C 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.722A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 317 through 325 removed outlier: 6.109A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.589A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 337 through 342 removed outlier: 6.472A pdb=" N GLU B 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N SER D 341 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS B 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLU D 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER C 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.414A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 350 through 362 removed outlier: 6.944A pdb=" N LEU B 357 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP D 358 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN B 359 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE D 360 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR B 361 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N HIS D 362 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL C 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LYS D 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER C 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N GLY D 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE C 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU D 357 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N SER C 356 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 10.428A pdb=" N ASN D 359 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N ASP C 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N THR D 361 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N ILE C 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 368 through 378 removed outlier: 6.484A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE D 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 213 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: 2.09 Time building geometry restraints manager: 5.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 3582 1.12 - 1.29: 570 1.29 - 1.46: 1011 1.46 - 1.64: 1917 1.64 - 1.81: 6 Bond restraints: 7086 Sorted by residual: bond pdb=" N LEU F 325 " pdb=" H LEU F 325 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLU E 372 " pdb=" H GLU E 372 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" ND2 ASN A 368 " pdb="HD21 ASN A 368 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N TYR F 310 " pdb=" H TYR F 310 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LYS E 311 " pdb=" H LYS E 311 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 96.32 - 102.88: 31 102.88 - 109.43: 5175 109.43 - 115.99: 4054 115.99 - 122.55: 2975 122.55 - 129.11: 677 Bond angle restraints: 12912 Sorted by residual: angle pdb=" C ASP E 348 " pdb=" N ARG E 349 " pdb=" CA ARG E 349 " ideal model delta sigma weight residual 121.56 128.79 -7.23 1.56e+00 4.11e-01 2.15e+01 angle pdb=" CB HIS B 329 " pdb=" CG HIS B 329 " pdb=" CD2 HIS B 329 " ideal model delta sigma weight residual 131.20 125.24 5.96 1.30e+00 5.92e-01 2.10e+01 angle pdb=" C ASP B 348 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " ideal model delta sigma weight residual 121.56 128.65 -7.09 1.56e+00 4.11e-01 2.06e+01 angle pdb=" CB HIS B 330 " pdb=" CG HIS B 330 " pdb=" CD2 HIS B 330 " ideal model delta sigma weight residual 131.20 125.40 5.80 1.30e+00 5.92e-01 1.99e+01 angle pdb=" CB HIS D 329 " pdb=" CG HIS D 329 " pdb=" CD2 HIS D 329 " ideal model delta sigma weight residual 131.20 125.41 5.79 1.30e+00 5.92e-01 1.98e+01 ... (remaining 12907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.31: 2902 14.31 - 28.62: 164 28.62 - 42.93: 76 42.93 - 57.24: 64 57.24 - 71.55: 58 Dihedral angle restraints: 3264 sinusoidal: 1866 harmonic: 1398 Sorted by residual: dihedral pdb=" CA LYS C 317 " pdb=" C LYS C 317 " pdb=" N VAL C 318 " pdb=" CA VAL C 318 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA LYS F 317 " pdb=" C LYS F 317 " pdb=" N VAL F 318 " pdb=" CA VAL F 318 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA LYS D 317 " pdb=" C LYS D 317 " pdb=" N VAL D 318 " pdb=" CA VAL D 318 " ideal model delta harmonic sigma weight residual 180.00 157.34 22.66 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.062: 296 0.062 - 0.123: 181 0.123 - 0.184: 36 0.184 - 0.245: 5 0.245 - 0.306: 10 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS B 311 " pdb=" N LYS B 311 " pdb=" C LYS B 311 " pdb=" CB LYS B 311 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA LYS E 311 " pdb=" N LYS E 311 " pdb=" C LYS E 311 " pdb=" CB LYS E 311 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 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 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 525 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.111 2.00e-02 2.50e+03 4.99e-02 7.48e+01 pdb=" CG TYR E 310 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.106 2.00e-02 2.50e+03 pdb=" HD1 TYR E 310 " -0.009 2.00e-02 2.50e+03 pdb=" HD2 TYR E 310 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 TYR E 310 " -0.025 2.00e-02 2.50e+03 pdb=" HE2 TYR E 310 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " 0.089 2.00e-02 2.50e+03 4.05e-02 4.91e+01 pdb=" CG TYR B 310 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " 0.086 2.00e-02 2.50e+03 pdb=" HD1 TYR B 310 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR B 310 " -0.029 2.00e-02 2.50e+03 pdb=" HE1 TYR B 310 " -0.025 2.00e-02 2.50e+03 pdb=" HE2 TYR B 310 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.088 2.00e-02 2.50e+03 4.03e-02 4.86e+01 pdb=" CG TYR F 310 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.086 2.00e-02 2.50e+03 pdb=" HD1 TYR F 310 " -0.007 2.00e-02 2.50e+03 pdb=" HD2 TYR F 310 " -0.029 2.00e-02 2.50e+03 pdb=" HE1 TYR F 310 " -0.019 2.00e-02 2.50e+03 pdb=" HE2 TYR F 310 " -0.009 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 539 2.17 - 2.78: 12128 2.78 - 3.39: 17832 3.39 - 3.99: 24552 3.99 - 4.60: 34219 Nonbonded interactions: 89270 Sorted by model distance: nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.563 1.850 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.565 1.850 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.578 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.585 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.629 1.850 ... (remaining 89265 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.270 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: 0.110 Extract box with map and model: 11.620 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.500 Find NCS groups from input model: 0.320 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 0.035 3498 Z= 0.714 Angle : 1.788 7.231 4680 Z= 1.193 Chirality : 0.082 0.306 528 Planarity : 0.011 0.058 594 Dihedral : 10.912 67.422 1344 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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: -1.61 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS F 330 PHE 0.038 0.012 PHE C 346 TYR 0.099 0.031 TYR E 310 ARG 0.002 0.001 ARG A 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 124 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7699 (mttt) cc_final: 0.7377 (mtpt) REVERT: A 321 LYS cc_start: 0.8409 (mttt) cc_final: 0.8085 (mttm) REVERT: A 349 ARG cc_start: 0.7435 (mtm180) cc_final: 0.6805 (ptt-90) REVERT: B 311 LYS cc_start: 0.7901 (mttt) cc_final: 0.7221 (mttm) REVERT: B 317 LYS cc_start: 0.6550 (mttt) cc_final: 0.5941 (mtpt) REVERT: B 340 LYS cc_start: 0.7548 (tttt) cc_final: 0.7052 (mmtt) REVERT: C 349 ARG cc_start: 0.7443 (mtm180) cc_final: 0.6917 (ptt-90) REVERT: D 311 LYS cc_start: 0.8244 (mttt) cc_final: 0.8013 (mtmt) REVERT: D 338 GLU cc_start: 0.7606 (tt0) cc_final: 0.7392 (tt0) REVERT: D 345 ASP cc_start: 0.8015 (t0) cc_final: 0.7813 (m-30) REVERT: D 349 ARG cc_start: 0.6871 (mtm180) cc_final: 0.6564 (mtt-85) REVERT: D 372 GLU cc_start: 0.7662 (tt0) cc_final: 0.7382 (tt0) REVERT: E 317 LYS cc_start: 0.6489 (mttt) cc_final: 0.6042 (mtpt) REVERT: E 340 LYS cc_start: 0.7682 (tttt) cc_final: 0.7181 (mmtt) REVERT: E 353 LYS cc_start: 0.6414 (mttt) cc_final: 0.6197 (tttm) REVERT: F 317 LYS cc_start: 0.6333 (mttt) cc_final: 0.5848 (mtpt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.7207 time to fit residues: 98.0246 Evaluate side-chains 81 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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: 1.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN C 307 GLN D 307 GLN E 307 GLN F 307 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3498 Z= 0.353 Angle : 0.542 4.123 4680 Z= 0.292 Chirality : 0.050 0.139 528 Planarity : 0.005 0.039 594 Dihedral : 6.067 21.200 462 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.52 % Allowed : 4.55 % Favored : 93.94 % 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: -1.32 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 374 PHE 0.008 0.001 PHE D 346 TYR 0.009 0.002 TYR F 310 ARG 0.001 0.000 ARG A 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 84 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7484 (mtm180) cc_final: 0.7044 (mtt180) REVERT: B 311 LYS cc_start: 0.8070 (mttt) cc_final: 0.7708 (mtpt) REVERT: B 317 LYS cc_start: 0.6590 (mttt) cc_final: 0.6153 (mtmt) REVERT: B 340 LYS cc_start: 0.7614 (tttt) cc_final: 0.7231 (mmtt) REVERT: C 349 ARG cc_start: 0.7471 (mtm180) cc_final: 0.6885 (ptt-90) REVERT: D 349 ARG cc_start: 0.6812 (mtm180) cc_final: 0.6462 (mtt180) REVERT: E 311 LYS cc_start: 0.7978 (mttt) cc_final: 0.7760 (mtmt) REVERT: E 317 LYS cc_start: 0.6602 (mttt) cc_final: 0.6114 (mtpt) REVERT: E 340 LYS cc_start: 0.7565 (tttt) cc_final: 0.7093 (mmtt) outliers start: 6 outliers final: 6 residues processed: 84 average time/residue: 0.6728 time to fit residues: 62.7589 Evaluate side-chains 77 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER 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: 7.9990 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3498 Z= 0.240 Angle : 0.481 3.993 4680 Z= 0.251 Chirality : 0.050 0.128 528 Planarity : 0.004 0.031 594 Dihedral : 5.388 18.134 462 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.52 % Allowed : 5.05 % Favored : 93.43 % 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: -1.04 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.78 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.009 0.001 PHE D 346 TYR 0.008 0.002 TYR F 310 ARG 0.002 0.000 ARG B 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 78 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7556 (mtm180) cc_final: 0.7111 (mtt180) REVERT: B 311 LYS cc_start: 0.7935 (mttt) cc_final: 0.7640 (mtmt) REVERT: B 317 LYS cc_start: 0.6635 (mttt) cc_final: 0.6134 (mtmt) REVERT: B 340 LYS cc_start: 0.7647 (tttt) cc_final: 0.7241 (mmtt) REVERT: B 345 ASP cc_start: 0.8192 (t0) cc_final: 0.7953 (t0) REVERT: B 347 LYS cc_start: 0.8937 (mttm) cc_final: 0.8703 (mmtm) REVERT: C 349 ARG cc_start: 0.7560 (mtm180) cc_final: 0.6963 (ptt-90) REVERT: D 349 ARG cc_start: 0.6895 (mtm180) cc_final: 0.6548 (mtt-85) REVERT: E 311 LYS cc_start: 0.7897 (mttt) cc_final: 0.7628 (mtmt) REVERT: E 317 LYS cc_start: 0.6729 (mttt) cc_final: 0.6114 (mtpt) REVERT: E 340 LYS cc_start: 0.7570 (tttt) cc_final: 0.7125 (mmtt) outliers start: 6 outliers final: 6 residues processed: 78 average time/residue: 0.6778 time to fit residues: 58.7798 Evaluate side-chains 76 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.0370 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 20 optimal weight: 0.0770 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.3620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3498 Z= 0.154 Angle : 0.439 3.945 4680 Z= 0.224 Chirality : 0.050 0.128 528 Planarity : 0.003 0.026 594 Dihedral : 4.894 15.005 462 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.52 % Allowed : 6.06 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.39), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.68 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.005 0.001 PHE F 346 TYR 0.006 0.001 TYR F 310 ARG 0.001 0.000 ARG F 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 78 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7532 (mtm180) cc_final: 0.7115 (mtt-85) REVERT: A 353 LYS cc_start: 0.7250 (mttt) cc_final: 0.7019 (tttm) REVERT: B 311 LYS cc_start: 0.7961 (mttt) cc_final: 0.7685 (mtmt) REVERT: B 317 LYS cc_start: 0.6583 (mttt) cc_final: 0.6079 (mtpt) REVERT: B 349 ARG cc_start: 0.4804 (mmp-170) cc_final: 0.4522 (tpm170) REVERT: C 349 ARG cc_start: 0.7585 (mtm180) cc_final: 0.6984 (ptt-90) REVERT: D 349 ARG cc_start: 0.6879 (mtm180) cc_final: 0.6403 (mtt90) REVERT: E 311 LYS cc_start: 0.7984 (mttt) cc_final: 0.7732 (mtmt) REVERT: E 340 LYS cc_start: 0.7493 (tttt) cc_final: 0.7052 (mmtt) outliers start: 6 outliers final: 6 residues processed: 78 average time/residue: 0.6652 time to fit residues: 58.1725 Evaluate side-chains 74 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 34 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3498 Z= 0.109 Angle : 0.421 3.842 4680 Z= 0.211 Chirality : 0.051 0.129 528 Planarity : 0.003 0.023 594 Dihedral : 4.463 12.702 462 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 0.76 % Allowed : 7.07 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.39), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.58 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 362 PHE 0.005 0.001 PHE F 346 TYR 0.005 0.001 TYR F 310 ARG 0.001 0.000 ARG D 379 *********************** 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 75 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7529 (mtm180) cc_final: 0.7074 (mtt180) REVERT: B 311 LYS cc_start: 0.7962 (mttt) cc_final: 0.7695 (mtmt) REVERT: B 317 LYS cc_start: 0.6646 (mttt) cc_final: 0.6127 (mtpt) REVERT: B 340 LYS cc_start: 0.7794 (mtpp) cc_final: 0.6752 (mmtt) REVERT: B 349 ARG cc_start: 0.5051 (mmp-170) cc_final: 0.4838 (tpm170) REVERT: C 349 ARG cc_start: 0.7640 (mtm180) cc_final: 0.6580 (pmt-80) REVERT: D 349 ARG cc_start: 0.6907 (mtm180) cc_final: 0.6446 (mtt90) REVERT: E 311 LYS cc_start: 0.7914 (mttt) cc_final: 0.7702 (mtmt) REVERT: E 340 LYS cc_start: 0.7468 (tttt) cc_final: 0.7059 (mmtt) outliers start: 3 outliers final: 3 residues processed: 75 average time/residue: 0.6382 time to fit residues: 53.4489 Evaluate side-chains 70 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3498 Z= 0.162 Angle : 0.418 3.883 4680 Z= 0.212 Chirality : 0.050 0.128 528 Planarity : 0.003 0.024 594 Dihedral : 4.507 12.738 462 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 2.02 % Allowed : 5.81 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.40), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.54 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 330 PHE 0.006 0.001 PHE D 378 TYR 0.007 0.002 TYR F 310 ARG 0.001 0.000 ARG B 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 80 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7569 (mtm180) cc_final: 0.7070 (mtt180) REVERT: B 311 LYS cc_start: 0.7895 (mttt) cc_final: 0.7571 (mtmt) REVERT: B 317 LYS cc_start: 0.6628 (mttt) cc_final: 0.6102 (mtpt) REVERT: B 340 LYS cc_start: 0.7761 (mtpp) cc_final: 0.6745 (mmtt) REVERT: B 349 ARG cc_start: 0.4956 (mmp-170) cc_final: 0.4734 (tpm170) REVERT: C 349 ARG cc_start: 0.7663 (mtm180) cc_final: 0.6610 (pmt-80) REVERT: D 349 ARG cc_start: 0.6932 (mtm180) cc_final: 0.6471 (mtt90) REVERT: E 311 LYS cc_start: 0.7990 (mttt) cc_final: 0.7722 (mtmt) REVERT: E 340 LYS cc_start: 0.7445 (tttt) cc_final: 0.7057 (mmtt) outliers start: 8 outliers final: 6 residues processed: 79 average time/residue: 0.6640 time to fit residues: 58.8002 Evaluate side-chains 76 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3498 Z= 0.115 Angle : 0.404 3.789 4680 Z= 0.202 Chirality : 0.050 0.127 528 Planarity : 0.003 0.023 594 Dihedral : 4.261 12.027 462 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.52 % Allowed : 6.31 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.41), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.50 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 362 PHE 0.004 0.001 PHE B 346 TYR 0.005 0.001 TYR F 310 ARG 0.001 0.000 ARG B 379 *********************** 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 76 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7570 (mtm180) cc_final: 0.7102 (mtt180) REVERT: B 311 LYS cc_start: 0.7947 (mttt) cc_final: 0.7662 (mtmt) REVERT: B 317 LYS cc_start: 0.6540 (mttt) cc_final: 0.6088 (mtpt) REVERT: B 340 LYS cc_start: 0.7773 (mtpp) cc_final: 0.6906 (mmtt) REVERT: B 349 ARG cc_start: 0.4924 (mmp-170) cc_final: 0.4685 (tpm170) REVERT: C 349 ARG cc_start: 0.7676 (mtm180) cc_final: 0.6610 (pmt-80) REVERT: D 349 ARG cc_start: 0.6953 (mtm180) cc_final: 0.6491 (mtt90) REVERT: E 311 LYS cc_start: 0.7978 (mttt) cc_final: 0.7747 (mtmt) REVERT: E 340 LYS cc_start: 0.7425 (tttt) cc_final: 0.7051 (mmtt) outliers start: 6 outliers final: 6 residues processed: 76 average time/residue: 0.6618 time to fit residues: 56.4395 Evaluate side-chains 75 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3498 Z= 0.230 Angle : 0.428 3.905 4680 Z= 0.218 Chirality : 0.049 0.121 528 Planarity : 0.003 0.025 594 Dihedral : 4.586 12.833 462 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.52 % Allowed : 6.31 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.41), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.52 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.006 0.001 PHE F 378 TYR 0.009 0.002 TYR D 310 ARG 0.002 0.000 ARG B 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 78 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7559 (mtm180) cc_final: 0.7102 (mtt180) REVERT: B 311 LYS cc_start: 0.7928 (mttt) cc_final: 0.7584 (mtmt) REVERT: B 317 LYS cc_start: 0.6596 (mttt) cc_final: 0.6066 (mtpt) REVERT: B 340 LYS cc_start: 0.7756 (mtpp) cc_final: 0.6840 (mmtt) REVERT: B 349 ARG cc_start: 0.4946 (mmp-170) cc_final: 0.4662 (tpm170) REVERT: C 349 ARG cc_start: 0.7679 (mtm180) cc_final: 0.6585 (pmt-80) REVERT: D 349 ARG cc_start: 0.6971 (mtm180) cc_final: 0.6510 (mtt90) REVERT: E 311 LYS cc_start: 0.7975 (mttt) cc_final: 0.7642 (mtmt) REVERT: E 340 LYS cc_start: 0.7461 (tttt) cc_final: 0.7051 (mmtt) outliers start: 6 outliers final: 6 residues processed: 78 average time/residue: 0.6423 time to fit residues: 56.2771 Evaluate side-chains 76 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3498 Z= 0.159 Angle : 0.411 3.845 4680 Z= 0.207 Chirality : 0.050 0.123 528 Planarity : 0.003 0.024 594 Dihedral : 4.427 12.154 462 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.52 % Allowed : 6.57 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.41), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.56 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 329 PHE 0.004 0.001 PHE F 378 TYR 0.007 0.002 TYR F 310 ARG 0.001 0.000 ARG B 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 77 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7550 (mtm180) cc_final: 0.7095 (mtt180) REVERT: B 311 LYS cc_start: 0.7901 (mttt) cc_final: 0.7557 (mtmt) REVERT: B 317 LYS cc_start: 0.6528 (mttt) cc_final: 0.6029 (mtpt) REVERT: B 340 LYS cc_start: 0.7744 (mtpp) cc_final: 0.6907 (mmtt) REVERT: B 349 ARG cc_start: 0.4939 (mmp-170) cc_final: 0.4641 (tpm170) REVERT: C 349 ARG cc_start: 0.7674 (mtm180) cc_final: 0.6584 (pmt-80) REVERT: D 349 ARG cc_start: 0.6988 (mtm180) cc_final: 0.6569 (mtt90) REVERT: E 311 LYS cc_start: 0.8055 (mttt) cc_final: 0.7755 (mtmt) REVERT: E 340 LYS cc_start: 0.7443 (tttt) cc_final: 0.7037 (mmtt) outliers start: 6 outliers final: 6 residues processed: 77 average time/residue: 0.6264 time to fit residues: 54.1108 Evaluate side-chains 76 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3498 Z= 0.263 Angle : 0.442 3.961 4680 Z= 0.225 Chirality : 0.049 0.122 528 Planarity : 0.003 0.026 594 Dihedral : 4.707 12.949 462 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.52 % Allowed : 6.57 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.41), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.60 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 374 PHE 0.003 0.001 PHE D 378 TYR 0.009 0.002 TYR D 310 ARG 0.003 0.000 ARG B 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 76 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7582 (mtm180) cc_final: 0.7122 (mtt180) REVERT: B 311 LYS cc_start: 0.8006 (mttt) cc_final: 0.7619 (mtmt) REVERT: B 317 LYS cc_start: 0.6628 (mttt) cc_final: 0.6105 (mtpt) REVERT: B 340 LYS cc_start: 0.7733 (mtpp) cc_final: 0.6858 (mmtt) REVERT: B 349 ARG cc_start: 0.4968 (mmp-170) cc_final: 0.4667 (tpm170) REVERT: C 349 ARG cc_start: 0.7697 (mtm180) cc_final: 0.6588 (pmt-80) REVERT: C 353 LYS cc_start: 0.7199 (mttt) cc_final: 0.6833 (tttm) REVERT: D 349 ARG cc_start: 0.7039 (mtm180) cc_final: 0.6689 (mtt180) REVERT: D 372 GLU cc_start: 0.7769 (tt0) cc_final: 0.7311 (tt0) REVERT: E 311 LYS cc_start: 0.8031 (mttt) cc_final: 0.7680 (mtmt) REVERT: E 340 LYS cc_start: 0.7477 (tttt) cc_final: 0.7039 (mmtt) outliers start: 6 outliers final: 6 residues processed: 76 average time/residue: 0.6319 time to fit residues: 53.9314 Evaluate side-chains 75 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 0.0980 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.136229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.119366 restraints weight = 13391.195| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.69 r_work: 0.3909 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3498 Z= 0.145 Angle : 0.414 3.861 4680 Z= 0.207 Chirality : 0.050 0.123 528 Planarity : 0.003 0.024 594 Dihedral : 4.431 11.753 462 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.52 % Allowed : 7.32 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.41), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.58 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 330 PHE 0.003 0.001 PHE F 378 TYR 0.006 0.001 TYR F 310 ARG 0.001 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3032.31 seconds wall clock time: 54 minutes 2.10 seconds (3242.10 seconds total)