Starting phenix.real_space_refine on Mon Mar 11 03:21:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9j_18283/03_2024/8q9j_18283.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9j_18283/03_2024/8q9j_18283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9j_18283/03_2024/8q9j_18283.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9j_18283/03_2024/8q9j_18283.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9j_18283/03_2024/8q9j_18283.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9j_18283/03_2024/8q9j_18283.pdb" } resolution = 2.96 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 2106 2.51 5 N 606 2.21 5 O 624 1.98 5 H 3480 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 372": "OE1" <-> "OE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 372": "OE1" <-> "OE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 372": "OE1" <-> "OE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F GLU 372": "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: 6822 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "B" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 3.50, per 1000 atoms: 0.51 Number of scatterers: 6822 At special positions: 0 Unit cell: (119.228, 100.326, 50.163, 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 624 8.00 N 606 7.00 C 2106 6.00 H 3480 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: 4.78 Conformation dependent library (CDL) restraints added in 737.8 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 50.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.376A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 7.127A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.375A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330 removed outlier: 5.771A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN A 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.459A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLU A 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N SER E 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS A 340 " --> pdb=" O SER E 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.525A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 357 Processing sheet with id=AA8, first strand: chain 'C' and resid 360 through 362 Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 377 removed outlier: 6.426A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.598A pdb=" N GLN B 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N TYR F 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 7.090A pdb=" N VAL B 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 322 removed outlier: 6.466A pdb=" N LYS B 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N SER F 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR B 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N CYS F 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS B 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 325 through 330 removed outlier: 5.905A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY F 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN B 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.433A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLU D 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER B 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.592A pdb=" N ASP B 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.490A pdb=" N GLN B 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE F 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS B 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N SER F 356 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLY B 355 " --> pdb=" O SER F 356 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.484A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 369 through 377 removed outlier: 6.447A pdb=" N LYS B 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N GLU F 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE B 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N HIS F 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR B 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LEU F 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS B 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 222 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: 2.23 Time building geometry restraints manager: 5.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3474 1.12 - 1.29: 560 1.29 - 1.47: 1022 1.47 - 1.64: 1814 1.64 - 1.81: 6 Bond restraints: 6876 Sorted by residual: bond pdb=" CD2 HIS E 330 " pdb=" HD2 HIS E 330 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N LYS D 353 " pdb=" H LYS D 353 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" ND2 ASN C 327 " pdb="HD21 ASN C 327 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY E 323 " pdb=" H GLY E 323 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CE2 TYR D 310 " pdb=" HE2 TYR D 310 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 6871 not shown) Histogram of bond angle deviations from ideal: 96.55 - 102.98: 18 102.98 - 109.40: 4980 109.40 - 115.82: 3995 115.82 - 122.25: 2753 122.25 - 128.67: 800 Bond angle restraints: 12546 Sorted by residual: angle pdb=" C GLY F 334 " pdb=" N GLY F 335 " pdb=" CA GLY F 335 " ideal model delta sigma weight residual 120.60 125.80 -5.20 1.01e+00 9.80e-01 2.65e+01 angle pdb=" CB HIS F 374 " pdb=" CG HIS F 374 " pdb=" CD2 HIS F 374 " ideal model delta sigma weight residual 131.20 124.53 6.67 1.30e+00 5.92e-01 2.64e+01 angle pdb=" CB HIS B 374 " pdb=" CG HIS B 374 " pdb=" CD2 HIS B 374 " ideal model delta sigma weight residual 131.20 125.03 6.17 1.30e+00 5.92e-01 2.25e+01 angle pdb=" CB HIS C 329 " pdb=" CG HIS C 329 " pdb=" CD2 HIS C 329 " ideal model delta sigma weight residual 131.20 125.31 5.89 1.30e+00 5.92e-01 2.06e+01 angle pdb=" CB HIS A 329 " pdb=" CG HIS A 329 " pdb=" CD2 HIS A 329 " ideal model delta sigma weight residual 131.20 125.32 5.88 1.30e+00 5.92e-01 2.05e+01 ... (remaining 12541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.69: 2747 13.69 - 27.38: 214 27.38 - 41.07: 69 41.07 - 54.76: 53 54.76 - 68.45: 85 Dihedral angle restraints: 3168 sinusoidal: 1806 harmonic: 1362 Sorted by residual: dihedral pdb=" CA GLY F 323 " pdb=" C GLY F 323 " pdb=" N SER F 324 " pdb=" CA SER F 324 " ideal model delta harmonic sigma weight residual 180.00 155.29 24.71 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA ILE E 360 " pdb=" C ILE E 360 " pdb=" N THR E 361 " pdb=" CA THR E 361 " ideal model delta harmonic sigma weight residual 180.00 155.37 24.63 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLY E 323 " pdb=" C GLY E 323 " pdb=" N SER E 324 " pdb=" CA SER E 324 " ideal model delta harmonic sigma weight residual 180.00 155.42 24.58 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 3165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 296 0.067 - 0.134: 165 0.134 - 0.202: 45 0.202 - 0.269: 7 0.269 - 0.336: 3 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA LYS B 317 " pdb=" N LYS B 317 " pdb=" C LYS B 317 " pdb=" CB LYS B 317 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA LYS D 343 " pdb=" N LYS D 343 " pdb=" C LYS D 343 " pdb=" CB LYS D 343 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA LYS A 317 " pdb=" N LYS A 317 " pdb=" C LYS A 317 " pdb=" CB LYS A 317 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 513 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " -0.099 2.00e-02 2.50e+03 4.49e-02 6.06e+01 pdb=" CG TYR C 310 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.025 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " -0.098 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " 0.012 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " -0.102 2.00e-02 2.50e+03 4.34e-02 5.65e+01 pdb=" CG TYR D 310 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " -0.084 2.00e-02 2.50e+03 pdb=" HD1 TYR D 310 " 0.007 2.00e-02 2.50e+03 pdb=" HD2 TYR D 310 " 0.030 2.00e-02 2.50e+03 pdb=" HE1 TYR D 310 " 0.017 2.00e-02 2.50e+03 pdb=" HE2 TYR D 310 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.090 2.00e-02 2.50e+03 3.94e-02 4.65e+01 pdb=" CG TYR A 310 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.081 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " 0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " 0.004 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 503 2.18 - 2.79: 11907 2.79 - 3.39: 17566 3.39 - 4.00: 24456 4.00 - 4.60: 33504 Nonbonded interactions: 87936 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.577 1.850 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.578 1.850 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.581 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.598 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.600 1.850 ... (remaining 87931 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: 3.580 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: 11.590 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 24.800 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 0.039 3396 Z= 0.751 Angle : 1.860 9.801 4548 Z= 1.236 Chirality : 0.087 0.336 516 Planarity : 0.011 0.062 576 Dihedral : 10.827 61.776 1296 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -1.24 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.004 HIS A 330 PHE 0.035 0.010 PHE A 346 TYR 0.093 0.031 TYR D 310 ARG 0.005 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8164 (mttt) cc_final: 0.7955 (mttp) REVERT: A 369 LYS cc_start: 0.7068 (mttt) cc_final: 0.6703 (mtpt) REVERT: A 370 LYS cc_start: 0.6981 (tttm) cc_final: 0.6741 (tttp) REVERT: A 372 GLU cc_start: 0.6509 (tt0) cc_final: 0.6164 (tp30) REVERT: C 321 LYS cc_start: 0.6612 (ttpt) cc_final: 0.6290 (ptpp) REVERT: C 340 LYS cc_start: 0.7883 (mtpt) cc_final: 0.7417 (tppt) REVERT: C 347 LYS cc_start: 0.7812 (mttt) cc_final: 0.7100 (mmpt) REVERT: C 349 ARG cc_start: 0.7390 (mtt180) cc_final: 0.5704 (mmp-170) REVERT: C 369 LYS cc_start: 0.7035 (mttt) cc_final: 0.6763 (mtpt) REVERT: C 370 LYS cc_start: 0.8097 (tttm) cc_final: 0.7155 (mptt) REVERT: C 372 GLU cc_start: 0.7646 (tt0) cc_final: 0.7197 (mp0) REVERT: C 375 LYS cc_start: 0.5780 (tttt) cc_final: 0.5237 (tppt) REVERT: E 311 LYS cc_start: 0.7113 (ttpt) cc_final: 0.6611 (pttp) REVERT: E 340 LYS cc_start: 0.8295 (mtpt) cc_final: 0.7915 (ttpt) REVERT: E 342 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7509 (tm-30) REVERT: E 372 GLU cc_start: 0.5843 (tt0) cc_final: 0.5550 (tp30) REVERT: E 375 LYS cc_start: 0.7300 (tttt) cc_final: 0.6876 (ttmt) REVERT: B 310 TYR cc_start: 0.4789 (t80) cc_final: 0.4539 (t80) REVERT: B 321 LYS cc_start: 0.7361 (ttpt) cc_final: 0.7004 (mttm) REVERT: B 342 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7732 (mt-10) REVERT: B 349 ARG cc_start: 0.7404 (mtt180) cc_final: 0.7168 (mtp85) REVERT: D 342 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7903 (mt-10) REVERT: D 349 ARG cc_start: 0.7546 (mtt180) cc_final: 0.5794 (mmp-170) REVERT: D 372 GLU cc_start: 0.7736 (tt0) cc_final: 0.7404 (tt0) REVERT: F 317 LYS cc_start: 0.7346 (pttt) cc_final: 0.7128 (ptpp) REVERT: F 320 SER cc_start: 0.7986 (t) cc_final: 0.7425 (p) REVERT: F 321 LYS cc_start: 0.8009 (ttpt) cc_final: 0.7645 (mttm) REVERT: F 342 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8007 (mt-10) REVERT: F 349 ARG cc_start: 0.7596 (mtt180) cc_final: 0.5966 (mtm180) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 2.9379 time to fit residues: 378.3066 Evaluate side-chains 79 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 362 HIS E 362 HIS B 362 HIS D 362 HIS F 307 GLN F 351 GLN F 362 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3396 Z= 0.192 Angle : 0.585 4.760 4548 Z= 0.304 Chirality : 0.053 0.145 516 Planarity : 0.003 0.024 576 Dihedral : 6.437 19.725 444 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.82 % Allowed : 12.24 % Favored : 85.94 % 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 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.009 0.001 PHE B 346 TYR 0.008 0.002 TYR F 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6889 (mtp85) REVERT: C 340 LYS cc_start: 0.8015 (mtpt) cc_final: 0.7627 (tppt) REVERT: C 349 ARG cc_start: 0.7271 (mtt180) cc_final: 0.5776 (mtp180) REVERT: E 311 LYS cc_start: 0.7083 (ttpt) cc_final: 0.6638 (pttp) REVERT: E 338 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: E 342 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7349 (tm-30) REVERT: E 347 LYS cc_start: 0.8144 (mttt) cc_final: 0.7181 (mtmt) REVERT: B 321 LYS cc_start: 0.7576 (ttpt) cc_final: 0.7042 (mttm) REVERT: B 342 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7677 (mt-10) REVERT: D 349 ARG cc_start: 0.7479 (mtt180) cc_final: 0.5772 (mmp-170) REVERT: F 320 SER cc_start: 0.8166 (t) cc_final: 0.7465 (p) REVERT: F 321 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7515 (mttm) REVERT: F 342 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8018 (mt-10) REVERT: F 349 ARG cc_start: 0.7504 (mtt180) cc_final: 0.5845 (mtm180) REVERT: F 375 LYS cc_start: 0.6521 (tttt) cc_final: 0.6134 (ttmp) outliers start: 7 outliers final: 2 residues processed: 77 average time/residue: 3.0504 time to fit residues: 240.2289 Evaluate side-chains 59 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 37 optimal weight: 0.2980 chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3396 Z= 0.277 Angle : 0.585 4.640 4548 Z= 0.306 Chirality : 0.052 0.143 516 Planarity : 0.003 0.033 576 Dihedral : 6.008 18.795 444 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.34 % Allowed : 14.84 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 329 PHE 0.007 0.002 PHE D 346 TYR 0.010 0.002 TYR F 310 ARG 0.004 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 LYS cc_start: 0.7040 (mttt) cc_final: 0.6739 (mtpt) REVERT: A 373 THR cc_start: 0.5982 (m) cc_final: 0.5568 (p) REVERT: C 340 LYS cc_start: 0.8030 (mtpt) cc_final: 0.7650 (tppt) REVERT: C 349 ARG cc_start: 0.7316 (mtt180) cc_final: 0.7110 (mtt90) REVERT: E 338 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: E 347 LYS cc_start: 0.8173 (mttt) cc_final: 0.7252 (mtmt) REVERT: E 372 GLU cc_start: 0.6944 (tt0) cc_final: 0.5886 (mt-10) REVERT: B 321 LYS cc_start: 0.7596 (ttpt) cc_final: 0.7002 (mttm) REVERT: B 342 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7610 (mt-10) REVERT: D 342 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7392 (mp0) REVERT: D 349 ARG cc_start: 0.7474 (mtt180) cc_final: 0.5745 (mmp-170) REVERT: D 372 GLU cc_start: 0.7678 (tt0) cc_final: 0.7426 (tt0) REVERT: F 320 SER cc_start: 0.8201 (t) cc_final: 0.7740 (t) REVERT: F 321 LYS cc_start: 0.7966 (ttpt) cc_final: 0.7422 (mttp) REVERT: F 342 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8043 (mt-10) REVERT: F 349 ARG cc_start: 0.7558 (mtt180) cc_final: 0.5874 (mtm180) REVERT: F 375 LYS cc_start: 0.6659 (tttt) cc_final: 0.6089 (ttmm) outliers start: 9 outliers final: 2 residues processed: 71 average time/residue: 2.7948 time to fit residues: 203.4811 Evaluate side-chains 68 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 0.1980 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3396 Z= 0.173 Angle : 0.511 3.889 4548 Z= 0.263 Chirality : 0.051 0.134 516 Planarity : 0.003 0.029 576 Dihedral : 5.356 17.858 444 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.08 % Allowed : 16.67 % Favored : 81.25 % 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: -1.62 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 329 PHE 0.004 0.001 PHE E 378 TYR 0.010 0.001 TYR F 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6710 (mtt90) REVERT: A 369 LYS cc_start: 0.7024 (mttt) cc_final: 0.6695 (mtpt) REVERT: A 373 THR cc_start: 0.6011 (m) cc_final: 0.5602 (p) REVERT: C 340 LYS cc_start: 0.7996 (mtpt) cc_final: 0.7653 (tppt) REVERT: C 348 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8091 (t0) REVERT: C 349 ARG cc_start: 0.7280 (mtt180) cc_final: 0.7037 (mtt90) REVERT: E 338 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: E 342 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7279 (tm-30) REVERT: E 347 LYS cc_start: 0.8161 (mttt) cc_final: 0.7227 (mtmt) REVERT: E 375 LYS cc_start: 0.7510 (tttt) cc_final: 0.7013 (ttmt) REVERT: B 321 LYS cc_start: 0.7564 (ttpt) cc_final: 0.7000 (mttm) REVERT: B 342 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7603 (mt-10) REVERT: D 342 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7436 (mp0) REVERT: D 349 ARG cc_start: 0.7524 (mtt180) cc_final: 0.5759 (mmp-170) REVERT: D 372 GLU cc_start: 0.7638 (tt0) cc_final: 0.7352 (tt0) REVERT: F 320 SER cc_start: 0.8136 (t) cc_final: 0.7670 (t) REVERT: F 321 LYS cc_start: 0.7928 (ttpt) cc_final: 0.7379 (mttp) REVERT: F 342 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8067 (mt-10) REVERT: F 349 ARG cc_start: 0.7510 (mtt180) cc_final: 0.5848 (mtm180) REVERT: F 375 LYS cc_start: 0.6621 (tttt) cc_final: 0.6130 (ttmm) outliers start: 8 outliers final: 1 residues processed: 70 average time/residue: 2.7701 time to fit residues: 198.8699 Evaluate side-chains 65 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 28 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3396 Z= 0.179 Angle : 0.502 3.824 4548 Z= 0.258 Chirality : 0.051 0.133 516 Planarity : 0.003 0.029 576 Dihedral : 5.158 17.366 444 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.82 % Allowed : 17.19 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.004 0.001 PHE E 378 TYR 0.010 0.002 TYR F 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6777 (mtt90) REVERT: A 353 LYS cc_start: 0.8364 (mttm) cc_final: 0.8084 (mttt) REVERT: A 369 LYS cc_start: 0.7029 (mttt) cc_final: 0.6719 (mtpt) REVERT: A 373 THR cc_start: 0.6140 (m) cc_final: 0.5745 (p) REVERT: C 338 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7436 (tt0) REVERT: C 348 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8045 (t0) REVERT: C 349 ARG cc_start: 0.7311 (mtt180) cc_final: 0.7052 (mtt90) REVERT: E 338 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: E 347 LYS cc_start: 0.8150 (mttt) cc_final: 0.7207 (mtmt) REVERT: E 372 GLU cc_start: 0.7077 (tt0) cc_final: 0.6010 (mp0) REVERT: E 375 LYS cc_start: 0.7517 (tttt) cc_final: 0.7001 (ttmt) REVERT: B 321 LYS cc_start: 0.7557 (ttpt) cc_final: 0.6924 (mttm) REVERT: B 342 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7622 (mt-10) REVERT: D 308 ILE cc_start: 0.7073 (mt) cc_final: 0.6808 (mp) REVERT: D 342 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7458 (mp0) REVERT: D 349 ARG cc_start: 0.7510 (mtt180) cc_final: 0.5731 (mmp-170) REVERT: D 372 GLU cc_start: 0.7641 (tt0) cc_final: 0.7368 (tt0) REVERT: F 320 SER cc_start: 0.8104 (t) cc_final: 0.7585 (t) REVERT: F 321 LYS cc_start: 0.7943 (ttpt) cc_final: 0.7390 (mttp) REVERT: F 342 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8079 (mt-10) REVERT: F 349 ARG cc_start: 0.7544 (mtt180) cc_final: 0.5876 (mtm180) REVERT: F 375 LYS cc_start: 0.6634 (tttt) cc_final: 0.6063 (ttmm) outliers start: 7 outliers final: 1 residues processed: 69 average time/residue: 2.9208 time to fit residues: 206.5690 Evaluate side-chains 66 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3396 Z= 0.220 Angle : 0.517 3.962 4548 Z= 0.266 Chirality : 0.051 0.136 516 Planarity : 0.003 0.029 576 Dihedral : 5.221 17.584 444 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.56 % Allowed : 16.67 % Favored : 81.77 % 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: -1.73 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.007 0.001 PHE E 378 TYR 0.012 0.002 TYR F 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.6853 (mtt90) REVERT: A 353 LYS cc_start: 0.8361 (mttm) cc_final: 0.8095 (mttt) REVERT: A 369 LYS cc_start: 0.7024 (mttt) cc_final: 0.6703 (mtpt) REVERT: A 373 THR cc_start: 0.6154 (m) cc_final: 0.5769 (p) REVERT: C 348 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8121 (t0) REVERT: C 349 ARG cc_start: 0.7322 (mtt180) cc_final: 0.7087 (mtt90) REVERT: E 338 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: E 347 LYS cc_start: 0.8138 (mttt) cc_final: 0.7194 (mtmt) REVERT: E 369 LYS cc_start: 0.7913 (mttt) cc_final: 0.7547 (mtpt) REVERT: E 372 GLU cc_start: 0.7102 (tt0) cc_final: 0.6071 (mp0) REVERT: E 375 LYS cc_start: 0.7506 (tttt) cc_final: 0.6976 (ttmt) REVERT: B 321 LYS cc_start: 0.7449 (ttpt) cc_final: 0.6898 (mttm) REVERT: B 342 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7595 (mt-10) REVERT: D 308 ILE cc_start: 0.7043 (mt) cc_final: 0.6777 (mp) REVERT: D 342 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7505 (mp0) REVERT: D 349 ARG cc_start: 0.7499 (mtt180) cc_final: 0.5695 (mmp-170) REVERT: D 372 GLU cc_start: 0.7728 (tt0) cc_final: 0.7498 (tt0) REVERT: F 321 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7401 (mttp) REVERT: F 342 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8056 (mt-10) REVERT: F 349 ARG cc_start: 0.7560 (mtt180) cc_final: 0.5882 (mtm180) REVERT: F 375 LYS cc_start: 0.6703 (tttt) cc_final: 0.6110 (ttmm) outliers start: 6 outliers final: 2 residues processed: 70 average time/residue: 3.1431 time to fit residues: 225.3885 Evaluate side-chains 69 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 358 ASP 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: 3.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3396 Z= 0.152 Angle : 0.483 3.753 4548 Z= 0.247 Chirality : 0.051 0.134 516 Planarity : 0.003 0.029 576 Dihedral : 4.908 16.919 444 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.78 % Allowed : 17.97 % Favored : 81.25 % 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: -1.75 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 329 PHE 0.004 0.001 PHE E 378 TYR 0.010 0.001 TYR F 310 ARG 0.000 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.6861 (mtt90) REVERT: A 353 LYS cc_start: 0.8340 (mttm) cc_final: 0.8096 (mttt) REVERT: A 369 LYS cc_start: 0.7051 (mttt) cc_final: 0.6768 (mtpt) REVERT: A 373 THR cc_start: 0.6168 (m) cc_final: 0.5795 (p) REVERT: C 348 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8093 (t0) REVERT: C 349 ARG cc_start: 0.7373 (mtt180) cc_final: 0.7130 (mtt90) REVERT: E 347 LYS cc_start: 0.8155 (mttt) cc_final: 0.7202 (mtmt) REVERT: E 375 LYS cc_start: 0.7479 (tttt) cc_final: 0.6967 (ttmt) REVERT: B 321 LYS cc_start: 0.7425 (ttpt) cc_final: 0.6906 (mttm) REVERT: B 342 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7578 (mt-10) REVERT: D 308 ILE cc_start: 0.7049 (mt) cc_final: 0.6780 (mp) REVERT: D 342 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7461 (mp0) REVERT: D 349 ARG cc_start: 0.7509 (mtt180) cc_final: 0.5714 (mmp-170) REVERT: D 372 GLU cc_start: 0.7697 (tt0) cc_final: 0.7473 (tt0) REVERT: F 321 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7401 (mttp) REVERT: F 342 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8072 (mt-10) REVERT: F 349 ARG cc_start: 0.7556 (mtt180) cc_final: 0.5891 (mtm180) REVERT: F 375 LYS cc_start: 0.6716 (tttt) cc_final: 0.6144 (ttmm) outliers start: 3 outliers final: 1 residues processed: 66 average time/residue: 2.8915 time to fit residues: 195.6287 Evaluate side-chains 64 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3396 Z= 0.139 Angle : 0.466 3.656 4548 Z= 0.238 Chirality : 0.051 0.135 516 Planarity : 0.003 0.028 576 Dihedral : 4.669 16.346 444 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.78 % Allowed : 17.97 % Favored : 81.25 % 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: -1.75 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 330 PHE 0.003 0.000 PHE C 346 TYR 0.011 0.001 TYR F 310 ARG 0.000 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6876 (mtt90) REVERT: A 353 LYS cc_start: 0.8325 (mttm) cc_final: 0.8074 (mttt) REVERT: A 369 LYS cc_start: 0.7053 (mttt) cc_final: 0.6761 (mtpt) REVERT: A 373 THR cc_start: 0.6191 (m) cc_final: 0.5822 (p) REVERT: C 319 THR cc_start: 0.7903 (m) cc_final: 0.7492 (p) REVERT: C 348 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8045 (t0) REVERT: C 349 ARG cc_start: 0.7384 (mtt180) cc_final: 0.7159 (mtt90) REVERT: E 375 LYS cc_start: 0.7515 (tttt) cc_final: 0.7033 (ttmt) REVERT: B 321 LYS cc_start: 0.7435 (ttpt) cc_final: 0.6905 (mttm) REVERT: B 342 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7569 (mt-10) REVERT: D 308 ILE cc_start: 0.7035 (mt) cc_final: 0.6774 (mp) REVERT: D 342 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7451 (mp0) REVERT: D 349 ARG cc_start: 0.7532 (mtt180) cc_final: 0.5717 (mmp-170) REVERT: D 372 GLU cc_start: 0.7659 (tt0) cc_final: 0.7447 (tt0) REVERT: F 321 LYS cc_start: 0.7905 (ttpt) cc_final: 0.7384 (mttp) REVERT: F 342 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8064 (mt-10) REVERT: F 349 ARG cc_start: 0.7571 (mtt180) cc_final: 0.5990 (mtm180) REVERT: F 375 LYS cc_start: 0.6684 (tttt) cc_final: 0.6091 (ttmm) outliers start: 3 outliers final: 0 residues processed: 63 average time/residue: 2.9298 time to fit residues: 188.9982 Evaluate side-chains 63 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 0.0270 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 27 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3396 Z= 0.118 Angle : 0.451 3.486 4548 Z= 0.229 Chirality : 0.051 0.137 516 Planarity : 0.003 0.027 576 Dihedral : 4.378 15.394 444 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.52 % Allowed : 18.23 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 330 PHE 0.003 0.000 PHE C 346 TYR 0.010 0.001 TYR F 310 ARG 0.000 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.571 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: 0.7446 (OUTLIER) cc_final: 0.6896 (mtt90) REVERT: A 353 LYS cc_start: 0.8296 (mttm) cc_final: 0.8059 (mttt) REVERT: A 369 LYS cc_start: 0.7027 (mttt) cc_final: 0.6752 (mtpt) REVERT: A 373 THR cc_start: 0.6182 (m) cc_final: 0.5786 (p) REVERT: C 319 THR cc_start: 0.7882 (m) cc_final: 0.7556 (p) REVERT: C 348 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7998 (t0) REVERT: C 349 ARG cc_start: 0.7363 (mtt180) cc_final: 0.7141 (mtt90) REVERT: E 342 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7255 (tm-30) REVERT: E 347 LYS cc_start: 0.7268 (mtmt) cc_final: 0.6391 (mtmt) REVERT: E 375 LYS cc_start: 0.7546 (tttt) cc_final: 0.7052 (ttmt) REVERT: B 321 LYS cc_start: 0.7433 (ttpt) cc_final: 0.6925 (mttm) REVERT: B 342 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7570 (mt-10) REVERT: D 349 ARG cc_start: 0.7554 (mtt180) cc_final: 0.5714 (mmp-170) REVERT: D 372 GLU cc_start: 0.7661 (tt0) cc_final: 0.7409 (tt0) REVERT: F 321 LYS cc_start: 0.7854 (ttpt) cc_final: 0.7346 (mttp) REVERT: F 349 ARG cc_start: 0.7565 (mtt180) cc_final: 0.6033 (mtm180) REVERT: F 375 LYS cc_start: 0.6754 (tttt) cc_final: 0.6177 (ttmm) outliers start: 2 outliers final: 0 residues processed: 71 average time/residue: 2.7183 time to fit residues: 197.9619 Evaluate side-chains 67 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3396 Z= 0.149 Angle : 0.465 3.489 4548 Z= 0.238 Chirality : 0.051 0.132 516 Planarity : 0.003 0.025 576 Dihedral : 4.514 15.669 444 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.04 % Allowed : 18.49 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 374 PHE 0.004 0.001 PHE C 346 TYR 0.016 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) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LYS cc_start: 0.8325 (mttm) cc_final: 0.8080 (mttt) REVERT: A 369 LYS cc_start: 0.7031 (mttt) cc_final: 0.6707 (mtpt) REVERT: A 373 THR cc_start: 0.6207 (m) cc_final: 0.5859 (p) REVERT: C 319 THR cc_start: 0.7945 (m) cc_final: 0.7599 (p) REVERT: C 349 ARG cc_start: 0.7352 (mtt180) cc_final: 0.5887 (mmp-170) REVERT: E 347 LYS cc_start: 0.7277 (mtmt) cc_final: 0.6395 (mtmt) REVERT: E 375 LYS cc_start: 0.7565 (tttt) cc_final: 0.7061 (ttmt) REVERT: B 321 LYS cc_start: 0.7422 (ttpt) cc_final: 0.6910 (mttm) REVERT: B 342 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7590 (mt-10) REVERT: D 349 ARG cc_start: 0.7544 (mtt180) cc_final: 0.5756 (mmp-170) REVERT: D 372 GLU cc_start: 0.7644 (tt0) cc_final: 0.7399 (tt0) REVERT: F 321 LYS cc_start: 0.7892 (ttpt) cc_final: 0.7376 (mttp) REVERT: F 349 ARG cc_start: 0.7608 (mtt180) cc_final: 0.6013 (mtm180) REVERT: F 375 LYS cc_start: 0.6768 (tttt) cc_final: 0.6160 (ttmm) outliers start: 4 outliers final: 0 residues processed: 63 average time/residue: 3.1289 time to fit residues: 201.7032 Evaluate side-chains 59 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.154771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.137652 restraints weight = 11500.384| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.64 r_work: 0.3963 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3884 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3396 Z= 0.173 Angle : 0.482 3.574 4548 Z= 0.247 Chirality : 0.051 0.133 516 Planarity : 0.003 0.026 576 Dihedral : 4.682 16.277 444 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.52 % Allowed : 19.79 % Favored : 79.69 % 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: -1.65 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 329 PHE 0.004 0.001 PHE E 378 TYR 0.017 0.002 TYR B 310 ARG 0.005 0.001 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4617.84 seconds wall clock time: 81 minutes 18.28 seconds (4878.28 seconds total)