Starting phenix.real_space_refine on Sat Aug 3 04:03:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9g_18280/08_2024/8q9g_18280.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9g_18280/08_2024/8q9g_18280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9g_18280/08_2024/8q9g_18280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9g_18280/08_2024/8q9g_18280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9g_18280/08_2024/8q9g_18280.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9g_18280/08_2024/8q9g_18280.cif" } resolution = 2.65 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 PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 372": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 372": "OE1" <-> "OE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 372": "OE1" <-> "OE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 372": "OE1" <-> "OE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 4.60, per 1000 atoms: 0.67 Number of scatterers: 6822 At special positions: 0 Unit cell: (150.489, 92.329, 42.166, 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: 5.51 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 6.518A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.556A 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: 6.339A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.298A 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: 5.949A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.779A 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: 6.755A pdb=" N GLU A 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N SER E 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS A 340 " --> pdb=" O SER E 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.611A 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 removed outlier: 6.508A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N SER E 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY A 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.417A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 377 Processing sheet with id=AB1, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.801A pdb=" N ILE B 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.658A 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: 6.250A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 325 through 330 removed outlier: 5.981A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY F 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.800A 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 Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.676A 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: 6.546A pdb=" N GLN B 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE F 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS B 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N SER F 356 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.254A 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: 6.350A 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: 6.233A pdb=" N LYS B 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N THR D 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU B 372 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LYS D 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N HIS B 374 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N THR D 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 376 " --> pdb=" O THR D 377 " (cutoff:3.500A) 83 hydrogen bonds defined for protein. 249 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: 2.10 Time building geometry restraints manager: 5.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 3474 1.11 - 1.29: 558 1.29 - 1.46: 916 1.46 - 1.63: 1922 1.63 - 1.81: 6 Bond restraints: 6876 Sorted by residual: bond pdb=" N SER F 324 " pdb=" H SER F 324 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CD1 TYR B 310 " pdb=" HD1 TYR B 310 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N TYR A 310 " pdb=" H TYR A 310 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" NE2 GLN E 336 " pdb="HE21 GLN E 336 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" NE2 HIS B 362 " pdb=" HE2 HIS B 362 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 ... (remaining 6871 not shown) Histogram of bond angle deviations from ideal: 97.13 - 103.51: 48 103.51 - 109.89: 6042 109.89 - 116.28: 2935 116.28 - 122.66: 2824 122.66 - 129.04: 697 Bond angle restraints: 12546 Sorted by residual: angle pdb=" N SER B 316 " pdb=" CA SER B 316 " pdb=" C SER B 316 " ideal model delta sigma weight residual 110.53 117.64 -7.11 1.32e+00 5.74e-01 2.90e+01 angle pdb=" N GLY B 326 " pdb=" CA GLY B 326 " pdb=" C GLY B 326 " ideal model delta sigma weight residual 110.69 117.25 -6.56 1.33e+00 5.65e-01 2.43e+01 angle pdb=" N GLU F 372 " pdb=" CA GLU F 372 " pdb=" CB GLU F 372 " ideal model delta sigma weight residual 111.13 102.34 8.79 1.79e+00 3.12e-01 2.41e+01 angle pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " pdb=" CD2 HIS E 374 " ideal model delta sigma weight residual 131.20 124.85 6.35 1.30e+00 5.92e-01 2.38e+01 angle pdb=" CB HIS D 329 " pdb=" CG HIS D 329 " pdb=" CD2 HIS D 329 " ideal model delta sigma weight residual 131.20 124.85 6.35 1.30e+00 5.92e-01 2.38e+01 ... (remaining 12541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.63: 2843 14.63 - 29.25: 115 29.25 - 43.87: 81 43.87 - 58.50: 80 58.50 - 73.12: 49 Dihedral angle restraints: 3168 sinusoidal: 1806 harmonic: 1362 Sorted by residual: dihedral pdb=" C LYS C 343 " pdb=" N LYS C 343 " pdb=" CA LYS C 343 " pdb=" CB LYS C 343 " ideal model delta harmonic sigma weight residual -122.60 -132.81 10.21 0 2.50e+00 1.60e-01 1.67e+01 dihedral pdb=" CA ILE A 360 " pdb=" C ILE A 360 " pdb=" N THR A 361 " pdb=" CA THR A 361 " ideal model delta harmonic sigma weight residual 180.00 161.38 18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA LYS A 369 " pdb=" C LYS A 369 " pdb=" N LYS A 370 " pdb=" CA LYS A 370 " ideal model delta harmonic sigma weight residual 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 3165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 303 0.066 - 0.132: 152 0.132 - 0.198: 46 0.198 - 0.264: 13 0.264 - 0.329: 2 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA LYS C 343 " pdb=" N LYS C 343 " pdb=" C LYS C 343 " pdb=" CB LYS C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA ASP D 358 " pdb=" N ASP D 358 " pdb=" C ASP D 358 " pdb=" CB ASP D 358 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 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 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 513 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 362 " -0.075 2.00e-02 2.50e+03 4.52e-02 4.59e+01 pdb=" CG HIS B 362 " 0.054 2.00e-02 2.50e+03 pdb=" ND1 HIS B 362 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 HIS B 362 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 HIS B 362 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS B 362 " 0.039 2.00e-02 2.50e+03 pdb=" HD2 HIS B 362 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 HIS B 362 " -0.035 2.00e-02 2.50e+03 pdb=" HE2 HIS B 362 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " -0.088 2.00e-02 2.50e+03 3.90e-02 4.56e+01 pdb=" CG TYR D 310 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " -0.083 2.00e-02 2.50e+03 pdb=" HD1 TYR D 310 " 0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR D 310 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 TYR D 310 " 0.009 2.00e-02 2.50e+03 pdb=" HE2 TYR D 310 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.079 2.00e-02 2.50e+03 3.54e-02 3.76e+01 pdb=" CG TYR C 310 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.076 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " -0.014 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 616 2.20 - 2.80: 12494 2.80 - 3.40: 17578 3.40 - 4.00: 24431 4.00 - 4.60: 33683 Nonbonded interactions: 88802 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.603 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.610 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.627 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.644 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.653 2.450 ... (remaining 88797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.880 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: 0.080 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 28.070 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 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 0.038 3396 Z= 0.756 Angle : 1.947 8.792 4548 Z= 1.280 Chirality : 0.085 0.329 516 Planarity : 0.009 0.055 576 Dihedral : 10.250 57.110 1296 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % 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: -1.98 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.005 HIS A 330 PHE 0.043 0.014 PHE C 346 TYR 0.082 0.024 TYR D 310 ARG 0.006 0.001 ARG C 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 133 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7097 (mtpt) cc_final: 0.6748 (mttm) REVERT: A 351 GLN cc_start: 0.7879 (mt0) cc_final: 0.7615 (mt0) REVERT: A 358 ASP cc_start: 0.8773 (m-30) cc_final: 0.8567 (m-30) REVERT: C 311 LYS cc_start: 0.5407 (ttpt) cc_final: 0.5090 (mmtm) REVERT: C 321 LYS cc_start: 0.7275 (mtpt) cc_final: 0.6624 (mttt) REVERT: C 345 ASP cc_start: 0.7808 (t0) cc_final: 0.7314 (t70) REVERT: C 349 ARG cc_start: 0.7392 (mtt180) cc_final: 0.5388 (mmp-170) REVERT: C 369 LYS cc_start: 0.6597 (mttt) cc_final: 0.6299 (mttp) REVERT: C 372 GLU cc_start: 0.7657 (tt0) cc_final: 0.7193 (tp30) REVERT: E 321 LYS cc_start: 0.7934 (mtpt) cc_final: 0.7620 (mttp) REVERT: E 345 ASP cc_start: 0.8028 (t0) cc_final: 0.7684 (t0) REVERT: E 347 LYS cc_start: 0.7772 (mttt) cc_final: 0.6817 (pttm) REVERT: B 314 ASP cc_start: 0.5622 (t0) cc_final: 0.5104 (t0) REVERT: B 320 SER cc_start: 0.7792 (t) cc_final: 0.6924 (p) REVERT: B 321 LYS cc_start: 0.7391 (mtpt) cc_final: 0.6989 (mttt) REVERT: B 345 ASP cc_start: 0.6889 (t0) cc_final: 0.6689 (m-30) REVERT: B 369 LYS cc_start: 0.6550 (mttt) cc_final: 0.6131 (mtpp) REVERT: B 375 LYS cc_start: 0.4806 (tttt) cc_final: 0.4483 (ttmm) REVERT: D 320 SER cc_start: 0.8259 (t) cc_final: 0.7998 (p) REVERT: D 321 LYS cc_start: 0.7452 (mtpt) cc_final: 0.7146 (mtmm) REVERT: D 345 ASP cc_start: 0.6786 (t0) cc_final: 0.6586 (p0) REVERT: D 349 ARG cc_start: 0.7661 (mtt180) cc_final: 0.6544 (mmp-170) REVERT: D 375 LYS cc_start: 0.4901 (tttt) cc_final: 0.4679 (tttm) REVERT: F 314 ASP cc_start: 0.5583 (t0) cc_final: 0.5371 (t0) REVERT: F 316 SER cc_start: 0.6735 (m) cc_final: 0.6453 (p) REVERT: F 320 SER cc_start: 0.7944 (t) cc_final: 0.7290 (p) REVERT: F 349 ARG cc_start: 0.6698 (mtt180) cc_final: 0.6472 (ptt-90) REVERT: F 375 LYS cc_start: 0.6681 (tttt) cc_final: 0.6255 (ttmm) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 2.9471 time to fit residues: 400.7334 Evaluate side-chains 94 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 307 GLN E 336 GLN E 362 HIS B 362 HIS F 362 HIS F 368 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3396 Z= 0.256 Angle : 0.605 4.840 4548 Z= 0.319 Chirality : 0.051 0.135 516 Planarity : 0.003 0.034 576 Dihedral : 5.533 16.503 444 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.08 % Allowed : 11.46 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 362 PHE 0.009 0.002 PHE C 346 TYR 0.008 0.002 TYR B 310 ARG 0.004 0.001 ARG E 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 103 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 320 SER cc_start: 0.8048 (t) cc_final: 0.7634 (p) REVERT: A 349 ARG cc_start: 0.7071 (mtm180) cc_final: 0.6868 (mtt180) REVERT: C 311 LYS cc_start: 0.5375 (ttpt) cc_final: 0.5023 (mmtt) REVERT: C 347 LYS cc_start: 0.7825 (mttt) cc_final: 0.7576 (mmtt) REVERT: C 349 ARG cc_start: 0.7419 (mtt180) cc_final: 0.5474 (mmp-170) REVERT: C 369 LYS cc_start: 0.6584 (mttt) cc_final: 0.6321 (mttp) REVERT: C 372 GLU cc_start: 0.7518 (tt0) cc_final: 0.7024 (tp30) REVERT: E 314 ASP cc_start: 0.5663 (t0) cc_final: 0.5372 (t0) REVERT: E 347 LYS cc_start: 0.7796 (mttt) cc_final: 0.6839 (pttm) REVERT: E 349 ARG cc_start: 0.7169 (mtm180) cc_final: 0.6854 (mtt180) REVERT: B 320 SER cc_start: 0.7898 (t) cc_final: 0.7202 (p) REVERT: B 321 LYS cc_start: 0.7378 (mtpt) cc_final: 0.6981 (mttt) REVERT: B 342 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6699 (tt0) REVERT: B 345 ASP cc_start: 0.7036 (t0) cc_final: 0.6671 (m-30) REVERT: B 349 ARG cc_start: 0.7379 (mtp85) cc_final: 0.7102 (mtp85) REVERT: B 375 LYS cc_start: 0.4722 (tttt) cc_final: 0.4313 (ttmm) REVERT: D 320 SER cc_start: 0.8433 (t) cc_final: 0.8180 (p) REVERT: D 321 LYS cc_start: 0.7546 (mtpt) cc_final: 0.7231 (mttm) REVERT: D 345 ASP cc_start: 0.6976 (t0) cc_final: 0.6649 (p0) REVERT: D 349 ARG cc_start: 0.7704 (mtt180) cc_final: 0.6411 (mmp-170) REVERT: D 369 LYS cc_start: 0.6797 (mttt) cc_final: 0.6466 (ttmm) REVERT: D 375 LYS cc_start: 0.5302 (tttt) cc_final: 0.5000 (ttmm) REVERT: F 316 SER cc_start: 0.6821 (m) cc_final: 0.6561 (p) REVERT: F 320 SER cc_start: 0.7614 (t) cc_final: 0.6979 (p) REVERT: F 349 ARG cc_start: 0.6473 (mtt180) cc_final: 0.6037 (pmt-80) REVERT: F 369 LYS cc_start: 0.7386 (mttt) cc_final: 0.6985 (ttmm) REVERT: F 375 LYS cc_start: 0.6755 (tttt) cc_final: 0.6489 (mtpp) outliers start: 8 outliers final: 3 residues processed: 96 average time/residue: 2.6788 time to fit residues: 263.0601 Evaluate side-chains 94 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN E 336 GLN E 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3396 Z= 0.337 Angle : 0.615 4.307 4548 Z= 0.329 Chirality : 0.051 0.143 516 Planarity : 0.003 0.026 576 Dihedral : 5.398 16.677 444 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.12 % Allowed : 13.28 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 374 PHE 0.009 0.002 PHE E 346 TYR 0.010 0.003 TYR C 310 ARG 0.004 0.001 ARG C 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 101 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 SER cc_start: 0.8019 (t) cc_final: 0.7659 (p) REVERT: C 311 LYS cc_start: 0.5316 (ttpt) cc_final: 0.4977 (mmtm) REVERT: C 320 SER cc_start: 0.8412 (t) cc_final: 0.8193 (p) REVERT: C 321 LYS cc_start: 0.7376 (mtmt) cc_final: 0.6951 (mttp) REVERT: C 347 LYS cc_start: 0.7844 (mttt) cc_final: 0.7521 (mmmm) REVERT: C 349 ARG cc_start: 0.7439 (mtt180) cc_final: 0.5459 (mmp-170) REVERT: C 372 GLU cc_start: 0.7689 (tt0) cc_final: 0.7159 (tp30) REVERT: E 338 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6918 (tt0) REVERT: E 347 LYS cc_start: 0.7911 (mttt) cc_final: 0.6996 (pmtt) REVERT: B 320 SER cc_start: 0.8050 (t) cc_final: 0.7405 (p) REVERT: B 321 LYS cc_start: 0.7297 (mtpt) cc_final: 0.6937 (mttt) REVERT: B 342 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6796 (tt0) REVERT: B 349 ARG cc_start: 0.7472 (mtp85) cc_final: 0.7216 (mtp85) REVERT: D 320 SER cc_start: 0.8467 (t) cc_final: 0.8244 (p) REVERT: D 321 LYS cc_start: 0.7436 (mtpt) cc_final: 0.7135 (mttp) REVERT: D 349 ARG cc_start: 0.7762 (mtt180) cc_final: 0.6460 (mmp-170) REVERT: D 369 LYS cc_start: 0.6778 (mttt) cc_final: 0.6450 (ttmm) REVERT: D 375 LYS cc_start: 0.5236 (tttt) cc_final: 0.4783 (ttmm) REVERT: F 316 SER cc_start: 0.6649 (m) cc_final: 0.6418 (p) REVERT: F 349 ARG cc_start: 0.6387 (mtt180) cc_final: 0.6034 (pmt-80) REVERT: F 369 LYS cc_start: 0.7374 (mttt) cc_final: 0.7038 (ttmm) REVERT: F 375 LYS cc_start: 0.6716 (tttt) cc_final: 0.6455 (mtpp) outliers start: 12 outliers final: 7 residues processed: 92 average time/residue: 2.8939 time to fit residues: 272.2883 Evaluate side-chains 95 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3396 Z= 0.263 Angle : 0.568 4.156 4548 Z= 0.298 Chirality : 0.051 0.139 516 Planarity : 0.003 0.024 576 Dihedral : 5.209 16.611 444 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.86 % Allowed : 14.06 % Favored : 83.07 % 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: -2.20 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.007 0.002 PHE E 378 TYR 0.009 0.002 TYR B 310 ARG 0.003 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 98 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 320 SER cc_start: 0.8020 (t) cc_final: 0.7668 (p) REVERT: C 311 LYS cc_start: 0.5277 (ttpt) cc_final: 0.4945 (mmtm) REVERT: C 320 SER cc_start: 0.8408 (t) cc_final: 0.8200 (p) REVERT: C 321 LYS cc_start: 0.7406 (mtmt) cc_final: 0.7008 (mttp) REVERT: C 347 LYS cc_start: 0.7826 (mttt) cc_final: 0.7500 (mmmm) REVERT: C 349 ARG cc_start: 0.7522 (mtt180) cc_final: 0.5617 (mmp-170) REVERT: C 372 GLU cc_start: 0.7723 (tt0) cc_final: 0.7212 (tp30) REVERT: E 336 GLN cc_start: 0.7824 (tt0) cc_final: 0.7301 (tt0) REVERT: E 338 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6562 (mt-10) REVERT: E 347 LYS cc_start: 0.7952 (mttt) cc_final: 0.6995 (pmtt) REVERT: B 320 SER cc_start: 0.8149 (t) cc_final: 0.7547 (p) REVERT: B 321 LYS cc_start: 0.7296 (mtpt) cc_final: 0.6943 (mttt) REVERT: B 349 ARG cc_start: 0.7497 (mtp85) cc_final: 0.7244 (mtp85) REVERT: D 320 SER cc_start: 0.8450 (t) cc_final: 0.8222 (p) REVERT: D 321 LYS cc_start: 0.7474 (mtpt) cc_final: 0.7172 (mttp) REVERT: D 349 ARG cc_start: 0.7773 (mtt180) cc_final: 0.6493 (mmp-170) REVERT: D 369 LYS cc_start: 0.6777 (mttt) cc_final: 0.6424 (ttmm) REVERT: D 375 LYS cc_start: 0.5259 (tttt) cc_final: 0.4829 (ttmm) REVERT: F 345 ASP cc_start: 0.6404 (OUTLIER) cc_final: 0.6162 (p0) REVERT: F 349 ARG cc_start: 0.6402 (mtt180) cc_final: 0.6046 (pmt-80) REVERT: F 369 LYS cc_start: 0.7407 (mttt) cc_final: 0.7052 (ttmm) outliers start: 11 outliers final: 6 residues processed: 88 average time/residue: 3.0016 time to fit residues: 270.3362 Evaluate side-chains 91 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3396 Z= 0.332 Angle : 0.598 4.221 4548 Z= 0.317 Chirality : 0.050 0.140 516 Planarity : 0.003 0.023 576 Dihedral : 5.278 16.375 444 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.34 % Allowed : 15.62 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.007 0.002 PHE E 346 TYR 0.010 0.003 TYR B 310 ARG 0.003 0.000 ARG C 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 92 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 320 SER cc_start: 0.8027 (t) cc_final: 0.7690 (p) REVERT: C 311 LYS cc_start: 0.5258 (ttpt) cc_final: 0.4957 (mmtm) REVERT: C 320 SER cc_start: 0.8427 (t) cc_final: 0.8210 (p) REVERT: C 321 LYS cc_start: 0.7423 (mtmt) cc_final: 0.7015 (mttp) REVERT: C 347 LYS cc_start: 0.7910 (mttt) cc_final: 0.7556 (mmmm) REVERT: C 349 ARG cc_start: 0.7505 (mtt180) cc_final: 0.5620 (mmp-170) REVERT: C 372 GLU cc_start: 0.7703 (tt0) cc_final: 0.7178 (tp30) REVERT: E 336 GLN cc_start: 0.7880 (tt0) cc_final: 0.7265 (tt0) REVERT: E 338 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6679 (mt-10) REVERT: E 347 LYS cc_start: 0.7971 (mttt) cc_final: 0.7031 (pmtt) REVERT: B 320 SER cc_start: 0.8156 (t) cc_final: 0.7528 (p) REVERT: B 321 LYS cc_start: 0.7292 (mtpt) cc_final: 0.6982 (mttt) REVERT: D 320 SER cc_start: 0.8454 (t) cc_final: 0.8221 (p) REVERT: D 321 LYS cc_start: 0.7434 (mtpt) cc_final: 0.7109 (mttm) REVERT: D 349 ARG cc_start: 0.7770 (mtt180) cc_final: 0.6522 (mmp-170) REVERT: D 369 LYS cc_start: 0.6789 (mttt) cc_final: 0.6431 (ttmm) REVERT: F 345 ASP cc_start: 0.6511 (OUTLIER) cc_final: 0.6282 (p0) REVERT: F 349 ARG cc_start: 0.6500 (mtt180) cc_final: 0.6056 (pmt-80) REVERT: F 369 LYS cc_start: 0.7427 (mttt) cc_final: 0.7067 (ttmm) outliers start: 9 outliers final: 5 residues processed: 84 average time/residue: 3.0006 time to fit residues: 257.8897 Evaluate side-chains 87 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3396 Z= 0.185 Angle : 0.529 4.751 4548 Z= 0.273 Chirality : 0.050 0.137 516 Planarity : 0.002 0.022 576 Dihedral : 4.958 15.631 444 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.82 % Allowed : 16.15 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.004 0.001 PHE C 346 TYR 0.009 0.002 TYR B 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 91 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 320 SER cc_start: 0.8022 (t) cc_final: 0.7686 (p) REVERT: C 311 LYS cc_start: 0.5303 (ttpt) cc_final: 0.4975 (mmtt) REVERT: C 321 LYS cc_start: 0.7429 (mtmt) cc_final: 0.7028 (mttp) REVERT: C 338 GLU cc_start: 0.7171 (tp30) cc_final: 0.6912 (tp30) REVERT: C 347 LYS cc_start: 0.7862 (mttt) cc_final: 0.7531 (mmmm) REVERT: C 349 ARG cc_start: 0.7493 (mtt180) cc_final: 0.5619 (mmp-170) REVERT: C 372 GLU cc_start: 0.7754 (tt0) cc_final: 0.7219 (tp30) REVERT: E 336 GLN cc_start: 0.7885 (tt0) cc_final: 0.7201 (tt0) REVERT: E 338 GLU cc_start: 0.7107 (tt0) cc_final: 0.6712 (mt-10) REVERT: E 347 LYS cc_start: 0.7952 (mttt) cc_final: 0.7018 (pmtt) REVERT: B 320 SER cc_start: 0.8159 (t) cc_final: 0.7622 (p) REVERT: B 321 LYS cc_start: 0.7280 (mtpt) cc_final: 0.6939 (mttt) REVERT: B 349 ARG cc_start: 0.7380 (mtp85) cc_final: 0.7126 (mtp85) REVERT: D 320 SER cc_start: 0.8431 (t) cc_final: 0.8220 (p) REVERT: D 321 LYS cc_start: 0.7495 (mtpt) cc_final: 0.7203 (mttp) REVERT: D 349 ARG cc_start: 0.7752 (mtt180) cc_final: 0.6457 (mmp-170) REVERT: D 369 LYS cc_start: 0.6834 (mttt) cc_final: 0.6443 (ttmm) REVERT: F 345 ASP cc_start: 0.6526 (OUTLIER) cc_final: 0.6318 (p0) REVERT: F 349 ARG cc_start: 0.6479 (mtt180) cc_final: 0.6048 (pmt-80) REVERT: F 369 LYS cc_start: 0.7442 (mttt) cc_final: 0.7073 (ttmm) outliers start: 7 outliers final: 5 residues processed: 85 average time/residue: 3.0180 time to fit residues: 262.4379 Evaluate side-chains 88 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3396 Z= 0.334 Angle : 0.598 5.536 4548 Z= 0.316 Chirality : 0.050 0.138 516 Planarity : 0.003 0.027 576 Dihedral : 5.167 16.374 444 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.08 % Allowed : 17.19 % Favored : 80.73 % 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: -2.35 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.007 0.002 PHE E 346 TYR 0.011 0.003 TYR B 310 ARG 0.003 0.001 ARG C 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 87 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: C 311 LYS cc_start: 0.5222 (ttpt) cc_final: 0.4926 (mmtt) REVERT: C 321 LYS cc_start: 0.7396 (mtmt) cc_final: 0.6985 (mttp) REVERT: C 347 LYS cc_start: 0.7899 (mttt) cc_final: 0.7541 (mmmm) REVERT: C 349 ARG cc_start: 0.7479 (mtt180) cc_final: 0.5637 (mmp-170) REVERT: C 372 GLU cc_start: 0.7708 (tt0) cc_final: 0.7152 (tp30) REVERT: E 336 GLN cc_start: 0.7873 (tt0) cc_final: 0.7276 (tt0) REVERT: E 338 GLU cc_start: 0.7114 (tt0) cc_final: 0.6653 (mt-10) REVERT: E 347 LYS cc_start: 0.7939 (mttt) cc_final: 0.7046 (pmtt) REVERT: B 320 SER cc_start: 0.8169 (t) cc_final: 0.7532 (p) REVERT: B 321 LYS cc_start: 0.7280 (mtpt) cc_final: 0.6942 (mttt) REVERT: B 349 ARG cc_start: 0.7458 (mtp85) cc_final: 0.7213 (mtp85) REVERT: D 320 SER cc_start: 0.8452 (t) cc_final: 0.8214 (p) REVERT: D 321 LYS cc_start: 0.7457 (mtpt) cc_final: 0.7133 (mttm) REVERT: D 349 ARG cc_start: 0.7783 (mtt180) cc_final: 0.6520 (mmp-170) REVERT: D 369 LYS cc_start: 0.6818 (mttt) cc_final: 0.6509 (ttmm) REVERT: F 345 ASP cc_start: 0.6562 (OUTLIER) cc_final: 0.6341 (p0) REVERT: F 349 ARG cc_start: 0.6593 (mtt180) cc_final: 0.6064 (pmt-80) REVERT: F 369 LYS cc_start: 0.7401 (mttt) cc_final: 0.7026 (ttmm) outliers start: 8 outliers final: 5 residues processed: 80 average time/residue: 3.1258 time to fit residues: 255.7831 Evaluate side-chains 84 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 0.0670 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3396 Z= 0.158 Angle : 0.511 4.826 4548 Z= 0.261 Chirality : 0.051 0.136 516 Planarity : 0.002 0.020 576 Dihedral : 4.741 14.798 444 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.56 % Allowed : 17.45 % 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: -2.25 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.003 0.001 PHE C 346 TYR 0.008 0.001 TYR B 310 ARG 0.001 0.000 ARG C 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 87 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 SER cc_start: 0.7985 (t) cc_final: 0.7649 (p) REVERT: C 311 LYS cc_start: 0.5388 (ttpt) cc_final: 0.5051 (mmtt) REVERT: C 321 LYS cc_start: 0.7459 (mtmt) cc_final: 0.7015 (mttp) REVERT: C 338 GLU cc_start: 0.7164 (tp30) cc_final: 0.6903 (tp30) REVERT: C 349 ARG cc_start: 0.7510 (mtt180) cc_final: 0.5583 (mmp-170) REVERT: C 372 GLU cc_start: 0.7774 (tt0) cc_final: 0.7267 (tp30) REVERT: E 336 GLN cc_start: 0.7902 (tt0) cc_final: 0.7140 (tt0) REVERT: E 338 GLU cc_start: 0.7089 (tt0) cc_final: 0.6744 (mt-10) REVERT: E 347 LYS cc_start: 0.7924 (mttt) cc_final: 0.6999 (pmtt) REVERT: E 375 LYS cc_start: 0.6779 (tttp) cc_final: 0.5975 (ttmm) REVERT: B 320 SER cc_start: 0.8143 (t) cc_final: 0.7617 (p) REVERT: B 321 LYS cc_start: 0.7285 (mtpt) cc_final: 0.6974 (mttt) REVERT: B 349 ARG cc_start: 0.7469 (mtp85) cc_final: 0.7238 (mtp85) REVERT: D 321 LYS cc_start: 0.7492 (mtpt) cc_final: 0.7194 (mttp) REVERT: D 349 ARG cc_start: 0.7762 (mtt180) cc_final: 0.6509 (mmp-170) REVERT: F 349 ARG cc_start: 0.6538 (mtt180) cc_final: 0.6064 (pmt-80) REVERT: F 369 LYS cc_start: 0.7440 (mttt) cc_final: 0.7066 (ttmm) outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 3.2071 time to fit residues: 269.0952 Evaluate side-chains 82 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E 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: 0.9990 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 0.0970 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3396 Z= 0.188 Angle : 0.532 6.059 4548 Z= 0.274 Chirality : 0.050 0.137 516 Planarity : 0.002 0.018 576 Dihedral : 4.661 15.056 444 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 1.91 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: -2.24 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.004 0.001 PHE E 346 TYR 0.009 0.002 TYR B 310 ARG 0.001 0.000 ARG C 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 81 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 SER cc_start: 0.7978 (t) cc_final: 0.7620 (p) REVERT: C 311 LYS cc_start: 0.5282 (ttpt) cc_final: 0.4967 (mmtt) REVERT: C 321 LYS cc_start: 0.7428 (mtmt) cc_final: 0.6990 (mttp) REVERT: C 338 GLU cc_start: 0.7161 (tp30) cc_final: 0.6899 (tp30) REVERT: C 347 LYS cc_start: 0.7872 (mttt) cc_final: 0.7518 (mmmm) REVERT: C 349 ARG cc_start: 0.7489 (mtt180) cc_final: 0.5601 (mmp-170) REVERT: C 372 GLU cc_start: 0.7829 (tt0) cc_final: 0.7280 (tp30) REVERT: E 336 GLN cc_start: 0.7877 (tt0) cc_final: 0.7255 (tt0) REVERT: E 338 GLU cc_start: 0.7085 (tt0) cc_final: 0.6663 (mt-10) REVERT: E 347 LYS cc_start: 0.7924 (mttt) cc_final: 0.7003 (pmtt) REVERT: B 320 SER cc_start: 0.8150 (t) cc_final: 0.7555 (p) REVERT: B 321 LYS cc_start: 0.7295 (mtpt) cc_final: 0.6988 (mttt) REVERT: B 349 ARG cc_start: 0.7505 (mtp85) cc_final: 0.7266 (mtp85) REVERT: D 321 LYS cc_start: 0.7469 (mtpt) cc_final: 0.7152 (mttp) REVERT: D 349 ARG cc_start: 0.7771 (mtt180) cc_final: 0.6523 (mmp-170) REVERT: F 349 ARG cc_start: 0.6598 (mtt180) cc_final: 0.6052 (pmt-80) REVERT: F 369 LYS cc_start: 0.7446 (mttt) cc_final: 0.7070 (ttmm) outliers start: 4 outliers final: 4 residues processed: 78 average time/residue: 3.1256 time to fit residues: 249.2812 Evaluate side-chains 80 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E 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: 0.7980 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3396 Z= 0.141 Angle : 0.490 6.285 4548 Z= 0.249 Chirality : 0.051 0.136 516 Planarity : 0.002 0.023 576 Dihedral : 4.395 13.735 444 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.56 % Allowed : 18.23 % Favored : 80.21 % 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: -2.18 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.003 0.000 PHE C 346 TYR 0.005 0.001 TYR B 310 ARG 0.000 0.000 ARG B 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 84 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 SER cc_start: 0.8045 (t) cc_final: 0.7678 (p) REVERT: C 311 LYS cc_start: 0.5349 (ttpt) cc_final: 0.5023 (mmtm) REVERT: C 321 LYS cc_start: 0.7496 (mtmt) cc_final: 0.7051 (mttp) REVERT: C 338 GLU cc_start: 0.7104 (tp30) cc_final: 0.6851 (tp30) REVERT: C 349 ARG cc_start: 0.7525 (mtt180) cc_final: 0.5590 (mmp-170) REVERT: C 372 GLU cc_start: 0.7784 (tt0) cc_final: 0.7245 (tp30) REVERT: E 336 GLN cc_start: 0.7885 (tt0) cc_final: 0.7267 (tt0) REVERT: E 338 GLU cc_start: 0.7074 (tt0) cc_final: 0.6775 (mt-10) REVERT: E 347 LYS cc_start: 0.7896 (mttt) cc_final: 0.6972 (pmtt) REVERT: E 375 LYS cc_start: 0.6751 (tttp) cc_final: 0.5951 (ttmm) REVERT: B 320 SER cc_start: 0.8118 (t) cc_final: 0.7586 (p) REVERT: B 321 LYS cc_start: 0.7269 (mtpt) cc_final: 0.6960 (mttt) REVERT: B 349 ARG cc_start: 0.7494 (mtp85) cc_final: 0.7266 (mtp85) REVERT: D 321 LYS cc_start: 0.7540 (mtpt) cc_final: 0.7220 (mttp) REVERT: D 336 GLN cc_start: 0.6519 (tt0) cc_final: 0.5932 (mm-40) REVERT: D 349 ARG cc_start: 0.7765 (mtt180) cc_final: 0.6516 (mmp-170) REVERT: F 349 ARG cc_start: 0.6645 (mtt180) cc_final: 0.5992 (pmt-80) outliers start: 6 outliers final: 3 residues processed: 79 average time/residue: 3.0558 time to fit residues: 246.9361 Evaluate side-chains 78 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.152138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.121466 restraints weight = 11355.129| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.64 r_work: 0.3756 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3396 Z= 0.233 Angle : 0.557 6.400 4548 Z= 0.292 Chirality : 0.050 0.137 516 Planarity : 0.003 0.021 576 Dihedral : 4.629 14.890 444 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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: -2.20 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.006 0.001 PHE D 346 TYR 0.011 0.002 TYR B 310 ARG 0.002 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5190.53 seconds wall clock time: 91 minutes 15.92 seconds (5475.92 seconds total)