Starting phenix.real_space_refine on Mon Mar 11 03:21:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9g_18280/03_2024/8q9g_18280.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9g_18280/03_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_18280/03_2024/8q9g_18280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9g_18280/03_2024/8q9g_18280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9g_18280/03_2024/8q9g_18280.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9g_18280/03_2024/8q9g_18280.pdb" } 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-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: 3.57, per 1000 atoms: 0.52 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: 4.95 Conformation dependent library (CDL) restraints added in 674.4 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: 6.518A 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: 2.22 Time building geometry restraints manager: 5.17 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 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.610 1.850 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.627 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.644 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.653 1.850 ... (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 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: 2.920 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: 0.100 Extract box with map and model: 11.850 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 25.250 Find NCS groups from input model: 0.310 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:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.200 ------------------------------------------------------------------------------- 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 : 0.559 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: 2.9535 time to fit residues: 401.5354 Evaluate side-chains 94 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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: 9.9990 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: 6.9990 chunk 38 optimal weight: 6.9990 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: 0.6552 moved from start: 0.3566 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= 0.253 Angle : 0.599 4.741 4548 Z= 0.315 Chirality : 0.051 0.142 516 Planarity : 0.003 0.032 576 Dihedral : 5.487 15.028 444 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.56 % Allowed : 11.72 % Favored : 86.72 % 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: -1.82 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 374 PHE 0.009 0.002 PHE C 346 TYR 0.007 0.002 TYR D 310 ARG 0.003 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 100 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 SER cc_start: 0.7974 (t) cc_final: 0.7569 (p) REVERT: C 311 LYS cc_start: 0.5269 (ttpt) cc_final: 0.4914 (mmtm) REVERT: C 321 LYS cc_start: 0.7296 (mtpt) cc_final: 0.6905 (mttm) REVERT: C 345 ASP cc_start: 0.7845 (t0) cc_final: 0.7641 (t70) REVERT: C 347 LYS cc_start: 0.7837 (mttt) cc_final: 0.7587 (mmtt) REVERT: C 349 ARG cc_start: 0.7395 (mtt180) cc_final: 0.5479 (mmp-170) REVERT: C 369 LYS cc_start: 0.6554 (mttt) cc_final: 0.6307 (mttp) REVERT: C 372 GLU cc_start: 0.7695 (tt0) cc_final: 0.7217 (tp30) REVERT: E 338 GLU cc_start: 0.7168 (tt0) cc_final: 0.6765 (pp20) REVERT: E 347 LYS cc_start: 0.7805 (mttt) cc_final: 0.6849 (pttm) REVERT: E 349 ARG cc_start: 0.7146 (mtm180) cc_final: 0.6871 (mtt180) REVERT: B 320 SER cc_start: 0.7834 (t) cc_final: 0.7167 (p) REVERT: B 321 LYS cc_start: 0.7358 (mtpt) cc_final: 0.6959 (mttt) REVERT: B 345 ASP cc_start: 0.7054 (t0) cc_final: 0.6679 (m-30) REVERT: B 349 ARG cc_start: 0.7285 (mtp85) cc_final: 0.7011 (mtp85) REVERT: B 375 LYS cc_start: 0.4895 (tttt) cc_final: 0.4573 (ttmm) REVERT: D 320 SER cc_start: 0.8466 (t) cc_final: 0.8210 (p) REVERT: D 321 LYS cc_start: 0.7494 (mtpt) cc_final: 0.7180 (mttm) REVERT: D 345 ASP cc_start: 0.6968 (t0) cc_final: 0.6633 (p0) REVERT: D 349 ARG cc_start: 0.7706 (mtt180) cc_final: 0.6400 (mmp-170) REVERT: D 369 LYS cc_start: 0.6603 (mttt) cc_final: 0.6303 (ttmm) REVERT: D 375 LYS cc_start: 0.4976 (tttt) cc_final: 0.4684 (ttmm) REVERT: F 316 SER cc_start: 0.6717 (m) cc_final: 0.6360 (p) REVERT: F 320 SER cc_start: 0.7587 (t) cc_final: 0.6947 (p) REVERT: F 375 LYS cc_start: 0.6763 (tttt) cc_final: 0.6332 (tttm) outliers start: 6 outliers final: 2 residues processed: 94 average time/residue: 3.0643 time to fit residues: 294.4475 Evaluate side-chains 92 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 348 ASP 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: 9.9990 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 19 optimal weight: 7.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.4080 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= 0.221 Angle : 0.545 4.330 4548 Z= 0.289 Chirality : 0.050 0.140 516 Planarity : 0.002 0.018 576 Dihedral : 5.032 14.948 444 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.56 % Allowed : 14.58 % Favored : 83.85 % 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: -1.94 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 374 PHE 0.008 0.002 PHE C 346 TYR 0.009 0.002 TYR C 310 ARG 0.002 0.001 ARG E 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 96 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 SER cc_start: 0.7975 (t) cc_final: 0.7614 (p) REVERT: C 311 LYS cc_start: 0.5358 (ttpt) cc_final: 0.5032 (mmtm) REVERT: C 320 SER cc_start: 0.8421 (t) cc_final: 0.8196 (p) REVERT: C 321 LYS cc_start: 0.7273 (mtpt) cc_final: 0.6835 (mttp) REVERT: C 347 LYS cc_start: 0.7841 (mttt) cc_final: 0.7545 (mmmm) REVERT: C 349 ARG cc_start: 0.7464 (mtt180) cc_final: 0.5489 (mmp-170) REVERT: C 372 GLU cc_start: 0.7748 (tt0) cc_final: 0.7202 (tp30) REVERT: E 338 GLU cc_start: 0.7172 (tt0) cc_final: 0.6740 (pp20) REVERT: E 347 LYS cc_start: 0.7899 (mttt) cc_final: 0.6920 (pttm) REVERT: B 320 SER cc_start: 0.8067 (t) cc_final: 0.7444 (p) REVERT: B 321 LYS cc_start: 0.7316 (mtpt) cc_final: 0.6979 (mttt) REVERT: B 375 LYS cc_start: 0.4808 (tttt) cc_final: 0.4593 (tttp) REVERT: D 321 LYS cc_start: 0.7329 (mtpt) cc_final: 0.7012 (mttp) REVERT: D 349 ARG cc_start: 0.7752 (mtt180) cc_final: 0.6384 (mmp-170) REVERT: D 369 LYS cc_start: 0.6652 (mttt) cc_final: 0.6332 (ttmm) REVERT: D 375 LYS cc_start: 0.4951 (tttt) cc_final: 0.4618 (tttm) REVERT: F 316 SER cc_start: 0.6603 (m) cc_final: 0.6368 (p) REVERT: F 349 ARG cc_start: 0.6138 (ptt-90) cc_final: 0.5798 (pmt-80) REVERT: F 375 LYS cc_start: 0.6775 (tttt) cc_final: 0.6331 (tttm) outliers start: 6 outliers final: 3 residues processed: 92 average time/residue: 2.9253 time to fit residues: 275.4012 Evaluate side-chains 87 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain E residue 348 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: 9.9990 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN E 368 ASN B 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3396 Z= 0.376 Angle : 0.621 4.357 4548 Z= 0.332 Chirality : 0.051 0.140 516 Planarity : 0.003 0.015 576 Dihedral : 5.368 15.940 444 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: -2.16 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 374 PHE 0.009 0.002 PHE E 378 TYR 0.011 0.003 TYR A 310 ARG 0.004 0.001 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 94 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 SER cc_start: 0.8016 (t) cc_final: 0.7659 (p) REVERT: C 311 LYS cc_start: 0.5229 (ttpt) cc_final: 0.4909 (mmtm) REVERT: C 321 LYS cc_start: 0.7319 (mtpt) cc_final: 0.6872 (mttp) REVERT: C 347 LYS cc_start: 0.7837 (mttt) cc_final: 0.7507 (mmmm) REVERT: C 349 ARG cc_start: 0.7489 (mtt180) cc_final: 0.5572 (mmp-170) REVERT: C 372 GLU cc_start: 0.7742 (tt0) cc_final: 0.7187 (tp30) REVERT: E 338 GLU cc_start: 0.7153 (tt0) cc_final: 0.6692 (pp20) REVERT: E 347 LYS cc_start: 0.7943 (mttt) cc_final: 0.7023 (pmtt) REVERT: B 320 SER cc_start: 0.8083 (t) cc_final: 0.7384 (p) REVERT: B 321 LYS cc_start: 0.7317 (mtpt) cc_final: 0.6964 (mttt) REVERT: D 321 LYS cc_start: 0.7298 (mtpt) cc_final: 0.6957 (mttm) REVERT: D 349 ARG cc_start: 0.7696 (mtt180) cc_final: 0.6426 (mmp-170) REVERT: D 369 LYS cc_start: 0.6635 (mttt) cc_final: 0.6344 (ttmm) REVERT: F 316 SER cc_start: 0.6576 (m) cc_final: 0.6330 (p) REVERT: F 345 ASP cc_start: 0.6512 (OUTLIER) cc_final: 0.6278 (p0) REVERT: F 375 LYS cc_start: 0.6742 (tttt) cc_final: 0.6495 (mtpp) outliers start: 9 outliers final: 5 residues processed: 86 average time/residue: 2.9917 time to fit residues: 263.3125 Evaluate side-chains 88 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 358 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: 2.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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: 0.6558 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3396 Z= 0.203 Angle : 0.525 4.102 4548 Z= 0.274 Chirality : 0.050 0.137 516 Planarity : 0.002 0.017 576 Dihedral : 4.969 15.088 444 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: -2.10 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 374 PHE 0.006 0.001 PHE C 346 TYR 0.008 0.002 TYR B 310 ARG 0.001 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 90 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 SER cc_start: 0.7973 (t) cc_final: 0.7629 (p) REVERT: C 311 LYS cc_start: 0.5222 (ttpt) cc_final: 0.4908 (mmtm) REVERT: C 321 LYS cc_start: 0.7296 (mtpt) cc_final: 0.6906 (mttp) REVERT: C 338 GLU cc_start: 0.7170 (tp30) cc_final: 0.6917 (tp30) REVERT: C 347 LYS cc_start: 0.7857 (mttt) cc_final: 0.7548 (mmmm) REVERT: C 349 ARG cc_start: 0.7489 (mtt180) cc_final: 0.5589 (mmp-170) REVERT: C 372 GLU cc_start: 0.7778 (tt0) cc_final: 0.7274 (tp30) REVERT: E 336 GLN cc_start: 0.7763 (tt0) cc_final: 0.7199 (tt0) REVERT: E 338 GLU cc_start: 0.7132 (tt0) cc_final: 0.6717 (mt-10) REVERT: E 347 LYS cc_start: 0.7946 (mttt) cc_final: 0.7018 (pmtt) REVERT: B 320 SER cc_start: 0.8081 (t) cc_final: 0.7518 (p) REVERT: B 321 LYS cc_start: 0.7296 (mtpt) cc_final: 0.6949 (mttt) REVERT: B 349 ARG cc_start: 0.7534 (ptp-170) cc_final: 0.7243 (ptp-110) REVERT: D 321 LYS cc_start: 0.7322 (mtpt) cc_final: 0.6979 (mttm) REVERT: D 349 ARG cc_start: 0.7703 (mtt180) cc_final: 0.6461 (mmp-170) REVERT: D 369 LYS cc_start: 0.6622 (mttt) cc_final: 0.6320 (ttmm) REVERT: F 349 ARG cc_start: 0.6141 (ptt-90) cc_final: 0.5783 (pmt-80) REVERT: F 375 LYS cc_start: 0.6752 (tttt) cc_final: 0.6540 (mtpp) outliers start: 6 outliers final: 5 residues processed: 85 average time/residue: 3.0387 time to fit residues: 264.6330 Evaluate side-chains 86 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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: 0.6564 moved from start: 0.4646 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= 0.255 Angle : 0.557 4.605 4548 Z= 0.293 Chirality : 0.050 0.139 516 Planarity : 0.002 0.019 576 Dihedral : 5.015 15.553 444 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.82 % Allowed : 17.45 % 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: -2.13 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.006 0.001 PHE C 346 TYR 0.009 0.002 TYR B 310 ARG 0.002 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 89 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 SER cc_start: 0.7932 (t) cc_final: 0.7564 (p) REVERT: C 311 LYS cc_start: 0.5212 (ttpt) cc_final: 0.4904 (mmtm) REVERT: C 321 LYS cc_start: 0.7310 (mtpt) cc_final: 0.6807 (mttp) REVERT: C 347 LYS cc_start: 0.7892 (mttt) cc_final: 0.7552 (mmmm) REVERT: C 349 ARG cc_start: 0.7483 (mtt180) cc_final: 0.5599 (mmp-170) REVERT: C 372 GLU cc_start: 0.7741 (tt0) cc_final: 0.7226 (tp30) REVERT: E 338 GLU cc_start: 0.7108 (tt0) cc_final: 0.6714 (pp20) REVERT: E 347 LYS cc_start: 0.7950 (mttt) cc_final: 0.7022 (pmtt) REVERT: B 320 SER cc_start: 0.8126 (t) cc_final: 0.7513 (p) REVERT: B 321 LYS cc_start: 0.7293 (mtpt) cc_final: 0.6951 (mttt) REVERT: D 321 LYS cc_start: 0.7351 (mtpt) cc_final: 0.7019 (mttm) REVERT: D 349 ARG cc_start: 0.7718 (mtt180) cc_final: 0.6439 (mmp-170) REVERT: D 369 LYS cc_start: 0.6614 (mttt) cc_final: 0.6317 (ttmm) REVERT: F 349 ARG cc_start: 0.6208 (ptt-90) cc_final: 0.5784 (pmt-80) REVERT: F 375 LYS cc_start: 0.6707 (tttt) cc_final: 0.6502 (mtpp) outliers start: 7 outliers final: 5 residues processed: 83 average time/residue: 3.0915 time to fit residues: 262.7668 Evaluate side-chains 84 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 369 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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: 0.6567 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3396 Z= 0.301 Angle : 0.585 5.016 4548 Z= 0.308 Chirality : 0.050 0.138 516 Planarity : 0.003 0.019 576 Dihedral : 5.125 15.649 444 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.82 % Allowed : 17.45 % 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: -2.18 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 374 PHE 0.007 0.002 PHE A 346 TYR 0.011 0.003 TYR B 310 ARG 0.002 0.000 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 88 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 SER cc_start: 0.7955 (t) cc_final: 0.7594 (p) REVERT: C 311 LYS cc_start: 0.5215 (ttpt) cc_final: 0.4898 (mmtm) REVERT: C 321 LYS cc_start: 0.7333 (mtpt) cc_final: 0.6830 (mttp) REVERT: C 347 LYS cc_start: 0.7888 (mttt) cc_final: 0.7544 (mmmm) REVERT: C 349 ARG cc_start: 0.7468 (mtt180) cc_final: 0.5607 (mmp-170) REVERT: C 372 GLU cc_start: 0.7765 (tt0) cc_final: 0.7204 (tp30) REVERT: E 338 GLU cc_start: 0.7185 (tt0) cc_final: 0.6788 (pp20) REVERT: E 347 LYS cc_start: 0.7956 (mttt) cc_final: 0.7031 (pmtt) REVERT: B 320 SER cc_start: 0.8106 (t) cc_final: 0.7463 (p) REVERT: B 321 LYS cc_start: 0.7299 (mtpt) cc_final: 0.6958 (mttt) REVERT: B 349 ARG cc_start: 0.7577 (ptp-170) cc_final: 0.7346 (ptp-110) REVERT: D 321 LYS cc_start: 0.7359 (mtpt) cc_final: 0.7027 (mttm) REVERT: D 349 ARG cc_start: 0.7694 (mtt180) cc_final: 0.6461 (mmp-170) REVERT: D 369 LYS cc_start: 0.6645 (mttt) cc_final: 0.6338 (ttmm) outliers start: 7 outliers final: 6 residues processed: 82 average time/residue: 3.0075 time to fit residues: 252.3348 Evaluate side-chains 84 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 369 LYS 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: 20.0000 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.6553 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3396 Z= 0.178 Angle : 0.513 4.000 4548 Z= 0.264 Chirality : 0.050 0.136 516 Planarity : 0.002 0.021 576 Dihedral : 4.796 15.111 444 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.08 % Allowed : 17.71 % 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: -2.09 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 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 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 88 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 SER cc_start: 0.7922 (t) cc_final: 0.7572 (p) REVERT: C 311 LYS cc_start: 0.5260 (ttpt) cc_final: 0.4936 (mmtm) REVERT: C 321 LYS cc_start: 0.7285 (mtpt) cc_final: 0.6797 (mttp) REVERT: C 338 GLU cc_start: 0.7158 (tp30) cc_final: 0.6898 (tp30) REVERT: C 347 LYS cc_start: 0.7877 (mttt) cc_final: 0.7529 (mmmm) REVERT: C 349 ARG cc_start: 0.7462 (mtt180) cc_final: 0.5593 (mmp-170) REVERT: C 372 GLU cc_start: 0.7822 (tt0) cc_final: 0.7327 (tp30) REVERT: E 338 GLU cc_start: 0.7097 (tt0) cc_final: 0.6757 (pp20) REVERT: E 347 LYS cc_start: 0.7942 (mttt) cc_final: 0.7038 (pmtt) REVERT: E 375 LYS cc_start: 0.6799 (tttp) cc_final: 0.5997 (ttmm) REVERT: B 320 SER cc_start: 0.8069 (t) cc_final: 0.7522 (p) REVERT: B 321 LYS cc_start: 0.7303 (mtpt) cc_final: 0.6963 (mttt) REVERT: B 349 ARG cc_start: 0.7582 (ptp-170) cc_final: 0.7339 (ptp-110) REVERT: D 321 LYS cc_start: 0.7327 (mtpt) cc_final: 0.6990 (mttt) REVERT: D 349 ARG cc_start: 0.7696 (mtt180) cc_final: 0.6458 (mmp-170) REVERT: D 369 LYS cc_start: 0.6636 (mttt) cc_final: 0.6323 (ttmm) REVERT: F 349 ARG cc_start: 0.6206 (ptt-90) cc_final: 0.5792 (pmt-80) outliers start: 8 outliers final: 6 residues processed: 82 average time/residue: 3.0071 time to fit residues: 252.1830 Evaluate side-chains 84 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 369 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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: 0.6564 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3396 Z= 0.276 Angle : 0.574 6.675 4548 Z= 0.302 Chirality : 0.050 0.138 516 Planarity : 0.003 0.022 576 Dihedral : 4.971 15.441 444 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.08 % Allowed : 18.49 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.006 0.001 PHE A 346 TYR 0.012 0.003 TYR B 310 ARG 0.002 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 87 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 311 LYS cc_start: 0.5204 (ttpt) cc_final: 0.4914 (mmtm) REVERT: C 321 LYS cc_start: 0.7299 (mtpt) cc_final: 0.6832 (mttp) REVERT: C 338 GLU cc_start: 0.7160 (tp30) cc_final: 0.6932 (tp30) REVERT: C 347 LYS cc_start: 0.7868 (mttt) cc_final: 0.7524 (mmmm) REVERT: C 349 ARG cc_start: 0.7455 (mtt180) cc_final: 0.5621 (mmp-170) REVERT: C 372 GLU cc_start: 0.7804 (tt0) cc_final: 0.7268 (tp30) REVERT: E 338 GLU cc_start: 0.7162 (tt0) cc_final: 0.6784 (pp20) REVERT: E 347 LYS cc_start: 0.7957 (mttt) cc_final: 0.7044 (pmtt) REVERT: B 320 SER cc_start: 0.8134 (t) cc_final: 0.7520 (p) REVERT: B 321 LYS cc_start: 0.7289 (mtpt) cc_final: 0.6949 (mttt) REVERT: D 321 LYS cc_start: 0.7340 (mtpt) cc_final: 0.7011 (mttt) REVERT: D 349 ARG cc_start: 0.7711 (mtt180) cc_final: 0.6456 (mmp-170) REVERT: D 369 LYS cc_start: 0.6675 (mttt) cc_final: 0.6421 (ttmm) REVERT: F 345 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6629 (p0) REVERT: F 349 ARG cc_start: 0.6223 (ptt-90) cc_final: 0.5813 (pmt-80) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 3.1302 time to fit residues: 256.5385 Evaluate side-chains 84 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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: 0.6556 moved from start: 0.4856 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= 0.187 Angle : 0.521 5.742 4548 Z= 0.272 Chirality : 0.050 0.136 516 Planarity : 0.002 0.019 576 Dihedral : 4.798 14.986 444 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.08 % Allowed : 18.23 % 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: -2.08 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 374 PHE 0.005 0.001 PHE C 346 TYR 0.009 0.002 TYR B 310 ARG 0.001 0.000 ARG E 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 85 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 SER cc_start: 0.7935 (t) cc_final: 0.7577 (p) REVERT: C 311 LYS cc_start: 0.5210 (ttpt) cc_final: 0.4899 (mmtt) REVERT: C 321 LYS cc_start: 0.7309 (mtpt) cc_final: 0.6823 (mttp) REVERT: C 338 GLU cc_start: 0.7186 (tp30) cc_final: 0.6917 (tp30) REVERT: C 347 LYS cc_start: 0.7871 (mttt) cc_final: 0.7528 (mmmm) REVERT: C 349 ARG cc_start: 0.7460 (mtt180) cc_final: 0.5619 (mmp-170) REVERT: C 372 GLU cc_start: 0.7814 (tt0) cc_final: 0.7298 (tp30) REVERT: E 338 GLU cc_start: 0.7165 (tt0) cc_final: 0.6782 (pp20) REVERT: E 347 LYS cc_start: 0.7937 (mttt) cc_final: 0.7018 (pmtt) REVERT: B 320 SER cc_start: 0.8110 (t) cc_final: 0.7532 (p) REVERT: B 321 LYS cc_start: 0.7293 (mtpt) cc_final: 0.6953 (mttt) REVERT: D 321 LYS cc_start: 0.7334 (mtpt) cc_final: 0.6997 (mttt) REVERT: D 349 ARG cc_start: 0.7694 (mtt180) cc_final: 0.6453 (mmp-170) REVERT: D 369 LYS cc_start: 0.6664 (mttt) cc_final: 0.6411 (ttmm) REVERT: F 345 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6624 (p0) REVERT: F 349 ARG cc_start: 0.6226 (ptt-90) cc_final: 0.5814 (pmt-80) outliers start: 8 outliers final: 6 residues processed: 78 average time/residue: 2.9966 time to fit residues: 239.2648 Evaluate side-chains 84 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.152296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.121704 restraints weight = 11268.566| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.64 r_work: 0.3757 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3396 Z= 0.163 Angle : 0.499 5.364 4548 Z= 0.257 Chirality : 0.050 0.135 516 Planarity : 0.002 0.022 576 Dihedral : 4.537 14.400 444 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.82 % Allowed : 19.01 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.004 0.001 PHE C 346 TYR 0.009 0.002 TYR B 310 ARG 0.001 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5138.54 seconds wall clock time: 90 minutes 1.97 seconds (5401.97 seconds total)