Starting phenix.real_space_refine on Mon Mar 11 03:20:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkx_14056/03_2024/7qkx_14056.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkx_14056/03_2024/7qkx_14056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkx_14056/03_2024/7qkx_14056.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkx_14056/03_2024/7qkx_14056.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkx_14056/03_2024/7qkx_14056.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkx_14056/03_2024/7qkx_14056.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2106 2.51 5 N 606 2.21 5 O 624 1.98 5 H 3480 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 372": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 372": "OE1" <-> "OE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 372": "OE1" <-> "OE2" Residue "G GLU 338": "OE1" <-> "OE2" Residue "G ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 372": "OE1" <-> "OE2" Residue "G PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 372": "OE1" <-> "OE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 372": "OE1" <-> "OE2" 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: "G" 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} Time building chain proxies: 3.55, per 1000 atoms: 0.52 Number of scatterers: 6822 At special positions: 0 Unit cell: (86.52, 146.672, 36.256, 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: 5.31 Conformation dependent library (CDL) restraints added in 735.3 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, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.442A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.925A 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 321 removed outlier: 6.307A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.174A 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: 5.913A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.772A 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 Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.430A 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: 6.521A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N SER E 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.410A 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: 6.427A 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 removed outlier: 6.597A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 307 through 310 removed outlier: 6.495A pdb=" N ILE G 308 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN G 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N TYR D 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL G 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.923A pdb=" N VAL G 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 317 through 321 Processing sheet with id=AB4, first strand: chain 'B' and resid 325 through 330 removed outlier: 5.930A pdb=" N GLY G 326 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N HIS B 329 " --> pdb=" O GLY G 326 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE G 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY D 326 " --> pdb=" O LEU G 325 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN G 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 337 through 342 removed outlier: 6.560A pdb=" N VAL G 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LYS B 340 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL G 339 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLU B 342 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER G 341 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.472A pdb=" N ASP G 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 350 through 357 removed outlier: 6.344A pdb=" N VAL G 350 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LYS B 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER G 352 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N GLY B 355 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE G 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU B 357 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER G 356 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN G 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE D 354 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS G 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N SER D 356 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY G 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.446A pdb=" N THR G 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 369 through 377 removed outlier: 6.626A pdb=" N LYS G 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLU D 372 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE G 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N HIS D 374 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR G 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N LEU D 376 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS G 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) 64 hydrogen bonds defined for protein. 192 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: 2.25 Time building geometry restraints manager: 5.54 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: 941 1.46 - 1.64: 1897 1.64 - 1.81: 6 Bond restraints: 6876 Sorted by residual: bond pdb=" N ASP C 345 " pdb=" H ASP C 345 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" N ARG C 349 " pdb=" H ARG C 349 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" N SER A 352 " pdb=" H SER A 352 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" N ILE D 360 " pdb=" H ILE D 360 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" N HIS B 329 " pdb=" H HIS B 329 " 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: 96.64 - 103.07: 28 103.07 - 109.50: 5251 109.50 - 115.94: 3712 115.94 - 122.37: 2833 122.37 - 128.81: 722 Bond angle restraints: 12546 Sorted by residual: angle pdb=" CA ASP G 345 " pdb=" CB ASP G 345 " pdb=" CG ASP G 345 " ideal model delta sigma weight residual 112.60 117.62 -5.02 1.00e+00 1.00e+00 2.52e+01 angle pdb=" OE1 GLN G 336 " pdb=" CD GLN G 336 " pdb=" NE2 GLN G 336 " ideal model delta sigma weight residual 122.60 117.64 4.96 1.00e+00 1.00e+00 2.46e+01 angle pdb=" CA ASP E 345 " pdb=" CB ASP E 345 " pdb=" CG ASP E 345 " ideal model delta sigma weight residual 112.60 117.54 -4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" CA ASP A 345 " pdb=" CB ASP A 345 " pdb=" CG ASP A 345 " ideal model delta sigma weight residual 112.60 117.47 -4.87 1.00e+00 1.00e+00 2.37e+01 angle pdb=" N GLY G 326 " pdb=" CA GLY G 326 " pdb=" C GLY G 326 " ideal model delta sigma weight residual 110.69 117.16 -6.47 1.33e+00 5.65e-01 2.36e+01 ... (remaining 12541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.51: 2745 13.51 - 27.02: 207 27.02 - 40.52: 84 40.52 - 54.03: 54 54.03 - 67.54: 78 Dihedral angle restraints: 3168 sinusoidal: 1806 harmonic: 1362 Sorted by residual: dihedral pdb=" CA LYS G 375 " pdb=" C LYS G 375 " pdb=" N LEU G 376 " pdb=" CA LEU G 376 " ideal model delta harmonic sigma weight residual 180.00 151.10 28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA THR B 377 " pdb=" C THR B 377 " pdb=" N PHE B 378 " pdb=" CA PHE B 378 " ideal model delta harmonic sigma weight residual -180.00 -152.40 -27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA LYS G 369 " pdb=" C LYS G 369 " pdb=" N LYS G 370 " pdb=" CA LYS G 370 " ideal model delta harmonic sigma weight residual 180.00 157.11 22.89 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 3165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 286 0.067 - 0.133: 165 0.133 - 0.199: 48 0.199 - 0.265: 13 0.265 - 0.332: 4 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA LEU G 376 " pdb=" N LEU G 376 " pdb=" C LEU G 376 " pdb=" CB LEU G 376 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 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 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA LYS A 317 " pdb=" N LYS A 317 " pdb=" C LYS A 317 " pdb=" CB LYS A 317 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 513 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.076 2.00e-02 2.50e+03 3.17e-02 3.02e+01 pdb=" CG TYR C 310 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.045 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " 0.007 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 362 " 0.057 2.00e-02 2.50e+03 3.62e-02 2.95e+01 pdb=" CG HIS A 362 " -0.050 2.00e-02 2.50e+03 pdb=" ND1 HIS A 362 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS A 362 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 HIS A 362 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 HIS A 362 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 HIS A 362 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 HIS A 362 " 0.035 2.00e-02 2.50e+03 pdb=" HE2 HIS A 362 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 359 " 0.004 2.00e-02 2.50e+03 4.08e-02 2.50e+01 pdb=" CG ASN A 359 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 359 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 359 " -0.082 2.00e-02 2.50e+03 pdb="HD21 ASN A 359 " 0.046 2.00e-02 2.50e+03 pdb="HD22 ASN A 359 " 0.023 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 447 2.17 - 2.78: 11789 2.78 - 3.39: 17717 3.39 - 3.99: 24010 3.99 - 4.60: 33554 Nonbonded interactions: 87517 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.566 1.850 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.570 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.573 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.577 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.593 1.850 ... (remaining 87512 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 'G' } 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: 2.390 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: 0.120 Extract box with map and model: 11.550 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 25.710 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 0.037 3396 Z= 0.736 Angle : 1.820 6.465 4548 Z= 1.209 Chirality : 0.091 0.332 516 Planarity : 0.010 0.061 576 Dihedral : 10.510 53.065 1296 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.004 HIS A 330 PHE 0.032 0.011 PHE D 346 TYR 0.069 0.020 TYR C 310 ARG 0.002 0.000 ARG E 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 121 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 VAL cc_start: 0.2146 (t) cc_final: 0.1680 (t) REVERT: A 321 LYS cc_start: 0.7775 (ttpt) cc_final: 0.7228 (mttt) REVERT: A 369 LYS cc_start: 0.7304 (mttt) cc_final: 0.6679 (mtpt) REVERT: C 311 LYS cc_start: 0.7178 (ttpt) cc_final: 0.6637 (mmtt) REVERT: C 321 LYS cc_start: 0.7729 (ttpt) cc_final: 0.7233 (mttt) REVERT: C 349 ARG cc_start: 0.8240 (mtt180) cc_final: 0.6396 (mmm160) REVERT: C 369 LYS cc_start: 0.7273 (mttt) cc_final: 0.6942 (mtpt) REVERT: E 321 LYS cc_start: 0.8467 (ttpt) cc_final: 0.7985 (mttp) REVERT: E 349 ARG cc_start: 0.7507 (mtt180) cc_final: 0.6723 (pmt-80) REVERT: E 369 LYS cc_start: 0.7898 (mttt) cc_final: 0.7469 (mtpt) REVERT: E 375 LYS cc_start: 0.7042 (tttt) cc_final: 0.6663 (ttmm) REVERT: G 321 LYS cc_start: 0.7458 (ttmt) cc_final: 0.7081 (mttp) REVERT: G 369 LYS cc_start: 0.7227 (mttt) cc_final: 0.6697 (mtpt) REVERT: B 311 LYS cc_start: 0.7520 (ttpt) cc_final: 0.6909 (mmtt) REVERT: B 317 LYS cc_start: 0.6545 (pttt) cc_final: 0.6340 (pttp) REVERT: B 321 LYS cc_start: 0.7680 (ttpt) cc_final: 0.7144 (mttt) REVERT: B 349 ARG cc_start: 0.8213 (mtt180) cc_final: 0.6507 (mmm160) REVERT: B 369 LYS cc_start: 0.7323 (mttt) cc_final: 0.6984 (mtpt) REVERT: D 306 VAL cc_start: 0.3383 (t) cc_final: 0.3178 (t) REVERT: D 321 LYS cc_start: 0.8424 (ttpt) cc_final: 0.7906 (mttp) REVERT: D 349 ARG cc_start: 0.7721 (mtt180) cc_final: 0.6687 (pmt-80) REVERT: D 369 LYS cc_start: 0.7872 (mttt) cc_final: 0.7380 (mtpt) REVERT: D 375 LYS cc_start: 0.6926 (tttt) cc_final: 0.6421 (ttmm) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.5907 time to fit residues: 79.5388 Evaluate side-chains 81 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 362 HIS E 362 HIS G 362 HIS B 362 HIS D 362 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3396 Z= 0.171 Angle : 0.597 6.737 4548 Z= 0.310 Chirality : 0.052 0.136 516 Planarity : 0.003 0.023 576 Dihedral : 6.386 19.461 444 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % 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: -1.34 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 330 PHE 0.017 0.001 PHE B 378 TYR 0.009 0.002 TYR G 310 ARG 0.002 0.000 ARG G 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 77 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7781 (ttpt) cc_final: 0.7238 (mttm) REVERT: A 369 LYS cc_start: 0.7344 (mttt) cc_final: 0.6783 (mtpt) REVERT: C 321 LYS cc_start: 0.7684 (ttpt) cc_final: 0.7246 (mttt) REVERT: C 349 ARG cc_start: 0.8144 (mtt180) cc_final: 0.6305 (mmm160) REVERT: C 369 LYS cc_start: 0.7325 (mttt) cc_final: 0.7043 (mtpt) REVERT: E 321 LYS cc_start: 0.8400 (ttpt) cc_final: 0.8009 (mttm) REVERT: E 349 ARG cc_start: 0.7155 (mtt180) cc_final: 0.6612 (pmt-80) REVERT: E 369 LYS cc_start: 0.7932 (mttt) cc_final: 0.7427 (mtpt) REVERT: E 375 LYS cc_start: 0.7182 (tttt) cc_final: 0.6793 (ttmm) REVERT: G 369 LYS cc_start: 0.7190 (mttt) cc_final: 0.6748 (mtpt) REVERT: B 311 LYS cc_start: 0.7490 (ttpt) cc_final: 0.6895 (mmtt) REVERT: B 317 LYS cc_start: 0.6533 (pttt) cc_final: 0.6313 (pttp) REVERT: B 321 LYS cc_start: 0.7742 (ttpt) cc_final: 0.7250 (mttm) REVERT: B 349 ARG cc_start: 0.8262 (mtt180) cc_final: 0.6336 (mmm160) REVERT: B 369 LYS cc_start: 0.7212 (mttt) cc_final: 0.6832 (mtpt) REVERT: D 321 LYS cc_start: 0.8328 (ttpt) cc_final: 0.7892 (mttm) REVERT: D 369 LYS cc_start: 0.7803 (mttt) cc_final: 0.7319 (mtpt) REVERT: D 375 LYS cc_start: 0.7164 (tttt) cc_final: 0.6650 (ttmm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.6441 time to fit residues: 55.0786 Evaluate side-chains 70 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3396 Z= 0.302 Angle : 0.595 6.065 4548 Z= 0.313 Chirality : 0.052 0.136 516 Planarity : 0.003 0.020 576 Dihedral : 5.734 15.973 444 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.26 % Allowed : 11.46 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 329 PHE 0.012 0.002 PHE B 378 TYR 0.021 0.004 TYR G 310 ARG 0.004 0.001 ARG D 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 60 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7394 (mttm) REVERT: A 369 LYS cc_start: 0.7261 (mttt) cc_final: 0.6853 (mtpt) REVERT: A 375 LYS cc_start: 0.5873 (tttt) cc_final: 0.5522 (ttmm) REVERT: C 321 LYS cc_start: 0.7997 (ttpt) cc_final: 0.7525 (mttm) REVERT: C 349 ARG cc_start: 0.8195 (mtt180) cc_final: 0.6429 (mmm160) REVERT: C 369 LYS cc_start: 0.7235 (mttt) cc_final: 0.6918 (mtpt) REVERT: E 321 LYS cc_start: 0.8453 (ttpt) cc_final: 0.8052 (mttp) REVERT: E 349 ARG cc_start: 0.7566 (mtt180) cc_final: 0.6636 (pmt-80) REVERT: E 369 LYS cc_start: 0.7938 (mttt) cc_final: 0.7414 (mtpt) REVERT: E 375 LYS cc_start: 0.7394 (tttt) cc_final: 0.6894 (ttmm) REVERT: B 349 ARG cc_start: 0.8290 (mtt180) cc_final: 0.6462 (mmm160) REVERT: B 369 LYS cc_start: 0.7311 (mttt) cc_final: 0.6911 (mtpt) REVERT: D 321 LYS cc_start: 0.8404 (ttpt) cc_final: 0.7942 (mttm) REVERT: D 375 LYS cc_start: 0.7220 (tttt) cc_final: 0.6638 (ttmm) outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.6076 time to fit residues: 40.8833 Evaluate side-chains 51 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 0.1980 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- 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: 0.7867 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3396 Z= 0.199 Angle : 0.535 5.048 4548 Z= 0.275 Chirality : 0.050 0.134 516 Planarity : 0.002 0.017 576 Dihedral : 5.285 14.364 444 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.26 % Allowed : 12.24 % Favored : 87.50 % 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: -1.44 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.007 0.001 PHE B 378 TYR 0.012 0.002 TYR G 310 ARG 0.002 0.000 ARG E 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 57 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.579 Fit side-chains REVERT: A 321 LYS cc_start: 0.7889 (ttpt) cc_final: 0.7358 (mttm) REVERT: A 349 ARG cc_start: 0.7661 (mtp85) cc_final: 0.7351 (mtp85) REVERT: A 375 LYS cc_start: 0.5868 (tttt) cc_final: 0.5524 (ttmm) REVERT: C 321 LYS cc_start: 0.7896 (ttpt) cc_final: 0.7411 (mttm) REVERT: C 349 ARG cc_start: 0.8221 (mtt180) cc_final: 0.6398 (mmm160) REVERT: C 369 LYS cc_start: 0.7289 (mttt) cc_final: 0.6968 (mtpt) REVERT: E 321 LYS cc_start: 0.8473 (ttpt) cc_final: 0.8060 (mttp) REVERT: E 349 ARG cc_start: 0.7761 (mtt180) cc_final: 0.6583 (pmt-80) REVERT: E 375 LYS cc_start: 0.7381 (tttt) cc_final: 0.6875 (ttmm) REVERT: B 349 ARG cc_start: 0.8241 (mtt180) cc_final: 0.6416 (mmm160) REVERT: D 321 LYS cc_start: 0.8379 (ttpt) cc_final: 0.7917 (mttp) REVERT: D 375 LYS cc_start: 0.7262 (tttt) cc_final: 0.6675 (ttmm) outliers start: 1 outliers final: 1 residues processed: 57 average time/residue: 0.5224 time to fit residues: 34.1127 Evaluate side-chains 50 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.4980 chunk 8 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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: 0.7862 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3396 Z= 0.168 Angle : 0.502 4.749 4548 Z= 0.257 Chirality : 0.050 0.133 516 Planarity : 0.002 0.016 576 Dihedral : 4.934 13.392 444 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.26 % Allowed : 13.28 % 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: -1.47 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.005 0.001 PHE B 378 TYR 0.010 0.002 TYR G 310 ARG 0.001 0.000 ARG E 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 55 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7898 (ttpt) cc_final: 0.7486 (mttm) REVERT: A 349 ARG cc_start: 0.7685 (mtp85) cc_final: 0.7403 (mtp85) REVERT: A 375 LYS cc_start: 0.5883 (tttt) cc_final: 0.5518 (ttmm) REVERT: C 321 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7378 (mttm) REVERT: C 349 ARG cc_start: 0.8206 (mtt180) cc_final: 0.6392 (mmm160) REVERT: C 369 LYS cc_start: 0.7279 (mttt) cc_final: 0.6949 (mtpt) REVERT: E 321 LYS cc_start: 0.8426 (ttpt) cc_final: 0.8015 (mttp) REVERT: E 349 ARG cc_start: 0.7756 (mtt180) cc_final: 0.6640 (pmt-80) REVERT: E 375 LYS cc_start: 0.7408 (tttt) cc_final: 0.6866 (ttmm) REVERT: B 349 ARG cc_start: 0.8238 (mtt180) cc_final: 0.6407 (mmm160) REVERT: D 321 LYS cc_start: 0.8376 (ttpt) cc_final: 0.7857 (mttp) REVERT: D 375 LYS cc_start: 0.7318 (tttt) cc_final: 0.6718 (ttmm) outliers start: 1 outliers final: 1 residues processed: 55 average time/residue: 0.5204 time to fit residues: 32.9905 Evaluate side-chains 51 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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: 0.7870 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3396 Z= 0.201 Angle : 0.511 4.778 4548 Z= 0.263 Chirality : 0.050 0.134 516 Planarity : 0.002 0.016 576 Dihedral : 4.870 13.205 444 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.52 % Allowed : 13.80 % Favored : 85.68 % 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: -1.49 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.007 0.001 PHE B 378 TYR 0.013 0.002 TYR G 310 ARG 0.001 0.000 ARG G 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 51 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7918 (ttpt) cc_final: 0.7435 (mttp) REVERT: A 349 ARG cc_start: 0.7735 (mtp85) cc_final: 0.7497 (mtp85) REVERT: A 375 LYS cc_start: 0.5912 (tttt) cc_final: 0.5539 (ttmm) REVERT: C 321 LYS cc_start: 0.7890 (ttpt) cc_final: 0.7359 (mttm) REVERT: C 349 ARG cc_start: 0.8228 (mtt180) cc_final: 0.6388 (mmm160) REVERT: C 369 LYS cc_start: 0.7269 (mttt) cc_final: 0.6934 (mtpt) REVERT: E 321 LYS cc_start: 0.8432 (ttpt) cc_final: 0.7983 (mttp) REVERT: E 349 ARG cc_start: 0.7889 (mtt180) cc_final: 0.6617 (pmt-80) REVERT: E 375 LYS cc_start: 0.7399 (tttt) cc_final: 0.6827 (ttmm) REVERT: B 349 ARG cc_start: 0.8260 (mtt180) cc_final: 0.6454 (mmm160) REVERT: D 321 LYS cc_start: 0.8394 (ttpt) cc_final: 0.7852 (mttm) REVERT: D 375 LYS cc_start: 0.7367 (tttt) cc_final: 0.6750 (ttmm) outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.5116 time to fit residues: 29.5318 Evaluate side-chains 51 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.7881 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3396 Z= 0.242 Angle : 0.530 5.040 4548 Z= 0.273 Chirality : 0.050 0.138 516 Planarity : 0.002 0.017 576 Dihedral : 4.954 13.296 444 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.52 % Allowed : 14.32 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.007 0.001 PHE B 378 TYR 0.015 0.003 TYR G 310 ARG 0.002 0.000 ARG G 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 48 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.609 Fit side-chains REVERT: A 321 LYS cc_start: 0.7930 (ttpt) cc_final: 0.7444 (mttp) REVERT: A 349 ARG cc_start: 0.7778 (mtp85) cc_final: 0.7374 (mtt-85) REVERT: A 375 LYS cc_start: 0.5917 (tttt) cc_final: 0.5559 (ttmm) REVERT: C 349 ARG cc_start: 0.8265 (mtt180) cc_final: 0.6409 (mmm160) REVERT: C 369 LYS cc_start: 0.7308 (mttt) cc_final: 0.6970 (mtpt) REVERT: E 321 LYS cc_start: 0.8433 (ttpt) cc_final: 0.7957 (mttp) REVERT: E 349 ARG cc_start: 0.8024 (mtt180) cc_final: 0.6546 (pmt-80) REVERT: B 349 ARG cc_start: 0.8270 (mtt180) cc_final: 0.6529 (mmm160) REVERT: D 321 LYS cc_start: 0.8382 (ttpt) cc_final: 0.7838 (mttp) outliers start: 2 outliers final: 2 residues processed: 47 average time/residue: 0.4375 time to fit residues: 24.3011 Evaluate side-chains 46 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3396 Z= 0.141 Angle : 0.488 4.581 4548 Z= 0.247 Chirality : 0.050 0.132 516 Planarity : 0.002 0.015 576 Dihedral : 4.646 12.709 444 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.52 % Allowed : 15.10 % Favored : 84.38 % 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: -1.55 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.003 0.001 PHE A 346 TYR 0.008 0.002 TYR G 310 ARG 0.001 0.000 ARG A 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 47 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.773 Fit side-chains REVERT: A 321 LYS cc_start: 0.7925 (ttpt) cc_final: 0.7409 (mttp) REVERT: A 375 LYS cc_start: 0.5869 (tttt) cc_final: 0.5492 (ttmm) REVERT: C 349 ARG cc_start: 0.8217 (mtt180) cc_final: 0.6372 (mmm160) REVERT: C 369 LYS cc_start: 0.7253 (mttt) cc_final: 0.6929 (mtpt) REVERT: E 349 ARG cc_start: 0.7954 (mtt180) cc_final: 0.6557 (pmt-80) REVERT: B 349 ARG cc_start: 0.8241 (mtt180) cc_final: 0.6512 (mmm160) REVERT: D 321 LYS cc_start: 0.8382 (ttpt) cc_final: 0.7825 (mttm) outliers start: 2 outliers final: 2 residues processed: 46 average time/residue: 0.4886 time to fit residues: 26.2983 Evaluate side-chains 44 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.7844 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3396 Z= 0.108 Angle : 0.466 4.210 4548 Z= 0.233 Chirality : 0.050 0.129 516 Planarity : 0.002 0.014 576 Dihedral : 4.280 11.832 444 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.26 % Allowed : 15.36 % Favored : 84.38 % 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: -1.50 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 330 PHE 0.002 0.000 PHE B 378 TYR 0.005 0.001 TYR G 310 ARG 0.004 0.001 ARG D 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 48 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.602 Fit side-chains REVERT: A 321 LYS cc_start: 0.7891 (ttpt) cc_final: 0.7394 (mttp) REVERT: A 349 ARG cc_start: 0.7777 (mtp85) cc_final: 0.7458 (mtt-85) REVERT: A 375 LYS cc_start: 0.5835 (tttt) cc_final: 0.5473 (ttmm) REVERT: C 349 ARG cc_start: 0.8154 (mtt180) cc_final: 0.6369 (mmm160) REVERT: C 369 LYS cc_start: 0.7271 (mttt) cc_final: 0.6944 (mtpt) REVERT: E 349 ARG cc_start: 0.7890 (mtt180) cc_final: 0.6464 (pmt-80) REVERT: B 349 ARG cc_start: 0.8210 (mtt180) cc_final: 0.6347 (mmm160) REVERT: D 321 LYS cc_start: 0.8353 (ttpt) cc_final: 0.7796 (mttp) outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.4666 time to fit residues: 26.5065 Evaluate side-chains 45 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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: 0.7855 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3396 Z= 0.141 Angle : 0.478 4.210 4548 Z= 0.242 Chirality : 0.050 0.131 516 Planarity : 0.002 0.016 576 Dihedral : 4.315 11.710 444 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.26 % Allowed : 15.89 % 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: -1.51 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS E 329 PHE 0.005 0.001 PHE B 378 TYR 0.009 0.002 TYR C 310 ARG 0.001 0.000 ARG D 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 44 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.654 Fit side-chains REVERT: A 321 LYS cc_start: 0.7904 (ttpt) cc_final: 0.7395 (mttp) REVERT: A 349 ARG cc_start: 0.7866 (mtp85) cc_final: 0.7536 (mtt-85) REVERT: A 375 LYS cc_start: 0.5862 (tttt) cc_final: 0.5506 (ttmm) REVERT: C 349 ARG cc_start: 0.8212 (mtt180) cc_final: 0.6409 (mmm160) REVERT: C 369 LYS cc_start: 0.7259 (mttt) cc_final: 0.6942 (mtpt) REVERT: E 349 ARG cc_start: 0.8010 (mtt180) cc_final: 0.6549 (pmt-80) REVERT: B 349 ARG cc_start: 0.8237 (mtt180) cc_final: 0.6473 (mmm160) REVERT: D 321 LYS cc_start: 0.8353 (ttpt) cc_final: 0.7806 (mttm) outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.5076 time to fit residues: 26.3271 Evaluate side-chains 43 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.135975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.121802 restraints weight = 13028.225| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 2.02 r_work: 0.4209 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4122 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3396 Z= 0.122 Angle : 0.468 4.134 4548 Z= 0.235 Chirality : 0.050 0.130 516 Planarity : 0.002 0.015 576 Dihedral : 4.225 11.326 444 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.26 % Allowed : 16.41 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.003 0.001 PHE B 378 TYR 0.007 0.002 TYR G 310 ARG 0.001 0.000 ARG G 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2735.47 seconds wall clock time: 49 minutes 0.57 seconds (2940.57 seconds total)