Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 03:28:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkx_14056/08_2023/7qkx_14056.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkx_14056/08_2023/7qkx_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_14056/08_2023/7qkx_14056.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkx_14056/08_2023/7qkx_14056.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkx_14056/08_2023/7qkx_14056.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkx_14056/08_2023/7qkx_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-1.21rc1-5044/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: 3.20, per 1000 atoms: 0.47 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: 4.88 Conformation dependent library (CDL) restraints added in 525.8 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 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: 2.05 Time building geometry restraints manager: 5.11 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: 2348 13.51 - 27.02: 175 27.02 - 40.52: 38 40.52 - 54.03: 23 54.03 - 67.54: 62 Dihedral angle restraints: 2646 sinusoidal: 1284 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 2643 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: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 11.840 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.690 Find NCS groups from input model: 0.290 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.980 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.557 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 outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.5850 time to fit residues: 78.7740 Evaluate side-chains 65 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6785 ------------------------------------------------------------------------------- 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: 1.9990 chunk 11 optimal weight: 0.9990 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: 0.7751 moved from start: 0.4479 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= 0.169 Angle : 0.622 6.854 4548 Z= 0.323 Chirality : 0.052 0.140 516 Planarity : 0.003 0.023 576 Dihedral : 6.436 20.359 444 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.00 % 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 *********************** 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 57 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.601 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 outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.4609 time to fit residues: 30.6673 Evaluate side-chains 52 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.601 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7400 ------------------------------------------------------------------------------- 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: 1.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 41 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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: 0.7806 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 3396 Z= 0.268 Angle : 0.582 5.871 4548 Z= 0.304 Chirality : 0.052 0.138 516 Planarity : 0.003 0.027 576 Dihedral : 5.634 16.317 444 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer Outliers : 0.26 % 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: -1.42 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.25), residues: 426 *********************** 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 50 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 50 average time/residue: 0.4324 time to fit residues: 25.5221 Evaluate side-chains 48 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.614 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0814 time to fit residues: 0.8099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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: 0.7779 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 3396 Z= 0.143 Angle : 0.512 5.232 4548 Z= 0.257 Chirality : 0.051 0.135 516 Planarity : 0.002 0.017 576 Dihedral : 4.923 14.195 444 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer Outliers : 0.00 % 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: -1.40 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.25), residues: 426 *********************** 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 53 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.646 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.4486 time to fit residues: 28.1670 Evaluate side-chains 40 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 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 327 ASN G 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 3396 Z= 0.288 Angle : 0.568 5.042 4548 Z= 0.296 Chirality : 0.051 0.138 516 Planarity : 0.003 0.021 576 Dihedral : 5.160 14.323 444 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 0.52 % 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 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.25), residues: 426 *********************** 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 46 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.652 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 46 average time/residue: 0.3982 time to fit residues: 22.3108 Evaluate side-chains 44 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.559 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0943 time to fit residues: 0.9818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 3396 Z= 0.145 Angle : 0.505 4.978 4548 Z= 0.254 Chirality : 0.050 0.132 516 Planarity : 0.002 0.017 576 Dihedral : 4.716 13.316 444 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer Outliers : 0.26 % 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: -1.53 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.25), residues: 426 *********************** 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 47 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.601 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.4241 time to fit residues: 23.0740 Evaluate side-chains 41 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.534 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1100 time to fit residues: 0.8326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.7833 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 3396 Z= 0.330 Angle : 0.583 5.037 4548 Z= 0.304 Chirality : 0.051 0.142 516 Planarity : 0.003 0.026 576 Dihedral : 5.107 14.355 444 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 0.26 % 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: -1.67 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.25), residues: 426 *********************** 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 46 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.4606 time to fit residues: 25.0211 Evaluate side-chains 43 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.628 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0887 time to fit residues: 0.8798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.7821 moved from start: 0.5765 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= 0.228 Angle : 0.542 5.343 4548 Z= 0.276 Chirality : 0.050 0.136 516 Planarity : 0.003 0.020 576 Dihedral : 4.910 13.940 444 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.25), residues: 426 *********************** 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 44 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.4456 time to fit residues: 23.1674 Evaluate side-chains 42 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.619 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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: 0.7796 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 3396 Z= 0.131 Angle : 0.496 4.810 4548 Z= 0.247 Chirality : 0.050 0.131 516 Planarity : 0.002 0.019 576 Dihedral : 4.472 12.930 444 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 0.26 % 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: -1.66 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.25), residues: 426 *********************** 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 46 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.598 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 0.4313 time to fit residues: 22.9827 Evaluate side-chains 43 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.621 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 3396 Z= 0.147 Angle : 0.502 4.176 4548 Z= 0.252 Chirality : 0.050 0.132 516 Planarity : 0.002 0.017 576 Dihedral : 4.407 12.710 444 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 0.00 % 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: -1.66 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.25), residues: 426 ********************** 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 43 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.693 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.4310 time to fit residues: 22.1362 Evaluate side-chains 43 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.670 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.131403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.118438 restraints weight = 14616.557| |-----------------------------------------------------------------------------| r_work (start): 0.4291 rms_B_bonded: 2.08 r_work: 0.4198 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4104 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.5892 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= 0.198 Angle : 0.518 4.289 4548 Z= 0.264 Chirality : 0.050 0.135 516 Planarity : 0.002 0.018 576 Dihedral : 4.554 12.655 444 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 0.00 % 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: -1.71 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.25), residues: 426 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2546.86 seconds wall clock time: 45 minutes 42.20 seconds (2742.20 seconds total)