Starting phenix.real_space_refine on Wed Nov 15 01:33:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9l_18285/11_2023/8q9l_18285.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9l_18285/11_2023/8q9l_18285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9l_18285/11_2023/8q9l_18285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9l_18285/11_2023/8q9l_18285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9l_18285/11_2023/8q9l_18285.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9l_18285/11_2023/8q9l_18285.pdb" } resolution = 2.76 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 9 5.16 5 C 3159 2.51 5 N 909 2.21 5 O 936 1.98 5 H 5220 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 372": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 372": "OE1" <-> "OE2" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 372": "OE1" <-> "OE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 372": "OE1" <-> "OE2" Residue "G ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 372": "OE1" <-> "OE2" Residue "H ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 372": "OE1" <-> "OE2" Residue "I GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 10233 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "B" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} 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: "H" 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: "I" 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: 5.63, per 1000 atoms: 0.55 Number of scatterers: 10233 At special positions: 0 Unit cell: (138.13, 136.676, 43.62, 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 9 16.00 O 936 8.00 N 909 7.00 C 3159 6.00 H 5220 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: 7.98 Conformation dependent library (CDL) restraints added in 1.1 seconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 55.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.400A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.818A 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 330 removed outlier: 6.399A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 9.483A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N ASN C 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER E 324 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 325 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN A 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 336 through 342 removed outlier: 6.711A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.540A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 355 removed outlier: 6.368A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LYS C 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER A 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLY C 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE A 354 " --> pdb=" O GLY C 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.323A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 369 through 377 removed outlier: 6.660A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.695A pdb=" N GLN B 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N TYR F 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.845A pdb=" N VAL B 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 317 through 330 removed outlier: 6.760A pdb=" N SER B 324 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU D 325 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY B 326 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN D 327 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER F 324 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU B 325 " --> pdb=" O SER F 324 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY F 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN B 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 336 through 342 removed outlier: 6.418A pdb=" N GLN B 336 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL F 339 " --> pdb=" O GLN B 336 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLU B 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N SER F 341 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS B 340 " --> pdb=" O SER F 341 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.489A pdb=" N ASP B 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 355 Processing sheet with id=AB6, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.357A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 369 through 377 removed outlier: 6.641A pdb=" N LYS B 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N GLU F 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N HIS F 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR B 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU F 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS B 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 307 through 310 removed outlier: 6.757A pdb=" N GLN G 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR I 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL G 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 313 through 314 removed outlier: 6.862A pdb=" N VAL G 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 317 through 330 removed outlier: 6.725A pdb=" N SER G 324 " --> pdb=" O GLY H 323 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU H 325 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY G 326 " --> pdb=" O LEU H 325 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN H 327 " --> pdb=" O GLY G 326 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER I 324 " --> pdb=" O GLY G 323 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU G 325 " --> pdb=" O SER I 324 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLY I 326 " --> pdb=" O LEU G 325 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN G 327 " --> pdb=" O GLY I 326 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 336 through 342 removed outlier: 6.661A pdb=" N VAL G 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LYS H 340 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL G 339 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N GLU H 342 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER G 341 " --> pdb=" O GLU H 342 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 345 through 346 removed outlier: 6.520A pdb=" N ASP G 345 " --> pdb=" O PHE I 346 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 350 through 355 removed outlier: 6.333A pdb=" N VAL G 350 " --> pdb=" O GLN H 351 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LYS H 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER G 352 " --> pdb=" O LYS H 353 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N GLY H 355 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE G 354 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLN G 351 " --> pdb=" O SER I 352 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ILE I 354 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS G 353 " --> pdb=" O ILE I 354 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N SER I 356 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY G 355 " --> pdb=" O SER I 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'H' and resid 360 through 362 removed outlier: 6.362A pdb=" N THR G 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 369 through 377 removed outlier: 6.631A pdb=" N LYS G 369 " --> pdb=" O LYS I 370 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N GLU I 372 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE G 371 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N HIS I 374 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR G 373 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU I 376 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS G 375 " --> pdb=" O LEU I 376 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 384 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: 3.50 Time building geometry restraints manager: 8.35 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: 5211 1.11 - 1.28: 837 1.28 - 1.46: 1329 1.46 - 1.63: 2928 1.63 - 1.81: 9 Bond restraints: 10314 Sorted by residual: bond pdb=" ND2 ASN H 359 " pdb="HD22 ASN H 359 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N LYS A 340 " pdb=" H LYS A 340 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N LYS I 347 " pdb=" H LYS I 347 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N ILE C 360 " pdb=" H ILE C 360 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" N THR A 361 " pdb=" H THR A 361 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 ... (remaining 10309 not shown) Histogram of bond angle deviations from ideal: 96.39 - 102.97: 39 102.97 - 109.56: 8016 109.56 - 116.14: 5528 116.14 - 122.73: 4260 122.73 - 129.31: 976 Bond angle restraints: 18819 Sorted by residual: angle pdb=" CB HIS F 374 " pdb=" CG HIS F 374 " pdb=" CD2 HIS F 374 " ideal model delta sigma weight residual 131.20 124.93 6.27 1.30e+00 5.92e-01 2.33e+01 angle pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 131.20 124.93 6.27 1.30e+00 5.92e-01 2.32e+01 angle pdb=" CB HIS I 374 " pdb=" CG HIS I 374 " pdb=" CD2 HIS I 374 " ideal model delta sigma weight residual 131.20 124.97 6.23 1.30e+00 5.92e-01 2.29e+01 angle pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " pdb=" CD2 HIS E 374 " ideal model delta sigma weight residual 131.20 125.02 6.18 1.30e+00 5.92e-01 2.26e+01 angle pdb=" CB HIS B 374 " pdb=" CG HIS B 374 " pdb=" CD2 HIS B 374 " ideal model delta sigma weight residual 131.20 125.10 6.10 1.30e+00 5.92e-01 2.20e+01 ... (remaining 18814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.54: 3540 13.54 - 27.08: 233 27.08 - 40.62: 52 40.62 - 54.16: 47 54.16 - 67.70: 97 Dihedral angle restraints: 3969 sinusoidal: 1926 harmonic: 2043 Sorted by residual: dihedral pdb=" CA ILE G 371 " pdb=" C ILE G 371 " pdb=" N GLU G 372 " pdb=" CA GLU G 372 " ideal model delta harmonic sigma weight residual -180.00 -157.59 -22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA SER H 316 " pdb=" C SER H 316 " pdb=" N LYS H 317 " pdb=" CA LYS H 317 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ILE A 371 " pdb=" C ILE A 371 " pdb=" N GLU A 372 " pdb=" CA GLU A 372 " ideal model delta harmonic sigma weight residual 180.00 -158.21 -21.79 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 3966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 435 0.064 - 0.129: 243 0.129 - 0.193: 72 0.193 - 0.258: 18 0.258 - 0.322: 6 Chirality restraints: 774 Sorted by residual: chirality pdb=" CA LYS H 317 " pdb=" N LYS H 317 " pdb=" C LYS H 317 " pdb=" CB LYS H 317 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA LYS C 317 " pdb=" N LYS C 317 " pdb=" C LYS C 317 " pdb=" CB LYS C 317 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA LYS D 317 " pdb=" N LYS D 317 " pdb=" C LYS D 317 " pdb=" CB LYS D 317 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 771 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 368 " 0.073 2.00e-02 2.50e+03 6.46e-02 6.25e+01 pdb=" CG ASN F 368 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN F 368 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN F 368 " -0.042 2.00e-02 2.50e+03 pdb="HD21 ASN F 368 " -0.061 2.00e-02 2.50e+03 pdb="HD22 ASN F 368 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 368 " -0.070 2.00e-02 2.50e+03 6.41e-02 6.16e+01 pdb=" CG ASN A 368 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 368 " 0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN A 368 " 0.031 2.00e-02 2.50e+03 pdb="HD21 ASN A 368 " 0.070 2.00e-02 2.50e+03 pdb="HD22 ASN A 368 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " -0.090 2.00e-02 2.50e+03 4.17e-02 5.23e+01 pdb=" CG TYR B 310 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " -0.085 2.00e-02 2.50e+03 pdb=" HD1 TYR B 310 " -0.007 2.00e-02 2.50e+03 pdb=" HD2 TYR B 310 " 0.035 2.00e-02 2.50e+03 pdb=" HE1 TYR B 310 " 0.029 2.00e-02 2.50e+03 pdb=" HE2 TYR B 310 " -0.005 2.00e-02 2.50e+03 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 873 2.18 - 2.79: 18013 2.79 - 3.39: 26435 3.39 - 4.00: 37363 4.00 - 4.60: 50819 Nonbonded interactions: 133503 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.581 1.850 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.581 1.850 nonbonded pdb=" OD1 ASP I 314 " pdb=" HG SER I 316 " model vdw 1.587 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.602 1.850 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.605 1.850 ... (remaining 133498 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 3.160 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: 0.160 Extract box with map and model: 11.960 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 36.300 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 0.034 5094 Z= 0.743 Angle : 1.762 8.654 6822 Z= 1.160 Chirality : 0.086 0.322 774 Planarity : 0.011 0.048 864 Dihedral : 11.628 51.205 1944 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.21), residues: 639 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 0.879 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: 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: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 272 average time/residue: 2.5405 time to fit residues: 717.4978 Evaluate side-chains 201 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2589 time to fit residues: 1.4560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN H 307 GLN I 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5094 Z= 0.280 Angle : 0.626 5.041 6822 Z= 0.331 Chirality : 0.052 0.138 774 Planarity : 0.003 0.021 864 Dihedral : 6.291 16.148 666 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 2.60 % Allowed : 20.66 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.21), residues: 639 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 194 average time/residue: 2.9497 time to fit residues: 591.1495 Evaluate side-chains 156 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 151 time to evaluate : 0.834 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 1.2647 time to fit residues: 3.7270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN D 307 GLN H 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.6381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5094 Z= 0.284 Angle : 0.587 4.481 6822 Z= 0.308 Chirality : 0.051 0.143 774 Planarity : 0.003 0.022 864 Dihedral : 5.662 16.027 666 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 3.12 % Allowed : 22.22 % Favored : 74.65 % 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: -1.85 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.21), residues: 639 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 149 average time/residue: 2.8765 time to fit residues: 443.5623 Evaluate side-chains 137 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 0.945 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 2 average time/residue: 1.3624 time to fit residues: 4.0965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 30 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 16 optimal weight: 0.0970 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN H 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.6542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5094 Z= 0.225 Angle : 0.541 4.211 6822 Z= 0.281 Chirality : 0.050 0.140 774 Planarity : 0.003 0.019 864 Dihedral : 5.319 15.263 666 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.39 % Allowed : 23.96 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.21), residues: 639 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 136 average time/residue: 2.8442 time to fit residues: 400.2553 Evaluate side-chains 124 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 0.832 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 1.2262 time to fit residues: 3.6291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 31 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.6549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5094 Z= 0.201 Angle : 0.523 5.177 6822 Z= 0.270 Chirality : 0.051 0.138 774 Planarity : 0.002 0.018 864 Dihedral : 5.049 14.691 666 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.39 % Allowed : 24.83 % Favored : 73.78 % 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: -1.97 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.21), residues: 639 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 129 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 132 average time/residue: 2.8314 time to fit residues: 387.6966 Evaluate side-chains 130 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 0.842 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 3 average time/residue: 1.6887 time to fit residues: 6.4263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 0.1980 chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN H 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.6621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5094 Z= 0.201 Angle : 0.522 6.174 6822 Z= 0.268 Chirality : 0.050 0.138 774 Planarity : 0.002 0.016 864 Dihedral : 4.935 14.423 666 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.56 % Allowed : 25.35 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.21), residues: 639 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 130 average time/residue: 2.6532 time to fit residues: 358.0605 Evaluate side-chains 131 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 125 time to evaluate : 0.822 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 4 average time/residue: 1.2582 time to fit residues: 6.4328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 37 optimal weight: 0.0060 chunk 28 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN D 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.6720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5094 Z= 0.172 Angle : 0.500 5.314 6822 Z= 0.257 Chirality : 0.051 0.135 774 Planarity : 0.002 0.013 864 Dihedral : 4.707 13.690 666 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.87 % Allowed : 25.87 % Favored : 73.26 % 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: -1.95 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.21), residues: 639 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 133 average time/residue: 2.6594 time to fit residues: 367.2331 Evaluate side-chains 131 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 0.944 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 1.2624 time to fit residues: 3.8481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.6716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5094 Z= 0.253 Angle : 0.541 5.588 6822 Z= 0.281 Chirality : 0.050 0.139 774 Planarity : 0.002 0.017 864 Dihedral : 5.055 14.796 666 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.39 % Allowed : 26.04 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.21), residues: 639 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 127 average time/residue: 2.8987 time to fit residues: 381.0291 Evaluate side-chains 126 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 1.2730 time to fit residues: 3.8416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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: 0.7673 moved from start: 0.6684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5094 Z= 0.332 Angle : 0.579 4.833 6822 Z= 0.302 Chirality : 0.051 0.140 774 Planarity : 0.003 0.017 864 Dihedral : 5.333 15.924 666 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.22 % Allowed : 25.87 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.21), residues: 639 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 124 average time/residue: 2.9004 time to fit residues: 372.6368 Evaluate side-chains 121 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 1.1851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.6707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5094 Z= 0.236 Angle : 0.541 6.433 6822 Z= 0.280 Chirality : 0.050 0.140 774 Planarity : 0.002 0.016 864 Dihedral : 5.084 15.113 666 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.69 % Allowed : 26.39 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.21), residues: 639 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 124 average time/residue: 2.8332 time to fit residues: 363.8098 Evaluate side-chains 124 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1164 time to fit residues: 1.3752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 51 optimal weight: 0.0370 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 overall best weight: 1.9862 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.156961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.133087 restraints weight = 18482.648| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.78 r_work: 0.3689 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.6757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5094 Z= 0.196 Angle : 0.522 6.582 6822 Z= 0.267 Chirality : 0.050 0.138 774 Planarity : 0.002 0.015 864 Dihedral : 4.817 14.161 666 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.69 % Allowed : 26.22 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.21), residues: 639 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6920.58 seconds wall clock time: 121 minutes 23.91 seconds (7283.91 seconds total)