Starting phenix.real_space_refine on Fri Dec 8 00:56:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9k_18284/12_2023/8q9k_18284.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9k_18284/12_2023/8q9k_18284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9k_18284/12_2023/8q9k_18284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9k_18284/12_2023/8q9k_18284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9k_18284/12_2023/8q9k_18284.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9k_18284/12_2023/8q9k_18284.pdb" } resolution = 3.2 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= 0.001 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 1932 2.51 5 N 570 2.21 5 O 582 1.98 5 H 3216 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6306 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "C" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "D" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "B" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "F" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Time building chain proxies: 3.67, per 1000 atoms: 0.58 Number of scatterers: 6306 At special positions: 0 Unit cell: (139.256, 84.048, 41.2, 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 582 8.00 N 570 7.00 C 1932 6.00 H 3216 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: 4.62 Conformation dependent library (CDL) restraints added in 703.1 milliseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 708 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 45.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 309 through 310 removed outlier: 6.552A pdb=" N VAL A 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.837A pdb=" N VAL A 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 317 through 322 removed outlier: 6.415A pdb=" N LYS A 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N SER F 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR A 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N CYS F 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS A 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 325 through 330 removed outlier: 6.913A pdb=" N GLY A 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN E 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY F 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN A 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 337 through 341 removed outlier: 6.613A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.648A pdb=" N ASP A 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 350 through 354 removed outlier: 6.381A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 357 through 362 removed outlier: 6.440A pdb=" N ASP A 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N THR F 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 360 " --> pdb=" O THR F 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 369 through 374 removed outlier: 6.568A pdb=" N LYS A 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLU F 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE A 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N HIS F 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR A 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 309 through 310 removed outlier: 6.488A pdb=" N VAL C 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL D 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.753A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL D 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.424A pdb=" N LYS C 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N SER D 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR C 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N CYS D 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS C 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS D 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N SER B 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR D 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N CYS B 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LYS D 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 325 through 330 removed outlier: 8.850A pdb=" N LEU C 325 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N ILE D 328 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN C 327 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N HIS D 330 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS C 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N LEU D 325 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N ILE B 328 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN D 327 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N HIS B 330 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N HIS D 329 " --> pdb=" O HIS B 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 337 through 340 Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.564A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP D 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 354 Processing sheet with id=AB8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.440A pdb=" N ASP C 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N THR D 361 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE C 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP D 358 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR B 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE D 360 " --> pdb=" O THR B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 369 through 374 removed outlier: 6.501A pdb=" N LYS C 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLU D 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE C 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N HIS D 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR C 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS D 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLU B 372 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE D 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N HIS B 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR D 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 47 hydrogen bonds defined for protein. 141 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: 1.95 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3210 1.12 - 1.29: 522 1.29 - 1.46: 891 1.46 - 1.63: 1725 1.63 - 1.81: 6 Bond restraints: 6354 Sorted by residual: bond pdb=" N SER C 324 " pdb=" H SER C 324 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE ARG A 349 " pdb=" HE ARG A 349 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CD2 PHE E 346 " pdb=" HD2 PHE E 346 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLU F 338 " pdb=" H GLU F 338 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LYS C 311 " pdb=" H LYS C 311 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 6349 not shown) Histogram of bond angle deviations from ideal: 97.00 - 103.39: 44 103.39 - 109.78: 5471 109.78 - 116.17: 2920 116.17 - 122.56: 2504 122.56 - 128.96: 665 Bond angle restraints: 11604 Sorted by residual: angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 110.69 117.98 -7.29 1.33e+00 5.65e-01 3.00e+01 angle pdb=" C LYS C 340 " pdb=" N SER C 341 " pdb=" H SER C 341 " ideal model delta sigma weight residual 123.83 108.35 15.48 3.00e+00 1.11e-01 2.66e+01 angle pdb=" C LYS B 340 " pdb=" N SER B 341 " pdb=" H SER B 341 " ideal model delta sigma weight residual 123.83 108.63 15.20 3.00e+00 1.11e-01 2.57e+01 angle pdb=" N ARG D 349 " pdb=" CA ARG D 349 " pdb=" C ARG D 349 " ideal model delta sigma weight residual 110.35 117.23 -6.88 1.36e+00 5.41e-01 2.56e+01 angle pdb=" C LYS D 340 " pdb=" N SER D 341 " pdb=" H SER D 341 " ideal model delta sigma weight residual 123.83 108.95 14.88 3.00e+00 1.11e-01 2.46e+01 ... (remaining 11599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.63: 2543 13.63 - 27.26: 141 27.26 - 40.89: 31 40.89 - 54.52: 9 54.52 - 68.15: 72 Dihedral angle restraints: 2796 sinusoidal: 1554 harmonic: 1242 Sorted by residual: dihedral pdb=" C ARG B 349 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " pdb=" CB ARG B 349 " ideal model delta harmonic sigma weight residual -122.60 -133.04 10.44 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" C ARG F 349 " pdb=" N ARG F 349 " pdb=" CA ARG F 349 " pdb=" CB ARG F 349 " ideal model delta harmonic sigma weight residual -122.60 -132.63 10.03 0 2.50e+00 1.60e-01 1.61e+01 dihedral pdb=" N ARG B 349 " pdb=" C ARG B 349 " pdb=" CA ARG B 349 " pdb=" CB ARG B 349 " ideal model delta harmonic sigma weight residual 122.80 131.83 -9.03 0 2.50e+00 1.60e-01 1.31e+01 ... (remaining 2793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 323 0.085 - 0.169: 124 0.169 - 0.254: 16 0.254 - 0.338: 2 0.338 - 0.423: 3 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA ARG B 349 " pdb=" N ARG B 349 " pdb=" C ARG B 349 " pdb=" CB ARG B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CA ARG F 349 " pdb=" N ARG F 349 " pdb=" C ARG F 349 " pdb=" CB ARG F 349 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA ARG D 349 " pdb=" N ARG D 349 " pdb=" C ARG D 349 " pdb=" CB ARG D 349 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.38 2.00e-01 2.50e+01 3.52e+00 ... (remaining 465 not shown) Planarity restraints: 918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 340 " 0.046 2.00e-02 2.50e+03 8.41e-02 7.07e+01 pdb=" N SER B 341 " -0.145 2.00e-02 2.50e+03 pdb=" CA SER B 341 " 0.045 2.00e-02 2.50e+03 pdb=" H SER B 341 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 340 " 0.044 2.00e-02 2.50e+03 7.88e-02 6.21e+01 pdb=" N SER C 341 " -0.136 2.00e-02 2.50e+03 pdb=" CA SER C 341 " 0.042 2.00e-02 2.50e+03 pdb=" H SER C 341 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 340 " 0.041 2.00e-02 2.50e+03 7.42e-02 5.51e+01 pdb=" N SER D 341 " -0.128 2.00e-02 2.50e+03 pdb=" CA SER D 341 " 0.039 2.00e-02 2.50e+03 pdb=" H SER D 341 " 0.048 2.00e-02 2.50e+03 ... (remaining 915 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 475 2.18 - 2.78: 10985 2.78 - 3.39: 16438 3.39 - 3.99: 21542 3.99 - 4.60: 30268 Nonbonded interactions: 79708 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.571 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.573 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.579 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.583 1.850 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.597 1.850 ... (remaining 79703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 11.780 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.310 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.038 3138 Z= 0.741 Angle : 1.997 7.291 4194 Z= 1.327 Chirality : 0.088 0.423 468 Planarity : 0.011 0.092 534 Dihedral : 9.094 65.306 1212 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.94 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.003 HIS B 330 PHE 0.037 0.018 PHE D 346 TYR 0.049 0.014 TYR D 310 ARG 0.007 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.527 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: 151 average time/residue: 0.5648 time to fit residues: 93.9877 Evaluate side-chains 91 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.714 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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: 0.8084 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3138 Z= 0.173 Angle : 0.555 4.281 4194 Z= 0.292 Chirality : 0.052 0.130 468 Planarity : 0.003 0.031 534 Dihedral : 5.560 18.735 414 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.41 % Allowed : 6.78 % Favored : 91.81 % 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: -1.86 (0.33), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.008 0.002 PHE A 346 TYR 0.003 0.001 TYR A 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.534 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: 103 average time/residue: 0.4703 time to fit residues: 54.8728 Evaluate side-chains 96 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.564 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0711 time to fit residues: 1.1910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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: 0.8098 moved from start: 0.6026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3138 Z= 0.187 Angle : 0.518 3.974 4194 Z= 0.266 Chirality : 0.051 0.133 468 Planarity : 0.004 0.033 534 Dihedral : 5.002 17.453 414 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.41 % Allowed : 7.63 % Favored : 90.96 % 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 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 329 PHE 0.005 0.001 PHE D 346 TYR 0.004 0.001 TYR E 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 94 average time/residue: 0.4646 time to fit residues: 49.6375 Evaluate side-chains 88 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.524 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0751 time to fit residues: 1.2904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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: 0.8117 moved from start: 0.6211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3138 Z= 0.208 Angle : 0.505 4.407 4194 Z= 0.261 Chirality : 0.051 0.130 468 Planarity : 0.004 0.036 534 Dihedral : 4.945 15.916 414 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.69 % Allowed : 8.47 % Favored : 89.83 % 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 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.005 0.001 PHE E 346 TYR 0.005 0.001 TYR E 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 86 average time/residue: 0.5030 time to fit residues: 48.6533 Evaluate side-chains 82 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.522 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0683 time to fit residues: 1.3688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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: 0.8130 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3138 Z= 0.229 Angle : 0.493 4.172 4194 Z= 0.255 Chirality : 0.051 0.130 468 Planarity : 0.004 0.038 534 Dihedral : 4.923 15.317 414 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % 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: -1.63 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 329 PHE 0.005 0.001 PHE E 346 TYR 0.005 0.001 TYR E 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.5523 time to fit residues: 52.3906 Evaluate side-chains 82 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8073 moved from start: 0.6738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3138 Z= 0.161 Angle : 0.479 4.015 4194 Z= 0.244 Chirality : 0.051 0.131 468 Planarity : 0.004 0.038 534 Dihedral : 4.596 15.063 414 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.13 % Allowed : 11.86 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 330 PHE 0.002 0.001 PHE A 346 TYR 0.004 0.001 TYR E 310 ARG 0.002 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 91 average time/residue: 0.5477 time to fit residues: 55.9578 Evaluate side-chains 85 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.566 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0719 time to fit residues: 1.2041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 9.9990 chunk 29 optimal weight: 0.0970 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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: 0.8042 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3138 Z= 0.155 Angle : 0.477 4.233 4194 Z= 0.240 Chirality : 0.051 0.132 468 Planarity : 0.004 0.039 534 Dihedral : 4.300 14.611 414 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.28 % Allowed : 12.43 % Favored : 87.29 % 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: -1.43 (0.35), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 330 PHE 0.002 0.001 PHE D 346 TYR 0.004 0.001 TYR E 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 90 average time/residue: 0.5391 time to fit residues: 54.9054 Evaluate side-chains 86 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.584 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0727 time to fit residues: 0.8546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.0170 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.6934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3138 Z= 0.177 Angle : 0.492 4.335 4194 Z= 0.250 Chirality : 0.051 0.131 468 Planarity : 0.004 0.042 534 Dihedral : 4.347 14.109 414 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.28 % Allowed : 14.12 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.35), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 329 PHE 0.004 0.001 PHE D 346 TYR 0.004 0.001 TYR E 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 89 average time/residue: 0.5109 time to fit residues: 51.4337 Evaluate side-chains 87 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.533 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0739 time to fit residues: 0.7867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 0.0370 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.0770 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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: 0.8028 moved from start: 0.7018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3138 Z= 0.153 Angle : 0.478 4.445 4194 Z= 0.240 Chirality : 0.051 0.130 468 Planarity : 0.004 0.040 534 Dihedral : 4.107 13.907 414 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.28 % Allowed : 14.12 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.35), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 374 PHE 0.004 0.001 PHE F 346 TYR 0.003 0.001 TYR A 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.5170 time to fit residues: 54.6334 Evaluate side-chains 87 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.589 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0745 time to fit residues: 0.8482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.8049 moved from start: 0.7081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3138 Z= 0.180 Angle : 0.503 4.701 4194 Z= 0.253 Chirality : 0.051 0.131 468 Planarity : 0.004 0.039 534 Dihedral : 4.165 13.517 414 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.56 % Allowed : 14.12 % Favored : 85.31 % 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: -1.35 (0.35), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 329 PHE 0.003 0.001 PHE D 346 TYR 0.003 0.001 TYR E 310 ARG 0.001 0.000 ARG E 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 89 average time/residue: 0.5172 time to fit residues: 52.1901 Evaluate side-chains 89 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.711 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0782 time to fit residues: 1.0720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 0.0050 chunk 1 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 overall best weight: 2.2000 ------------------------------------------------------------------------------- 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 = 0.4486 r_free = 0.4486 target = 0.171735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.135687 restraints weight = 10612.991| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 2.33 r_work: 0.4133 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4039 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.7056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3138 Z= 0.244 Angle : 0.535 4.742 4194 Z= 0.272 Chirality : 0.051 0.130 468 Planarity : 0.004 0.037 534 Dihedral : 4.608 14.032 414 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.28 % Allowed : 15.54 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.35), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 329 PHE 0.005 0.001 PHE E 346 TYR 0.003 0.001 TYR E 310 ARG 0.002 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2984.52 seconds wall clock time: 55 minutes 8.46 seconds (3308.46 seconds total)