Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 14:10:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4t_14316/10_2023/7r4t_14316.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4t_14316/10_2023/7r4t_14316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4t_14316/10_2023/7r4t_14316.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4t_14316/10_2023/7r4t_14316.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4t_14316/10_2023/7r4t_14316.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4t_14316/10_2023/7r4t_14316.pdb" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2172 2.51 5 N 642 2.21 5 O 648 1.98 5 H 3606 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 338": "OE1" <-> "OE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 358": "OD1" <-> "OD2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "F PHE 378": "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 "A ASP 358": "OD1" <-> "OD2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A PHE 378": "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 "B ASP 358": "OD1" <-> "OD2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B PHE 378": "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 "C ASP 358": "OD1" <-> "OD2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C PHE 378": "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 "D ASP 358": "OD1" <-> "OD2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D PHE 378": "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 "E ASP 358": "OD1" <-> "OD2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 7074 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "D" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 3.44, per 1000 atoms: 0.49 Number of scatterers: 7074 At special positions: 0 Unit cell: (132.664, 112.888, 40.376, 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 648 8.00 N 642 7.00 C 2172 6.00 H 3606 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: 4.98 Conformation dependent library (CDL) restraints added in 561.9 milliseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.595A pdb=" N GLN F 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N TYR D 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL F 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.708A pdb=" N VAL F 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 324 removed outlier: 6.178A pdb=" N LYS F 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N SER D 320 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR F 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N CYS D 322 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LYS F 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N SER D 324 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY F 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.368A pdb=" N ILE F 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 341 removed outlier: 6.467A pdb=" N GLN F 336 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL D 339 " --> pdb=" O GLN F 336 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU F 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N SER D 341 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS F 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.593A pdb=" N ASP F 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 350 through 354 removed outlier: 6.364A pdb=" N GLN F 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE D 354 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS F 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 357 through 362 removed outlier: 6.532A pdb=" N LEU F 357 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE B 360 " --> pdb=" O LEU F 357 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN F 359 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N HIS B 362 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR F 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP F 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR D 361 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE F 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 378 removed outlier: 6.509A pdb=" N LYS F 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLU D 372 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE F 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N HIS D 374 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N THR F 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU D 376 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS F 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N PHE D 378 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR F 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.723A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 324 removed outlier: 6.169A pdb=" N LYS A 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N SER E 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR A 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N CYS E 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS A 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N SER E 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY A 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.404A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 336 through 338 removed outlier: 6.501A pdb=" N GLN A 336 " --> pdb=" O VAL E 337 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.605A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.377A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.503A pdb=" N LEU A 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE C 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 368 through 378 removed outlier: 6.440A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N PHE E 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR A 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 5.24 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: 3600 1.12 - 1.29: 576 1.29 - 1.47: 1176 1.47 - 1.64: 1770 1.64 - 1.82: 6 Bond restraints: 7128 Sorted by residual: 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 5.70e+01 bond pdb=" N GLY F 335 " pdb=" H GLY F 335 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N SER F 341 " pdb=" H SER F 341 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE2 HIS D 374 " pdb=" HE2 HIS D 374 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD2 PHE B 346 " pdb=" HD2 PHE B 346 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 7123 not shown) Histogram of bond angle deviations from ideal: 97.20 - 103.53: 33 103.53 - 109.86: 6192 109.86 - 116.18: 3100 116.18 - 122.51: 2935 122.51 - 128.83: 724 Bond angle restraints: 12984 Sorted by residual: angle pdb=" C VAL C 339 " pdb=" N LYS C 340 " pdb=" H LYS C 340 " ideal model delta sigma weight residual 123.83 105.55 18.27 3.00e+00 1.11e-01 3.71e+01 angle pdb=" C VAL A 339 " pdb=" N LYS A 340 " pdb=" H LYS A 340 " ideal model delta sigma weight residual 123.83 106.86 16.96 3.00e+00 1.11e-01 3.20e+01 angle pdb=" C VAL E 339 " pdb=" N LYS E 340 " pdb=" H LYS E 340 " ideal model delta sigma weight residual 123.83 108.19 15.63 3.00e+00 1.11e-01 2.71e+01 angle pdb=" CB HIS F 362 " pdb=" CG HIS F 362 " pdb=" CD2 HIS F 362 " 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 A 329 " pdb=" CG HIS A 329 " pdb=" CD2 HIS A 329 " ideal model delta sigma weight residual 131.20 125.11 6.09 1.30e+00 5.92e-01 2.20e+01 ... (remaining 12979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.45: 2394 13.45 - 26.89: 204 26.89 - 40.34: 66 40.34 - 53.78: 19 53.78 - 67.23: 59 Dihedral angle restraints: 2742 sinusoidal: 1338 harmonic: 1404 Sorted by residual: dihedral pdb=" CA VAL E 350 " pdb=" C VAL E 350 " pdb=" N GLN E 351 " pdb=" CA GLN E 351 " ideal model delta harmonic sigma weight residual 180.00 153.90 26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA VAL D 350 " pdb=" C VAL D 350 " pdb=" N GLN D 351 " pdb=" CA GLN D 351 " ideal model delta harmonic sigma weight residual 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA VAL F 350 " pdb=" C VAL F 350 " pdb=" N GLN F 351 " pdb=" CA GLN F 351 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 2739 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.070: 310 0.070 - 0.138: 174 0.138 - 0.207: 31 0.207 - 0.276: 10 0.276 - 0.345: 3 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS F 340 " pdb=" N LYS F 340 " pdb=" C LYS F 340 " pdb=" CB LYS F 340 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA LYS A 340 " pdb=" N LYS A 340 " pdb=" C LYS A 340 " pdb=" CB LYS A 340 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA LYS B 340 " pdb=" N LYS B 340 " pdb=" C LYS B 340 " pdb=" CB LYS B 340 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 525 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 339 " 0.059 2.00e-02 2.50e+03 1.13e-01 1.29e+02 pdb=" N LYS A 340 " -0.196 2.00e-02 2.50e+03 pdb=" CA LYS A 340 " 0.059 2.00e-02 2.50e+03 pdb=" H LYS A 340 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 339 " 0.059 2.00e-02 2.50e+03 1.12e-01 1.26e+02 pdb=" N LYS C 340 " -0.194 2.00e-02 2.50e+03 pdb=" CA LYS C 340 " 0.060 2.00e-02 2.50e+03 pdb=" H LYS C 340 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 339 " 0.053 2.00e-02 2.50e+03 1.02e-01 1.03e+02 pdb=" N LYS E 340 " -0.176 2.00e-02 2.50e+03 pdb=" CA LYS E 340 " 0.053 2.00e-02 2.50e+03 pdb=" H LYS E 340 " 0.069 2.00e-02 2.50e+03 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 592 2.17 - 2.78: 11959 2.78 - 3.38: 18274 3.38 - 3.99: 25297 3.99 - 4.60: 34258 Nonbonded interactions: 90380 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.560 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.567 1.850 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.570 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.573 1.850 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.594 1.850 ... (remaining 90375 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: 2.740 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: 11.480 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.840 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 0.035 3522 Z= 0.721 Angle : 1.775 6.178 4710 Z= 1.174 Chirality : 0.085 0.345 528 Planarity : 0.009 0.050 600 Dihedral : 11.858 51.239 1350 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.26), residues: 444 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.587 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: 136 average time/residue: 2.9926 time to fit residues: 416.0438 Evaluate side-chains 76 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.613 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3522 Z= 0.210 Angle : 0.554 4.473 4710 Z= 0.286 Chirality : 0.050 0.131 528 Planarity : 0.003 0.020 600 Dihedral : 5.857 19.975 468 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.52 % Allowed : 16.16 % Favored : 82.32 % 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 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.646 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 83 average time/residue: 2.8144 time to fit residues: 239.6077 Evaluate side-chains 67 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.653 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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: 0.8378 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3522 Z= 0.166 Angle : 0.473 3.625 4710 Z= 0.238 Chirality : 0.050 0.124 528 Planarity : 0.002 0.014 600 Dihedral : 4.831 17.505 468 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.27 % Allowed : 16.92 % Favored : 80.81 % 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: -1.45 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.662 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 71 average time/residue: 2.8374 time to fit residues: 206.9144 Evaluate side-chains 68 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.0656 time to fit residues: 0.8690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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: 0.8392 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3522 Z= 0.185 Angle : 0.462 3.563 4710 Z= 0.230 Chirality : 0.050 0.128 528 Planarity : 0.002 0.015 600 Dihedral : 4.476 16.292 468 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.26 % Allowed : 17.68 % Favored : 81.06 % 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: -1.36 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.28), residues: 444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.629 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 69 average time/residue: 2.7935 time to fit residues: 197.9736 Evaluate side-chains 64 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.669 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.0740 time to fit residues: 0.9776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.0370 chunk 34 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- 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: 0.8391 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3522 Z= 0.156 Angle : 0.452 3.543 4710 Z= 0.225 Chirality : 0.050 0.126 528 Planarity : 0.002 0.012 600 Dihedral : 4.225 15.183 468 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.01 % Allowed : 19.44 % Favored : 79.55 % 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: -1.31 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.28), residues: 444 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.682 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 66 average time/residue: 2.5537 time to fit residues: 173.6208 Evaluate side-chains 63 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.635 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0793 time to fit residues: 0.9287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 0.0670 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN B 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3522 Z= 0.243 Angle : 0.482 3.557 4710 Z= 0.240 Chirality : 0.050 0.129 528 Planarity : 0.002 0.018 600 Dihedral : 4.344 14.645 468 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.26 % Allowed : 17.93 % Favored : 80.81 % 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: -1.31 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.28), residues: 444 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.685 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 62 average time/residue: 2.6283 time to fit residues: 167.8236 Evaluate side-chains 60 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.672 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.0807 time to fit residues: 1.0446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3522 Z= 0.253 Angle : 0.486 3.639 4710 Z= 0.244 Chirality : 0.050 0.129 528 Planarity : 0.002 0.018 600 Dihedral : 4.350 14.365 468 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.01 % Allowed : 17.68 % Favored : 81.31 % 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: -1.40 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.28), residues: 444 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.686 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 61 average time/residue: 2.6679 time to fit residues: 167.5724 Evaluate side-chains 59 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.646 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0809 time to fit residues: 0.9113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 0.0980 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 0.0030 chunk 11 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3522 Z= 0.148 Angle : 0.454 3.497 4710 Z= 0.224 Chirality : 0.050 0.126 528 Planarity : 0.002 0.012 600 Dihedral : 4.087 13.756 468 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.76 % Allowed : 18.43 % Favored : 80.81 % 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: -1.38 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.28), residues: 444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.633 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 62 average time/residue: 2.7268 time to fit residues: 173.8923 Evaluate side-chains 61 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.633 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.7831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN A 351 GLN D 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.6245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3522 Z= 0.190 Angle : 0.458 3.538 4710 Z= 0.227 Chirality : 0.050 0.127 528 Planarity : 0.002 0.013 600 Dihedral : 4.108 13.704 468 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.76 % Allowed : 18.43 % Favored : 80.81 % 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: -1.39 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.28), residues: 444 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.570 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 61 average time/residue: 2.6764 time to fit residues: 167.9098 Evaluate side-chains 61 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.7510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.0670 chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN A 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.6281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3522 Z= 0.142 Angle : 0.443 3.494 4710 Z= 0.218 Chirality : 0.050 0.125 528 Planarity : 0.001 0.012 600 Dihedral : 3.924 13.185 468 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.76 % Allowed : 18.43 % Favored : 80.81 % 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: -1.39 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.29), residues: 444 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.704 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 63 average time/residue: 2.8572 time to fit residues: 184.9155 Evaluate side-chains 63 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.644 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.7642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN A 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.122580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.112899 restraints weight = 12692.560| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.54 r_work: 0.3711 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3522 Z= 0.283 Angle : 0.488 3.577 4710 Z= 0.244 Chirality : 0.050 0.133 528 Planarity : 0.002 0.018 600 Dihedral : 4.245 13.975 468 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.01 % Allowed : 17.68 % Favored : 81.31 % 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: -1.45 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.28), residues: 444 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4484.35 seconds wall clock time: 78 minutes 59.78 seconds (4739.78 seconds total)