Starting phenix.real_space_refine on Thu Jan 18 00:44:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4t_14316/01_2024/7r4t_14316.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4t_14316/01_2024/7r4t_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_14316/01_2024/7r4t_14316.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4t_14316/01_2024/7r4t_14316.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4t_14316/01_2024/7r4t_14316.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4t_14316/01_2024/7r4t_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-1.21-5211/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: 3.65, per 1000 atoms: 0.52 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: 5.04 Conformation dependent library (CDL) restraints added in 702.2 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: 0.71 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: 2.47 Time building geometry restraints manager: 5.27 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: 2769 13.45 - 26.89: 233 26.89 - 40.34: 76 40.34 - 53.78: 25 53.78 - 67.23: 59 Dihedral angle restraints: 3162 sinusoidal: 1758 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 3159 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: 4.660 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: 11.580 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.800 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.640 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS D 330 PHE 0.047 0.018 PHE F 378 TYR 0.032 0.008 TYR D 310 ARG 0.005 0.001 ARG F 349 *********************** 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 : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 347 LYS cc_start: 0.8346 (ttpt) cc_final: 0.7938 (mptt) REVERT: A 347 LYS cc_start: 0.8450 (ttpt) cc_final: 0.7989 (mptt) REVERT: B 347 LYS cc_start: 0.8339 (ttpt) cc_final: 0.7944 (mmtm) REVERT: B 349 ARG cc_start: 0.8218 (mtt180) cc_final: 0.6371 (mmp-170) REVERT: C 347 LYS cc_start: 0.8400 (ttpt) cc_final: 0.7966 (mmtm) REVERT: C 349 ARG cc_start: 0.8156 (mtt180) cc_final: 0.6382 (mmp-170) REVERT: D 347 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8240 (mptt) REVERT: D 348 ASP cc_start: 0.8537 (t70) cc_final: 0.8029 (t0) REVERT: D 349 ARG cc_start: 0.7334 (mtt180) cc_final: 0.5925 (pmt-80) REVERT: E 347 LYS cc_start: 0.8447 (ttpt) cc_final: 0.8122 (mptt) REVERT: E 348 ASP cc_start: 0.8595 (t70) cc_final: 0.8148 (t0) REVERT: E 349 ARG cc_start: 0.7266 (mtt180) cc_final: 0.5882 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 2.9230 time to fit residues: 406.5089 Evaluate side-chains 88 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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: 0.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- 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: 0.8382 moved from start: 0.4063 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= 0.200 Angle : 0.549 4.441 4710 Z= 0.279 Chirality : 0.050 0.129 528 Planarity : 0.003 0.023 600 Dihedral : 5.855 20.029 468 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.02 % Allowed : 15.15 % Favored : 82.83 % 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: -1.53 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.010 0.001 PHE C 378 TYR 0.007 0.001 TYR E 310 ARG 0.004 0.001 ARG F 349 *********************** 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 102 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.627 Fit side-chains REVERT: F 347 LYS cc_start: 0.8336 (ttpt) cc_final: 0.7908 (mptt) REVERT: A 338 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: A 347 LYS cc_start: 0.8493 (ttpt) cc_final: 0.7994 (mptt) REVERT: A 349 ARG cc_start: 0.7692 (mtt180) cc_final: 0.7339 (mtt180) REVERT: B 345 ASP cc_start: 0.8313 (m-30) cc_final: 0.8062 (m-30) REVERT: B 347 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8009 (mmtm) REVERT: B 349 ARG cc_start: 0.8146 (mtt180) cc_final: 0.6349 (mmp80) REVERT: C 338 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: C 347 LYS cc_start: 0.8574 (ttpt) cc_final: 0.8078 (mmtm) REVERT: C 349 ARG cc_start: 0.8133 (mtt180) cc_final: 0.6261 (mmp-170) REVERT: D 347 LYS cc_start: 0.8473 (ttpt) cc_final: 0.8218 (mptt) REVERT: D 348 ASP cc_start: 0.8550 (t70) cc_final: 0.8074 (t0) REVERT: D 349 ARG cc_start: 0.7245 (mtt180) cc_final: 0.5968 (pmt-80) REVERT: E 338 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: E 340 LYS cc_start: 0.8361 (ptpp) cc_final: 0.8112 (ptpt) REVERT: E 347 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8139 (mptt) REVERT: E 348 ASP cc_start: 0.8550 (t70) cc_final: 0.8104 (t0) REVERT: E 349 ARG cc_start: 0.7085 (mtt180) cc_final: 0.5929 (pmt-80) outliers start: 8 outliers final: 0 residues processed: 95 average time/residue: 3.1278 time to fit residues: 304.1082 Evaluate side-chains 78 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.8411 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3522 Z= 0.163 Angle : 0.478 3.645 4710 Z= 0.239 Chirality : 0.050 0.125 528 Planarity : 0.002 0.016 600 Dihedral : 4.865 17.560 468 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.78 % Allowed : 16.67 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 374 PHE 0.004 0.001 PHE D 378 TYR 0.007 0.001 TYR A 310 ARG 0.002 0.000 ARG A 349 *********************** 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 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.543 Fit side-chains REVERT: F 349 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7496 (mtt180) REVERT: A 338 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: A 349 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7422 (mtt180) REVERT: B 345 ASP cc_start: 0.8296 (m-30) cc_final: 0.8051 (m-30) REVERT: B 347 LYS cc_start: 0.8412 (ttpt) cc_final: 0.8011 (mmtm) REVERT: B 349 ARG cc_start: 0.8202 (mtt180) cc_final: 0.6325 (mmp-170) REVERT: C 338 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: C 347 LYS cc_start: 0.8492 (ttpt) cc_final: 0.8069 (mmtm) REVERT: C 349 ARG cc_start: 0.8166 (mtt180) cc_final: 0.6249 (mmp-170) REVERT: D 347 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8197 (mptt) REVERT: D 348 ASP cc_start: 0.8544 (t70) cc_final: 0.8075 (t0) REVERT: D 349 ARG cc_start: 0.7338 (mtt180) cc_final: 0.6030 (pmt-80) REVERT: E 340 LYS cc_start: 0.8356 (ptpp) cc_final: 0.8148 (ptpt) REVERT: E 347 LYS cc_start: 0.8472 (ttpt) cc_final: 0.8121 (mptt) REVERT: E 348 ASP cc_start: 0.8564 (t70) cc_final: 0.8128 (t0) REVERT: E 349 ARG cc_start: 0.7194 (mtt180) cc_final: 0.5939 (pmt-80) outliers start: 11 outliers final: 4 residues processed: 78 average time/residue: 2.8998 time to fit residues: 231.6742 Evaluate side-chains 79 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 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: 0.8435 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3522 Z= 0.213 Angle : 0.475 3.526 4710 Z= 0.238 Chirality : 0.051 0.129 528 Planarity : 0.002 0.013 600 Dihedral : 4.614 16.556 468 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.02 % Allowed : 17.93 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.005 0.001 PHE D 378 TYR 0.006 0.001 TYR D 310 ARG 0.002 0.000 ARG A 349 *********************** 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 81 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.617 Fit side-chains REVERT: F 349 ARG cc_start: 0.7795 (mtm180) cc_final: 0.7581 (mtt180) REVERT: A 349 ARG cc_start: 0.7847 (mtt180) cc_final: 0.7472 (mtt180) REVERT: B 347 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8038 (mmtm) REVERT: B 349 ARG cc_start: 0.8215 (mtt180) cc_final: 0.6382 (mmp-170) REVERT: C 338 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: C 347 LYS cc_start: 0.8460 (ttpt) cc_final: 0.8052 (mmtm) REVERT: C 349 ARG cc_start: 0.8121 (mtt180) cc_final: 0.6334 (mmp-170) REVERT: D 347 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8207 (mptt) REVERT: D 348 ASP cc_start: 0.8530 (t70) cc_final: 0.8085 (t0) REVERT: D 349 ARG cc_start: 0.7439 (mtt180) cc_final: 0.6040 (pmt-80) REVERT: E 311 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8398 (ptmt) REVERT: E 338 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: E 347 LYS cc_start: 0.8560 (ttpt) cc_final: 0.8188 (mptt) REVERT: E 348 ASP cc_start: 0.8520 (t70) cc_final: 0.8117 (t0) REVERT: E 349 ARG cc_start: 0.7384 (mtt180) cc_final: 0.6031 (pmt-80) outliers start: 8 outliers final: 2 residues processed: 76 average time/residue: 2.9109 time to fit residues: 226.8951 Evaluate side-chains 71 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 0.0870 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 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: 2.0964 ------------------------------------------------------------------------------- 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: 0.8441 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3522 Z= 0.204 Angle : 0.477 3.670 4710 Z= 0.237 Chirality : 0.050 0.126 528 Planarity : 0.002 0.012 600 Dihedral : 4.444 16.005 468 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.03 % Allowed : 16.67 % Favored : 80.30 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.004 0.001 PHE D 378 TYR 0.005 0.001 TYR A 310 ARG 0.002 0.000 ARG E 379 *********************** 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 83 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.611 Fit side-chains REVERT: A 351 GLN cc_start: 0.8471 (tt0) cc_final: 0.8264 (tt0) REVERT: B 347 LYS cc_start: 0.8491 (ttpt) cc_final: 0.8049 (mmtm) REVERT: B 349 ARG cc_start: 0.8242 (mtt180) cc_final: 0.6349 (mmp-170) REVERT: C 347 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8018 (mmtm) REVERT: C 349 ARG cc_start: 0.8136 (mtt180) cc_final: 0.6411 (mmp-170) REVERT: D 347 LYS cc_start: 0.8502 (ttpt) cc_final: 0.8215 (mptt) REVERT: D 348 ASP cc_start: 0.8564 (t70) cc_final: 0.8034 (t0) REVERT: D 349 ARG cc_start: 0.7539 (mtt180) cc_final: 0.5912 (pmt-80) REVERT: E 311 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8378 (ptmt) REVERT: E 338 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6602 (mp0) REVERT: E 347 LYS cc_start: 0.8570 (ttpt) cc_final: 0.8191 (mptt) REVERT: E 348 ASP cc_start: 0.8531 (t70) cc_final: 0.8112 (t0) REVERT: E 349 ARG cc_start: 0.7529 (mtt180) cc_final: 0.5985 (pmt-80) outliers start: 12 outliers final: 4 residues processed: 77 average time/residue: 2.6483 time to fit residues: 209.3978 Evaluate side-chains 70 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 338 GLU 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: 0.9980 chunk 33 optimal weight: 0.0030 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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: 0.8416 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3522 Z= 0.129 Angle : 0.445 3.536 4710 Z= 0.218 Chirality : 0.050 0.127 528 Planarity : 0.002 0.012 600 Dihedral : 4.065 14.697 468 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.77 % Allowed : 17.93 % Favored : 80.30 % 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: -1.22 (0.38), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.92 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 374 PHE 0.005 0.001 PHE B 378 TYR 0.005 0.001 TYR A 310 ARG 0.002 0.000 ARG F 349 *********************** 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 74 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.687 Fit side-chains REVERT: F 347 LYS cc_start: 0.8359 (ttpt) cc_final: 0.7957 (mptt) REVERT: B 347 LYS cc_start: 0.8494 (ttpt) cc_final: 0.8014 (mmtm) REVERT: B 349 ARG cc_start: 0.8246 (mtt180) cc_final: 0.6411 (mmp-170) REVERT: C 347 LYS cc_start: 0.8468 (ttpt) cc_final: 0.8018 (mmtm) REVERT: C 349 ARG cc_start: 0.8171 (mtt180) cc_final: 0.6355 (mmp-170) REVERT: D 347 LYS cc_start: 0.8487 (ttpt) cc_final: 0.8227 (mptt) REVERT: D 348 ASP cc_start: 0.8544 (t70) cc_final: 0.8193 (t0) REVERT: D 349 ARG cc_start: 0.7607 (mtt180) cc_final: 0.6048 (pmt-80) REVERT: E 338 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: E 347 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8211 (mptt) REVERT: E 348 ASP cc_start: 0.8539 (t70) cc_final: 0.8053 (t0) REVERT: E 349 ARG cc_start: 0.7573 (mtt180) cc_final: 0.5999 (pmt-80) outliers start: 7 outliers final: 3 residues processed: 72 average time/residue: 2.9061 time to fit residues: 214.6148 Evaluate side-chains 67 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3522 Z= 0.201 Angle : 0.463 3.527 4710 Z= 0.229 Chirality : 0.050 0.127 528 Planarity : 0.002 0.014 600 Dihedral : 4.136 14.608 468 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 1.27 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: -1.26 (0.38), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 329 PHE 0.007 0.001 PHE B 378 TYR 0.005 0.001 TYR A 310 ARG 0.003 0.000 ARG B 379 *********************** 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 66 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.749 Fit side-chains REVERT: F 345 ASP cc_start: 0.8257 (m-30) cc_final: 0.8004 (m-30) REVERT: F 347 LYS cc_start: 0.8361 (ttpt) cc_final: 0.7919 (mptt) REVERT: B 347 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8052 (mmtm) REVERT: B 349 ARG cc_start: 0.8302 (mtt180) cc_final: 0.6469 (mmp-170) REVERT: C 347 LYS cc_start: 0.8475 (ttpt) cc_final: 0.8040 (mmtm) REVERT: C 349 ARG cc_start: 0.8175 (mtt180) cc_final: 0.6376 (mmp-170) REVERT: D 347 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8206 (mptt) REVERT: D 348 ASP cc_start: 0.8584 (t70) cc_final: 0.8218 (t0) REVERT: D 349 ARG cc_start: 0.7734 (mtt180) cc_final: 0.6050 (pmt-80) REVERT: E 347 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8206 (mptt) REVERT: E 348 ASP cc_start: 0.8566 (t70) cc_final: 0.8177 (t0) REVERT: E 349 ARG cc_start: 0.7664 (mtt180) cc_final: 0.6019 (pmt-80) outliers start: 3 outliers final: 3 residues processed: 65 average time/residue: 2.8641 time to fit residues: 191.0699 Evaluate side-chains 65 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain E residue 324 SER 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: 0.9980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.0030 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3522 Z= 0.131 Angle : 0.444 3.485 4710 Z= 0.217 Chirality : 0.050 0.127 528 Planarity : 0.002 0.011 600 Dihedral : 3.903 13.781 468 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.76 % Allowed : 17.68 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.38), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 374 PHE 0.005 0.001 PHE B 378 TYR 0.005 0.001 TYR A 310 ARG 0.002 0.000 ARG B 379 *********************** 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 66 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.586 Fit side-chains REVERT: F 345 ASP cc_start: 0.8265 (m-30) cc_final: 0.8013 (m-30) REVERT: F 347 LYS cc_start: 0.8346 (ttpt) cc_final: 0.7976 (mptt) REVERT: B 347 LYS cc_start: 0.8503 (ttpt) cc_final: 0.8003 (mmtm) REVERT: B 349 ARG cc_start: 0.8237 (mtt180) cc_final: 0.6416 (mmp-170) REVERT: C 347 LYS cc_start: 0.8470 (ttpt) cc_final: 0.8020 (mmtm) REVERT: C 349 ARG cc_start: 0.8142 (mtt180) cc_final: 0.6324 (mmp-170) REVERT: D 348 ASP cc_start: 0.8595 (t70) cc_final: 0.8092 (t0) REVERT: D 349 ARG cc_start: 0.7798 (mtt180) cc_final: 0.6024 (pmt-80) REVERT: E 347 LYS cc_start: 0.8624 (ttpt) cc_final: 0.8216 (mptt) REVERT: E 348 ASP cc_start: 0.8560 (t70) cc_final: 0.8181 (t0) REVERT: E 349 ARG cc_start: 0.7765 (mtt180) cc_final: 0.5984 (pmt-80) outliers start: 3 outliers final: 3 residues processed: 65 average time/residue: 2.7935 time to fit residues: 186.3943 Evaluate side-chains 64 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0020 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.4526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3522 Z= 0.118 Angle : 0.426 3.424 4710 Z= 0.207 Chirality : 0.050 0.123 528 Planarity : 0.002 0.011 600 Dihedral : 3.669 13.214 468 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.76 % Allowed : 17.42 % Favored : 81.82 % 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: -1.25 (0.38), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 374 PHE 0.002 0.001 PHE E 346 TYR 0.005 0.001 TYR A 310 ARG 0.002 0.000 ARG B 379 *********************** 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 70 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.567 Fit side-chains REVERT: F 347 LYS cc_start: 0.8356 (ttpt) cc_final: 0.7976 (mptt) REVERT: B 347 LYS cc_start: 0.8488 (ttpt) cc_final: 0.7998 (mmtm) REVERT: B 349 ARG cc_start: 0.8230 (mtt180) cc_final: 0.6391 (mmp-170) REVERT: C 347 LYS cc_start: 0.8450 (ttpt) cc_final: 0.7993 (mmtm) REVERT: C 349 ARG cc_start: 0.8088 (mtt180) cc_final: 0.6183 (mmp-170) REVERT: D 348 ASP cc_start: 0.8560 (t70) cc_final: 0.8184 (t0) REVERT: D 349 ARG cc_start: 0.7881 (mtt180) cc_final: 0.6057 (pmt-80) REVERT: E 347 LYS cc_start: 0.8627 (ttpt) cc_final: 0.8238 (mptt) REVERT: E 348 ASP cc_start: 0.8564 (t70) cc_final: 0.8155 (t0) REVERT: E 349 ARG cc_start: 0.7807 (mtt180) cc_final: 0.5981 (pmt-80) REVERT: E 351 GLN cc_start: 0.8628 (tt0) cc_final: 0.8412 (tt0) outliers start: 3 outliers final: 3 residues processed: 69 average time/residue: 2.6821 time to fit residues: 190.1036 Evaluate side-chains 66 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain E residue 324 SER 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: 4.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 0.0770 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN D 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3522 Z= 0.249 Angle : 0.478 3.539 4710 Z= 0.237 Chirality : 0.050 0.130 528 Planarity : 0.002 0.012 600 Dihedral : 4.064 14.117 468 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.76 % Allowed : 16.92 % 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: -1.28 (0.38), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.006 0.001 PHE D 378 TYR 0.005 0.001 TYR A 310 ARG 0.002 0.000 ARG C 349 ********************** 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 : 0.633 Fit side-chains REVERT: F 347 LYS cc_start: 0.8341 (ttpt) cc_final: 0.7912 (mptt) REVERT: B 349 ARG cc_start: 0.8242 (mtt180) cc_final: 0.6465 (mmp80) REVERT: C 347 LYS cc_start: 0.8432 (ttpt) cc_final: 0.8004 (mmtm) REVERT: C 349 ARG cc_start: 0.8130 (mtt180) cc_final: 0.6392 (mmp-170) REVERT: D 348 ASP cc_start: 0.8623 (t70) cc_final: 0.8065 (t0) REVERT: D 349 ARG cc_start: 0.7972 (mtt180) cc_final: 0.6028 (pmt-80) REVERT: E 347 LYS cc_start: 0.8625 (ttpt) cc_final: 0.8241 (mptt) REVERT: E 348 ASP cc_start: 0.8555 (t70) cc_final: 0.8342 (t70) REVERT: E 349 ARG cc_start: 0.7871 (mtt180) cc_final: 0.5943 (pmt-80) outliers start: 3 outliers final: 3 residues processed: 62 average time/residue: 2.7379 time to fit residues: 174.5004 Evaluate side-chains 63 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.125282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.115404 restraints weight = 13668.013| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.60 r_work: 0.3703 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3522 Z= 0.139 Angle : 0.439 3.514 4710 Z= 0.215 Chirality : 0.050 0.122 528 Planarity : 0.002 0.011 600 Dihedral : 3.863 13.654 468 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.76 % Allowed : 17.42 % Favored : 81.82 % 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: -1.28 (0.38), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 329 PHE 0.003 0.001 PHE D 378 TYR 0.005 0.001 TYR A 310 ARG 0.002 0.000 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4707.92 seconds wall clock time: 83 minutes 32.99 seconds (5012.99 seconds total)