Starting phenix.real_space_refine on Sat Aug 3 05:46:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8d_18251/08_2024/8q8d_18251.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8d_18251/08_2024/8q8d_18251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8d_18251/08_2024/8q8d_18251.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8d_18251/08_2024/8q8d_18251.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8d_18251/08_2024/8q8d_18251.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8d_18251/08_2024/8q8d_18251.cif" } resolution = 3.04 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 "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 345": "OD1" <-> "OD2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 372": "OE1" <-> "OE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 345": "OD1" <-> "OD2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 372": "OE1" <-> "OE2" Residue "F 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-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7074 Number of models: 1 Model: "" Number of chains: 6 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} 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} Time building chain proxies: 5.13, per 1000 atoms: 0.73 Number of scatterers: 7074 At special positions: 0 Unit cell: (119.48, 117.832, 39.552, 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: 4.90 Conformation dependent library (CDL) restraints added in 809.2 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 19 sheets defined 0.0% alpha, 48.7% 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 'C' and resid 306 through 310 removed outlier: 6.519A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 306 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL E 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.852A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 318 removed outlier: 6.441A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 321 through 322 removed outlier: 6.385A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.375A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.626A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.267A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 351 through 354 removed outlier: 6.409A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.460A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.380A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS A 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR E 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU A 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N LYS E 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N HIS A 374 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N THR E 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.491A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.800A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.243A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 328 through 330 Processing sheet with id=AB6, first strand: chain 'D' and resid 336 through 342 removed outlier: 6.389A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER B 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.817A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.730A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.514A pdb=" N ASP B 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR D 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE B 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 378 removed outlier: 6.424A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N PHE D 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 63 hydrogen bonds defined for protein. 189 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: 2.16 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 3600 1.12 - 1.29: 579 1.29 - 1.47: 1174 1.47 - 1.64: 1769 1.64 - 1.82: 6 Bond restraints: 7128 Sorted by residual: bond pdb=" N THR E 377 " pdb=" H THR E 377 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N GLU A 342 " pdb=" H GLU A 342 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ILE C 371 " pdb=" H ILE C 371 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N GLU E 342 " pdb=" H GLU E 342 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CZ PHE E 378 " pdb=" HZ PHE E 378 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 7123 not shown) Histogram of bond angle deviations from ideal: 96.45 - 102.99: 30 102.99 - 109.52: 5361 109.52 - 116.06: 3900 116.06 - 122.59: 2983 122.59 - 129.13: 710 Bond angle restraints: 12984 Sorted by residual: angle pdb=" CA ASP D 358 " pdb=" CB ASP D 358 " pdb=" CG ASP D 358 " ideal model delta sigma weight residual 112.60 118.99 -6.39 1.00e+00 1.00e+00 4.08e+01 angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 118.59 -5.99 1.00e+00 1.00e+00 3.59e+01 angle pdb=" C LYS C 331 " pdb=" CA LYS C 331 " pdb=" CB LYS C 331 " ideal model delta sigma weight residual 110.55 120.21 -9.66 1.66e+00 3.63e-01 3.39e+01 angle pdb=" N SER C 324 " pdb=" CA SER C 324 " pdb=" CB SER C 324 " ideal model delta sigma weight residual 111.24 102.10 9.14 1.58e+00 4.01e-01 3.35e+01 angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 119.34 -5.54 1.00e+00 1.00e+00 3.07e+01 ... (remaining 12979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 2940 17.99 - 35.98: 158 35.98 - 53.98: 83 53.98 - 71.97: 96 71.97 - 89.96: 5 Dihedral angle restraints: 3282 sinusoidal: 1878 harmonic: 1404 Sorted by residual: dihedral pdb=" CA GLY C 323 " pdb=" C GLY C 323 " pdb=" N SER C 324 " pdb=" CA SER C 324 " ideal model delta harmonic sigma weight residual 180.00 150.83 29.17 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA SER A 341 " pdb=" C SER A 341 " pdb=" N GLU A 342 " pdb=" CA GLU A 342 " ideal model delta harmonic sigma weight residual 180.00 151.25 28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA SER C 341 " pdb=" C SER C 341 " pdb=" N GLU C 342 " pdb=" CA GLU C 342 " ideal model delta harmonic sigma weight residual 180.00 151.64 28.36 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 3279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 323 0.073 - 0.145: 165 0.145 - 0.218: 34 0.218 - 0.290: 4 0.290 - 0.363: 2 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA CYS F 322 " pdb=" N CYS F 322 " pdb=" C CYS F 322 " pdb=" CB CYS F 322 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA SER C 324 " pdb=" N SER C 324 " pdb=" C SER C 324 " pdb=" CB SER C 324 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA LYS E 347 " pdb=" N LYS E 347 " pdb=" C LYS E 347 " pdb=" CB LYS E 347 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 525 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.178 2.00e-02 2.50e+03 7.97e-02 1.91e+02 pdb=" CG TYR E 310 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.172 2.00e-02 2.50e+03 pdb=" HD1 TYR E 310 " -0.021 2.00e-02 2.50e+03 pdb=" HD2 TYR E 310 " -0.049 2.00e-02 2.50e+03 pdb=" HE1 TYR E 310 " -0.036 2.00e-02 2.50e+03 pdb=" HE2 TYR E 310 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.127 2.00e-02 2.50e+03 5.36e-02 8.63e+01 pdb=" CG TYR A 310 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.105 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " -0.016 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " -0.041 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " -0.023 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " -0.083 2.00e-02 2.50e+03 3.78e-02 4.28e+01 pdb=" CG TYR B 310 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " -0.078 2.00e-02 2.50e+03 pdb=" HD1 TYR B 310 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR B 310 " 0.030 2.00e-02 2.50e+03 pdb=" HE1 TYR B 310 " 0.025 2.00e-02 2.50e+03 pdb=" HE2 TYR B 310 " 0.001 2.00e-02 2.50e+03 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 504 2.16 - 2.77: 11738 2.77 - 3.38: 18515 3.38 - 3.99: 25771 3.99 - 4.60: 35517 Nonbonded interactions: 92045 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.545 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.545 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.548 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.556 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.585 2.450 ... (remaining 92040 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 3.570 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: 0.120 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 26.620 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 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 0.064 3522 Z= 0.745 Angle : 1.850 10.333 4710 Z= 1.226 Chirality : 0.085 0.363 528 Planarity : 0.011 0.093 600 Dihedral : 13.263 89.960 1350 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Cbeta Deviations : 0.51 % 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: -1.65 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS A 330 PHE 0.033 0.010 PHE F 346 TYR 0.161 0.038 TYR E 310 ARG 0.003 0.001 ARG E 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 133 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.6939 (mttt) cc_final: 0.6655 (mtpt) REVERT: A 348 ASP cc_start: 0.7612 (t0) cc_final: 0.7404 (t70) REVERT: A 351 GLN cc_start: 0.7228 (mt0) cc_final: 0.6743 (mp10) REVERT: A 369 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6864 (mttp) REVERT: B 307 GLN cc_start: 0.7224 (tt0) cc_final: 0.6683 (mt0) REVERT: B 321 LYS cc_start: 0.7258 (mttt) cc_final: 0.7020 (mttp) REVERT: B 336 GLN cc_start: 0.7944 (mt0) cc_final: 0.7739 (mt0) REVERT: B 338 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6598 (tp30) REVERT: B 369 LYS cc_start: 0.7696 (tttt) cc_final: 0.7074 (ttmm) REVERT: B 375 LYS cc_start: 0.6979 (ttmt) cc_final: 0.6374 (tttm) REVERT: C 317 LYS cc_start: 0.7787 (mttt) cc_final: 0.7431 (mtpt) REVERT: C 340 LYS cc_start: 0.8536 (mttt) cc_final: 0.8290 (mmmm) REVERT: C 351 GLN cc_start: 0.7709 (mt0) cc_final: 0.7392 (mp10) REVERT: C 375 LYS cc_start: 0.7984 (ttmt) cc_final: 0.7699 (ttmt) REVERT: D 307 GLN cc_start: 0.7800 (tt0) cc_final: 0.7332 (mt0) REVERT: D 347 LYS cc_start: 0.8391 (mptt) cc_final: 0.6751 (mtmm) REVERT: D 357 LEU cc_start: 0.7731 (tp) cc_final: 0.7526 (mp) REVERT: D 369 LYS cc_start: 0.8370 (tttt) cc_final: 0.7654 (ttmm) REVERT: D 375 LYS cc_start: 0.8365 (ttmt) cc_final: 0.7853 (tttp) REVERT: E 343 LYS cc_start: 0.7281 (mtmt) cc_final: 0.7012 (mtpp) REVERT: E 351 GLN cc_start: 0.7114 (mt0) cc_final: 0.6728 (mp10) REVERT: E 369 LYS cc_start: 0.7479 (mtmt) cc_final: 0.6987 (mttp) REVERT: F 307 GLN cc_start: 0.7055 (tt0) cc_final: 0.6524 (mt0) REVERT: F 311 LYS cc_start: 0.7808 (mttt) cc_final: 0.6518 (tppt) REVERT: F 336 GLN cc_start: 0.7699 (mt0) cc_final: 0.7390 (mt0) REVERT: F 340 LYS cc_start: 0.7593 (ttpp) cc_final: 0.6789 (mmtt) REVERT: F 358 ASP cc_start: 0.7695 (m-30) cc_final: 0.7339 (m-30) REVERT: F 375 LYS cc_start: 0.7523 (ttmt) cc_final: 0.7080 (tttm) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.5816 time to fit residues: 86.2048 Evaluate side-chains 90 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3522 Z= 0.297 Angle : 0.613 4.222 4710 Z= 0.325 Chirality : 0.052 0.149 528 Planarity : 0.004 0.052 600 Dihedral : 6.566 23.115 468 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.01 % Allowed : 8.33 % Favored : 90.66 % 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: -1.55 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.007 0.001 PHE E 346 TYR 0.014 0.002 TYR A 310 ARG 0.002 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: 4 poor density : 98 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7718 (t0) cc_final: 0.7252 (t0) REVERT: A 317 LYS cc_start: 0.7075 (mttt) cc_final: 0.6771 (mtpt) REVERT: A 340 LYS cc_start: 0.7649 (mttt) cc_final: 0.7434 (mttm) REVERT: A 351 GLN cc_start: 0.7330 (mt0) cc_final: 0.6794 (mp10) REVERT: A 369 LYS cc_start: 0.7522 (mtmt) cc_final: 0.7031 (mttp) REVERT: B 307 GLN cc_start: 0.7293 (tt0) cc_final: 0.6823 (mt0) REVERT: B 314 ASP cc_start: 0.7877 (t0) cc_final: 0.7665 (t0) REVERT: B 321 LYS cc_start: 0.7491 (mttt) cc_final: 0.7230 (mttp) REVERT: B 340 LYS cc_start: 0.7553 (mtpp) cc_final: 0.6617 (mtmm) REVERT: B 369 LYS cc_start: 0.7758 (tttt) cc_final: 0.7146 (ttmm) REVERT: B 375 LYS cc_start: 0.7326 (ttmt) cc_final: 0.6614 (tttm) REVERT: C 317 LYS cc_start: 0.7651 (mttt) cc_final: 0.7328 (mtpt) REVERT: C 338 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7907 (mt-10) REVERT: C 340 LYS cc_start: 0.8621 (mttt) cc_final: 0.8335 (mmmm) REVERT: C 375 LYS cc_start: 0.8039 (ttmt) cc_final: 0.7787 (ttmt) REVERT: D 307 GLN cc_start: 0.7885 (tt0) cc_final: 0.7322 (mt0) REVERT: D 324 SER cc_start: 0.8319 (m) cc_final: 0.7882 (t) REVERT: D 347 LYS cc_start: 0.8285 (mptt) cc_final: 0.6722 (mtmt) REVERT: D 357 LEU cc_start: 0.7897 (tp) cc_final: 0.7651 (mp) REVERT: D 375 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7746 (tttp) REVERT: E 340 LYS cc_start: 0.7705 (mttt) cc_final: 0.7428 (mtmt) REVERT: E 351 GLN cc_start: 0.7316 (mt0) cc_final: 0.6821 (mp10) REVERT: E 369 LYS cc_start: 0.7647 (mtmt) cc_final: 0.7166 (mttp) REVERT: E 372 GLU cc_start: 0.8288 (tt0) cc_final: 0.7998 (tt0) REVERT: F 307 GLN cc_start: 0.7247 (tt0) cc_final: 0.6664 (mt0) REVERT: F 311 LYS cc_start: 0.7858 (mttt) cc_final: 0.6487 (tppt) REVERT: F 336 GLN cc_start: 0.7688 (mt0) cc_final: 0.7416 (mt0) REVERT: F 338 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6818 (tp30) REVERT: F 340 LYS cc_start: 0.7650 (ttpp) cc_final: 0.6827 (mmtt) REVERT: F 358 ASP cc_start: 0.7896 (m-30) cc_final: 0.7494 (m-30) REVERT: F 375 LYS cc_start: 0.7704 (ttmt) cc_final: 0.7196 (tttm) outliers start: 4 outliers final: 4 residues processed: 101 average time/residue: 0.6270 time to fit residues: 70.4675 Evaluate side-chains 95 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3522 Z= 0.149 Angle : 0.499 4.029 4710 Z= 0.261 Chirality : 0.052 0.135 528 Planarity : 0.003 0.028 600 Dihedral : 5.822 21.550 468 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.77 % Allowed : 8.84 % Favored : 89.39 % 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: -1.33 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.005 0.001 PHE E 346 TYR 0.010 0.002 TYR C 310 ARG 0.006 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 102 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7829 (t0) cc_final: 0.7358 (t0) REVERT: A 317 LYS cc_start: 0.7260 (mttt) cc_final: 0.6923 (mtpt) REVERT: A 340 LYS cc_start: 0.7735 (mttt) cc_final: 0.7530 (mttm) REVERT: A 348 ASP cc_start: 0.7744 (t0) cc_final: 0.7437 (t70) REVERT: A 351 GLN cc_start: 0.7264 (mt0) cc_final: 0.6777 (mp10) REVERT: A 369 LYS cc_start: 0.7553 (mtmt) cc_final: 0.7057 (mttp) REVERT: B 307 GLN cc_start: 0.7310 (tt0) cc_final: 0.6849 (mt0) REVERT: B 314 ASP cc_start: 0.7896 (t0) cc_final: 0.7632 (t0) REVERT: B 321 LYS cc_start: 0.7553 (mttt) cc_final: 0.7281 (mttp) REVERT: B 340 LYS cc_start: 0.7522 (mtpp) cc_final: 0.6658 (mtmm) REVERT: B 369 LYS cc_start: 0.7789 (tttt) cc_final: 0.7142 (ttmm) REVERT: B 375 LYS cc_start: 0.7347 (ttmt) cc_final: 0.6716 (tttm) REVERT: C 317 LYS cc_start: 0.7555 (mttt) cc_final: 0.7240 (mtpt) REVERT: C 375 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7868 (ttmt) REVERT: D 307 GLN cc_start: 0.7900 (tt0) cc_final: 0.7268 (mt0) REVERT: D 324 SER cc_start: 0.8344 (m) cc_final: 0.7858 (t) REVERT: D 336 GLN cc_start: 0.8256 (mt0) cc_final: 0.7947 (tt0) REVERT: D 347 LYS cc_start: 0.8275 (mptt) cc_final: 0.6574 (mtmm) REVERT: D 357 LEU cc_start: 0.7948 (tp) cc_final: 0.7661 (mp) REVERT: D 375 LYS cc_start: 0.8267 (ttmt) cc_final: 0.7758 (tttp) REVERT: E 340 LYS cc_start: 0.7803 (mttt) cc_final: 0.7581 (mtmt) REVERT: E 343 LYS cc_start: 0.7337 (mtpp) cc_final: 0.6129 (mmmt) REVERT: E 351 GLN cc_start: 0.7370 (mt0) cc_final: 0.6904 (mp10) REVERT: E 357 LEU cc_start: 0.8215 (mp) cc_final: 0.7999 (mp) REVERT: E 369 LYS cc_start: 0.7762 (mtmt) cc_final: 0.7276 (mttp) REVERT: F 307 GLN cc_start: 0.7298 (tt0) cc_final: 0.6705 (mt0) REVERT: F 311 LYS cc_start: 0.7834 (mttt) cc_final: 0.6467 (tppt) REVERT: F 336 GLN cc_start: 0.7683 (mt0) cc_final: 0.7454 (mt0) REVERT: F 340 LYS cc_start: 0.7598 (ttpp) cc_final: 0.6926 (mmpt) REVERT: F 358 ASP cc_start: 0.7938 (m-30) cc_final: 0.7550 (m-30) REVERT: F 375 LYS cc_start: 0.7729 (ttmt) cc_final: 0.7234 (tttm) outliers start: 7 outliers final: 6 residues processed: 98 average time/residue: 0.5988 time to fit residues: 65.9168 Evaluate side-chains 97 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3522 Z= 0.376 Angle : 0.557 4.071 4710 Z= 0.295 Chirality : 0.051 0.133 528 Planarity : 0.004 0.030 600 Dihedral : 5.844 23.903 468 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.77 % Allowed : 10.61 % Favored : 87.63 % 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: -1.27 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.005 0.001 PHE F 378 TYR 0.020 0.002 TYR A 310 ARG 0.002 0.000 ARG E 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 92 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7830 (t0) cc_final: 0.7334 (t0) REVERT: A 317 LYS cc_start: 0.7360 (mttt) cc_final: 0.6910 (mtpt) REVERT: A 340 LYS cc_start: 0.7851 (mttt) cc_final: 0.7619 (mttm) REVERT: A 351 GLN cc_start: 0.7301 (mt0) cc_final: 0.6829 (mp10) REVERT: A 369 LYS cc_start: 0.7619 (mtmt) cc_final: 0.7043 (mttp) REVERT: B 307 GLN cc_start: 0.7627 (tt0) cc_final: 0.6948 (mt0) REVERT: B 321 LYS cc_start: 0.7535 (mttt) cc_final: 0.7308 (mttp) REVERT: B 340 LYS cc_start: 0.7624 (mtpp) cc_final: 0.6727 (mtmm) REVERT: B 369 LYS cc_start: 0.7840 (tttt) cc_final: 0.7137 (ttmm) REVERT: B 375 LYS cc_start: 0.7507 (ttmt) cc_final: 0.6884 (tttp) REVERT: C 317 LYS cc_start: 0.7799 (mttt) cc_final: 0.7462 (mtpt) REVERT: C 375 LYS cc_start: 0.8340 (ttmt) cc_final: 0.8063 (ttmm) REVERT: D 307 GLN cc_start: 0.8032 (tt0) cc_final: 0.7419 (mt0) REVERT: D 324 SER cc_start: 0.8411 (m) cc_final: 0.7839 (t) REVERT: D 336 GLN cc_start: 0.8298 (mt0) cc_final: 0.7992 (tt0) REVERT: D 357 LEU cc_start: 0.7872 (tp) cc_final: 0.7638 (mp) REVERT: D 369 LYS cc_start: 0.8382 (tttt) cc_final: 0.7658 (ttmm) REVERT: D 375 LYS cc_start: 0.8423 (ttmt) cc_final: 0.7868 (tttp) REVERT: E 340 LYS cc_start: 0.7841 (mttt) cc_final: 0.7560 (mtmt) REVERT: E 351 GLN cc_start: 0.7393 (mt0) cc_final: 0.6847 (mp10) REVERT: E 369 LYS cc_start: 0.7716 (mtmt) cc_final: 0.7267 (mttp) REVERT: F 307 GLN cc_start: 0.7401 (tt0) cc_final: 0.6839 (mt0) REVERT: F 311 LYS cc_start: 0.7982 (mttt) cc_final: 0.6579 (tppt) REVERT: F 324 SER cc_start: 0.8546 (m) cc_final: 0.8238 (t) REVERT: F 336 GLN cc_start: 0.7768 (mt0) cc_final: 0.7455 (tt0) REVERT: F 338 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6908 (tp30) REVERT: F 340 LYS cc_start: 0.7539 (ttpp) cc_final: 0.6834 (mmtt) REVERT: F 347 LYS cc_start: 0.7976 (mmtm) cc_final: 0.7766 (mmtm) REVERT: F 358 ASP cc_start: 0.7984 (m-30) cc_final: 0.7640 (m-30) REVERT: F 375 LYS cc_start: 0.7836 (ttmt) cc_final: 0.7334 (tttm) outliers start: 7 outliers final: 7 residues processed: 89 average time/residue: 0.6630 time to fit residues: 65.6904 Evaluate side-chains 84 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 0.0370 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3522 Z= 0.210 Angle : 0.485 4.050 4710 Z= 0.254 Chirality : 0.051 0.128 528 Planarity : 0.003 0.027 600 Dihedral : 5.444 22.034 468 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.77 % Allowed : 11.11 % Favored : 87.12 % 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 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.003 0.001 PHE B 346 TYR 0.009 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** 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 89 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.663 Fit side-chains REVERT: A 314 ASP cc_start: 0.7872 (t0) cc_final: 0.7186 (t0) REVERT: A 317 LYS cc_start: 0.7421 (mttt) cc_final: 0.7030 (mtpt) REVERT: A 340 LYS cc_start: 0.7833 (mttt) cc_final: 0.7614 (mttm) REVERT: A 351 GLN cc_start: 0.7311 (mt0) cc_final: 0.6809 (mp10) REVERT: A 369 LYS cc_start: 0.7635 (mtmt) cc_final: 0.7018 (mttp) REVERT: A 370 LYS cc_start: 0.7754 (tttp) cc_final: 0.7346 (tttt) REVERT: B 321 LYS cc_start: 0.7577 (mttt) cc_final: 0.7371 (mttp) REVERT: B 340 LYS cc_start: 0.7588 (mtpp) cc_final: 0.6783 (mtmm) REVERT: B 369 LYS cc_start: 0.7840 (tttt) cc_final: 0.7190 (ttmm) REVERT: B 375 LYS cc_start: 0.7531 (ttmt) cc_final: 0.6918 (tttp) REVERT: C 314 ASP cc_start: 0.7802 (t0) cc_final: 0.7531 (t0) REVERT: C 317 LYS cc_start: 0.7746 (mttt) cc_final: 0.7409 (mtpt) REVERT: C 375 LYS cc_start: 0.8301 (ttmt) cc_final: 0.8019 (ttmm) REVERT: D 307 GLN cc_start: 0.8078 (tt0) cc_final: 0.7407 (mt0) REVERT: D 324 SER cc_start: 0.8421 (m) cc_final: 0.7869 (t) REVERT: D 336 GLN cc_start: 0.8313 (mt0) cc_final: 0.8001 (tt0) REVERT: D 357 LEU cc_start: 0.7848 (tp) cc_final: 0.7644 (mp) REVERT: D 375 LYS cc_start: 0.8408 (ttmt) cc_final: 0.7866 (tttp) REVERT: E 340 LYS cc_start: 0.7899 (mttt) cc_final: 0.7615 (mtmt) REVERT: E 343 LYS cc_start: 0.7538 (mtpp) cc_final: 0.6965 (ttpp) REVERT: E 351 GLN cc_start: 0.7416 (mt0) cc_final: 0.6844 (mp10) REVERT: E 369 LYS cc_start: 0.7869 (mtmt) cc_final: 0.7394 (mttp) REVERT: F 307 GLN cc_start: 0.7422 (tt0) cc_final: 0.6769 (mt0) REVERT: F 311 LYS cc_start: 0.7977 (mttt) cc_final: 0.6573 (tppt) REVERT: F 324 SER cc_start: 0.8524 (m) cc_final: 0.8212 (t) REVERT: F 336 GLN cc_start: 0.7763 (mt0) cc_final: 0.7496 (mt0) REVERT: F 338 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6916 (tp30) REVERT: F 340 LYS cc_start: 0.7566 (ttpp) cc_final: 0.6833 (mmtt) REVERT: F 347 LYS cc_start: 0.7991 (mmtm) cc_final: 0.7790 (mmtm) REVERT: F 358 ASP cc_start: 0.7973 (m-30) cc_final: 0.7525 (m-30) REVERT: F 375 LYS cc_start: 0.7785 (ttmt) cc_final: 0.7310 (tttm) outliers start: 7 outliers final: 6 residues processed: 86 average time/residue: 0.6285 time to fit residues: 60.6058 Evaluate side-chains 84 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5271 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= 0.189 Angle : 0.461 3.983 4710 Z= 0.240 Chirality : 0.051 0.131 528 Planarity : 0.003 0.026 600 Dihedral : 5.131 20.753 468 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.77 % Allowed : 10.86 % Favored : 87.37 % 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 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.92 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 330 PHE 0.002 0.000 PHE B 346 TYR 0.009 0.001 TYR A 310 ARG 0.003 0.000 ARG A 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 93 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.560 Fit side-chains REVERT: A 314 ASP cc_start: 0.7914 (t0) cc_final: 0.7341 (t0) REVERT: A 317 LYS cc_start: 0.7467 (mttt) cc_final: 0.7001 (mtpt) REVERT: A 340 LYS cc_start: 0.7800 (mttt) cc_final: 0.7589 (mttm) REVERT: A 369 LYS cc_start: 0.7637 (mtmt) cc_final: 0.7029 (mttp) REVERT: A 370 LYS cc_start: 0.7829 (tttp) cc_final: 0.7427 (tttt) REVERT: B 321 LYS cc_start: 0.7626 (mttt) cc_final: 0.7425 (mttp) REVERT: B 340 LYS cc_start: 0.7610 (mtpp) cc_final: 0.6710 (mtmm) REVERT: B 369 LYS cc_start: 0.7919 (tttt) cc_final: 0.7252 (ttmm) REVERT: B 375 LYS cc_start: 0.7567 (ttmt) cc_final: 0.7000 (tttp) REVERT: C 314 ASP cc_start: 0.7805 (t0) cc_final: 0.7549 (t0) REVERT: C 317 LYS cc_start: 0.7716 (mttt) cc_final: 0.7385 (mtpt) REVERT: C 348 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.6908 (p0) REVERT: C 372 GLU cc_start: 0.7872 (tt0) cc_final: 0.7571 (tt0) REVERT: C 375 LYS cc_start: 0.8361 (ttmt) cc_final: 0.8074 (ttmm) REVERT: D 307 GLN cc_start: 0.8116 (tt0) cc_final: 0.7361 (mt0) REVERT: D 324 SER cc_start: 0.8388 (m) cc_final: 0.7816 (t) REVERT: D 336 GLN cc_start: 0.8339 (mt0) cc_final: 0.8024 (tt0) REVERT: D 357 LEU cc_start: 0.7863 (tp) cc_final: 0.7647 (mp) REVERT: D 375 LYS cc_start: 0.8394 (ttmt) cc_final: 0.7864 (tttp) REVERT: E 340 LYS cc_start: 0.7954 (mttt) cc_final: 0.7684 (mtmt) REVERT: E 343 LYS cc_start: 0.7536 (mtpp) cc_final: 0.7039 (ttpp) REVERT: E 369 LYS cc_start: 0.7877 (mtmt) cc_final: 0.7404 (mttp) REVERT: F 307 GLN cc_start: 0.7419 (tt0) cc_final: 0.6797 (mt0) REVERT: F 311 LYS cc_start: 0.7956 (mttt) cc_final: 0.6553 (tppt) REVERT: F 324 SER cc_start: 0.8479 (m) cc_final: 0.8162 (t) REVERT: F 336 GLN cc_start: 0.7754 (mt0) cc_final: 0.7494 (mt0) REVERT: F 340 LYS cc_start: 0.7599 (ttpp) cc_final: 0.6882 (mmtt) REVERT: F 347 LYS cc_start: 0.8035 (mmtm) cc_final: 0.7820 (mmtm) REVERT: F 358 ASP cc_start: 0.8000 (m-30) cc_final: 0.7553 (m-30) REVERT: F 375 LYS cc_start: 0.7775 (ttmt) cc_final: 0.7314 (tttm) outliers start: 7 outliers final: 4 residues processed: 90 average time/residue: 0.5883 time to fit residues: 59.7769 Evaluate side-chains 86 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3522 Z= 0.316 Angle : 0.493 4.005 4710 Z= 0.258 Chirality : 0.050 0.125 528 Planarity : 0.003 0.024 600 Dihedral : 5.271 20.997 468 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.53 % Allowed : 11.36 % Favored : 86.11 % 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: -1.27 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.004 0.001 PHE E 346 TYR 0.006 0.001 TYR A 310 ARG 0.002 0.000 ARG E 349 *********************** 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 90 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7796 (t0) cc_final: 0.7103 (t0) REVERT: A 317 LYS cc_start: 0.7479 (mttt) cc_final: 0.7082 (mtpt) REVERT: A 340 LYS cc_start: 0.7849 (mttt) cc_final: 0.7624 (mttm) REVERT: A 369 LYS cc_start: 0.7656 (mtmt) cc_final: 0.7055 (mttp) REVERT: A 370 LYS cc_start: 0.7878 (tttp) cc_final: 0.7477 (tttp) REVERT: B 375 LYS cc_start: 0.7600 (ttmt) cc_final: 0.7012 (tttp) REVERT: C 314 ASP cc_start: 0.7879 (t0) cc_final: 0.7665 (t70) REVERT: C 317 LYS cc_start: 0.7833 (mttt) cc_final: 0.7485 (mtpt) REVERT: C 375 LYS cc_start: 0.8399 (ttmt) cc_final: 0.8109 (ttmm) REVERT: D 307 GLN cc_start: 0.8062 (tt0) cc_final: 0.7366 (mt0) REVERT: D 324 SER cc_start: 0.8376 (m) cc_final: 0.7803 (t) REVERT: D 336 GLN cc_start: 0.8337 (mt0) cc_final: 0.8004 (tt0) REVERT: D 357 LEU cc_start: 0.7844 (tp) cc_final: 0.7632 (mp) REVERT: D 369 LYS cc_start: 0.8331 (tttt) cc_final: 0.7800 (tttm) REVERT: D 375 LYS cc_start: 0.8430 (ttmt) cc_final: 0.7883 (tttp) REVERT: E 340 LYS cc_start: 0.7952 (mttt) cc_final: 0.7669 (mtmt) REVERT: E 343 LYS cc_start: 0.7532 (mtpp) cc_final: 0.7009 (ttpp) REVERT: E 369 LYS cc_start: 0.7831 (mtmt) cc_final: 0.7328 (mttp) REVERT: F 307 GLN cc_start: 0.7480 (tt0) cc_final: 0.6805 (mt0) REVERT: F 311 LYS cc_start: 0.7986 (mttt) cc_final: 0.7674 (mtpt) REVERT: F 324 SER cc_start: 0.8530 (m) cc_final: 0.8198 (t) REVERT: F 336 GLN cc_start: 0.7893 (mt0) cc_final: 0.7668 (mt0) REVERT: F 340 LYS cc_start: 0.7592 (ttpp) cc_final: 0.6878 (mmtt) REVERT: F 347 LYS cc_start: 0.8056 (mmtm) cc_final: 0.7826 (mmtm) REVERT: F 358 ASP cc_start: 0.8019 (m-30) cc_final: 0.7614 (m-30) REVERT: F 375 LYS cc_start: 0.7784 (ttmt) cc_final: 0.7316 (tttm) outliers start: 10 outliers final: 8 residues processed: 86 average time/residue: 0.6064 time to fit residues: 58.4900 Evaluate side-chains 84 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 0.0870 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3522 Z= 0.144 Angle : 0.449 3.975 4710 Z= 0.231 Chirality : 0.051 0.130 528 Planarity : 0.003 0.027 600 Dihedral : 4.902 19.964 468 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.52 % Allowed : 12.37 % Favored : 86.11 % 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 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 374 PHE 0.001 0.000 PHE B 378 TYR 0.007 0.001 TYR C 310 ARG 0.001 0.000 ARG A 349 *********************** 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 88 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.632 Fit side-chains REVERT: A 314 ASP cc_start: 0.7802 (t0) cc_final: 0.7166 (t0) REVERT: A 317 LYS cc_start: 0.7472 (mttt) cc_final: 0.7084 (mtpt) REVERT: A 340 LYS cc_start: 0.7746 (mttt) cc_final: 0.7517 (mttm) REVERT: A 369 LYS cc_start: 0.7642 (mtmt) cc_final: 0.7045 (mttp) REVERT: A 370 LYS cc_start: 0.7889 (tttp) cc_final: 0.7512 (tttp) REVERT: B 369 LYS cc_start: 0.7944 (tttt) cc_final: 0.7242 (ttmm) REVERT: B 375 LYS cc_start: 0.7585 (ttmt) cc_final: 0.7055 (tttm) REVERT: C 317 LYS cc_start: 0.7725 (mttt) cc_final: 0.7395 (mtpt) REVERT: C 348 ASP cc_start: 0.7269 (p0) cc_final: 0.6586 (p0) REVERT: C 372 GLU cc_start: 0.7918 (tt0) cc_final: 0.7685 (tt0) REVERT: C 375 LYS cc_start: 0.8376 (ttmt) cc_final: 0.8070 (ttmm) REVERT: D 307 GLN cc_start: 0.8054 (tt0) cc_final: 0.7316 (mt0) REVERT: D 324 SER cc_start: 0.8418 (m) cc_final: 0.7844 (t) REVERT: D 336 GLN cc_start: 0.8322 (mt0) cc_final: 0.7978 (tt0) REVERT: D 375 LYS cc_start: 0.8391 (ttmt) cc_final: 0.7879 (tttp) REVERT: E 340 LYS cc_start: 0.7983 (mttt) cc_final: 0.7725 (mtmt) REVERT: E 343 LYS cc_start: 0.7577 (mtpp) cc_final: 0.7102 (ttpp) REVERT: E 369 LYS cc_start: 0.7915 (mtmt) cc_final: 0.7401 (mttp) REVERT: E 375 LYS cc_start: 0.7732 (ttmt) cc_final: 0.7082 (ttmm) REVERT: F 307 GLN cc_start: 0.7421 (tt0) cc_final: 0.6741 (mt0) REVERT: F 311 LYS cc_start: 0.8000 (mttt) cc_final: 0.7681 (mtpt) REVERT: F 324 SER cc_start: 0.8474 (m) cc_final: 0.8151 (t) REVERT: F 336 GLN cc_start: 0.7878 (mt0) cc_final: 0.7657 (mt0) REVERT: F 340 LYS cc_start: 0.7630 (ttpp) cc_final: 0.6924 (mmtt) REVERT: F 347 LYS cc_start: 0.8067 (mmtm) cc_final: 0.7854 (mmtm) REVERT: F 358 ASP cc_start: 0.8030 (m-30) cc_final: 0.7565 (m-30) REVERT: F 375 LYS cc_start: 0.7813 (ttmt) cc_final: 0.7343 (tttm) outliers start: 6 outliers final: 6 residues processed: 86 average time/residue: 0.5765 time to fit residues: 56.2794 Evaluate side-chains 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3522 Z= 0.228 Angle : 0.467 3.900 4710 Z= 0.241 Chirality : 0.050 0.123 528 Planarity : 0.003 0.026 600 Dihedral : 4.932 19.269 468 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.52 % Allowed : 12.63 % Favored : 85.86 % 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: -1.27 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.003 0.001 PHE E 346 TYR 0.005 0.001 TYR A 310 ARG 0.001 0.000 ARG E 349 *********************** 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 83 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7752 (t0) cc_final: 0.7149 (t0) REVERT: A 317 LYS cc_start: 0.7495 (mttt) cc_final: 0.7089 (mtpt) REVERT: A 340 LYS cc_start: 0.7774 (mttt) cc_final: 0.7543 (mttm) REVERT: A 369 LYS cc_start: 0.7660 (mtmt) cc_final: 0.7063 (mttp) REVERT: A 370 LYS cc_start: 0.7946 (tttp) cc_final: 0.7546 (tttp) REVERT: B 375 LYS cc_start: 0.7608 (ttmt) cc_final: 0.7079 (tttm) REVERT: C 317 LYS cc_start: 0.7785 (mttt) cc_final: 0.7461 (mtpt) REVERT: C 372 GLU cc_start: 0.8015 (tt0) cc_final: 0.7711 (tt0) REVERT: C 375 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8105 (ttmm) REVERT: D 307 GLN cc_start: 0.8087 (tt0) cc_final: 0.7308 (mt0) REVERT: D 324 SER cc_start: 0.8406 (m) cc_final: 0.7829 (t) REVERT: D 336 GLN cc_start: 0.8365 (mt0) cc_final: 0.8019 (tt0) REVERT: D 375 LYS cc_start: 0.8437 (ttmt) cc_final: 0.7903 (tttp) REVERT: E 340 LYS cc_start: 0.7957 (mttt) cc_final: 0.7701 (mtmt) REVERT: E 343 LYS cc_start: 0.7565 (mtpp) cc_final: 0.7078 (ttpp) REVERT: E 369 LYS cc_start: 0.7898 (mtmt) cc_final: 0.7391 (mttp) REVERT: E 375 LYS cc_start: 0.7716 (ttmt) cc_final: 0.7035 (ttmm) REVERT: F 307 GLN cc_start: 0.7421 (tt0) cc_final: 0.6716 (mt0) REVERT: F 311 LYS cc_start: 0.8020 (mttt) cc_final: 0.7696 (mtpt) REVERT: F 324 SER cc_start: 0.8495 (m) cc_final: 0.8169 (t) REVERT: F 336 GLN cc_start: 0.7878 (mt0) cc_final: 0.7658 (mt0) REVERT: F 340 LYS cc_start: 0.7628 (ttpp) cc_final: 0.6914 (mmtt) REVERT: F 347 LYS cc_start: 0.8070 (mmtm) cc_final: 0.7855 (mmtm) REVERT: F 358 ASP cc_start: 0.7983 (m-30) cc_final: 0.7498 (m-30) REVERT: F 375 LYS cc_start: 0.7799 (ttmt) cc_final: 0.7337 (tttm) outliers start: 6 outliers final: 6 residues processed: 81 average time/residue: 0.6078 time to fit residues: 55.4246 Evaluate side-chains 83 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.5772 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= 0.134 Angle : 0.450 4.125 4710 Z= 0.229 Chirality : 0.051 0.128 528 Planarity : 0.003 0.027 600 Dihedral : 4.668 18.529 468 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.52 % Allowed : 13.13 % Favored : 85.35 % 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 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 362 PHE 0.002 0.000 PHE F 346 TYR 0.006 0.001 TYR C 310 ARG 0.002 0.000 ARG A 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 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.677 Fit side-chains REVERT: A 314 ASP cc_start: 0.7737 (t0) cc_final: 0.7132 (t0) REVERT: A 317 LYS cc_start: 0.7517 (mttt) cc_final: 0.7114 (mtpt) REVERT: A 340 LYS cc_start: 0.7674 (mttt) cc_final: 0.7443 (mttm) REVERT: A 343 LYS cc_start: 0.7847 (mtpp) cc_final: 0.7227 (ttpp) REVERT: A 369 LYS cc_start: 0.7627 (mtmt) cc_final: 0.7030 (mttp) REVERT: A 370 LYS cc_start: 0.7966 (tttp) cc_final: 0.7566 (tttp) REVERT: B 369 LYS cc_start: 0.7974 (tttt) cc_final: 0.7248 (ttmm) REVERT: B 375 LYS cc_start: 0.7627 (ttmt) cc_final: 0.7086 (tttm) REVERT: C 317 LYS cc_start: 0.7716 (mttt) cc_final: 0.7383 (mtpt) REVERT: C 348 ASP cc_start: 0.7170 (p0) cc_final: 0.6269 (p0) REVERT: C 372 GLU cc_start: 0.7987 (tt0) cc_final: 0.7643 (tt0) REVERT: C 375 LYS cc_start: 0.8389 (ttmt) cc_final: 0.8067 (ttmm) REVERT: D 307 GLN cc_start: 0.8039 (tt0) cc_final: 0.7298 (mt0) REVERT: D 324 SER cc_start: 0.8376 (m) cc_final: 0.7796 (t) REVERT: D 336 GLN cc_start: 0.8331 (mt0) cc_final: 0.7973 (tt0) REVERT: D 375 LYS cc_start: 0.8391 (ttmt) cc_final: 0.7883 (tttp) REVERT: E 340 LYS cc_start: 0.8000 (mttt) cc_final: 0.7756 (mtmt) REVERT: E 343 LYS cc_start: 0.7566 (mtpp) cc_final: 0.7149 (ttpp) REVERT: E 369 LYS cc_start: 0.7919 (mtmt) cc_final: 0.7402 (mttp) REVERT: E 375 LYS cc_start: 0.7686 (ttmt) cc_final: 0.7002 (ttmm) REVERT: F 307 GLN cc_start: 0.7416 (tt0) cc_final: 0.6705 (mt0) REVERT: F 311 LYS cc_start: 0.7988 (mttt) cc_final: 0.7672 (mtpt) REVERT: F 324 SER cc_start: 0.8469 (m) cc_final: 0.8140 (t) REVERT: F 336 GLN cc_start: 0.7875 (mt0) cc_final: 0.7655 (mt0) REVERT: F 340 LYS cc_start: 0.7644 (ttpp) cc_final: 0.6933 (mmtt) REVERT: F 347 LYS cc_start: 0.8086 (mmtm) cc_final: 0.7879 (mmtm) REVERT: F 358 ASP cc_start: 0.8013 (m-30) cc_final: 0.7538 (m-30) REVERT: F 375 LYS cc_start: 0.7787 (ttmt) cc_final: 0.7315 (tttm) outliers start: 6 outliers final: 6 residues processed: 84 average time/residue: 0.5576 time to fit residues: 53.2181 Evaluate side-chains 83 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.133307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.122657 restraints weight = 13797.976| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.64 r_work: 0.3789 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.5841 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= 0.157 Angle : 0.448 4.535 4710 Z= 0.231 Chirality : 0.051 0.123 528 Planarity : 0.003 0.027 600 Dihedral : 4.599 17.776 468 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.52 % Allowed : 13.13 % Favored : 85.35 % 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 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 330 PHE 0.002 0.000 PHE C 346 TYR 0.005 0.001 TYR C 310 ARG 0.001 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3037.62 seconds wall clock time: 53 minutes 46.16 seconds (3226.16 seconds total)