Starting phenix.real_space_refine on Mon Mar 11 05:00:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8d_18251/03_2024/8q8d_18251.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8d_18251/03_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_18251/03_2024/8q8d_18251.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8d_18251/03_2024/8q8d_18251.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8d_18251/03_2024/8q8d_18251.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8d_18251/03_2024/8q8d_18251.pdb" } 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-5265/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: 3.68, per 1000 atoms: 0.52 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: 5.49 Conformation dependent library (CDL) restraints added in 740.5 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: 0.69 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: 2.28 Time building geometry restraints manager: 5.67 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 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.545 1.850 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.548 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.556 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.585 1.850 ... (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 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: 4.900 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: 11.860 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 26.570 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.800 ------------------------------------------------------------------------------- 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 : 0.692 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: 0.5896 time to fit residues: 87.6785 Evaluate side-chains 90 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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: 1.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3522 Z= 0.281 Angle : 0.602 4.003 4710 Z= 0.319 Chirality : 0.050 0.159 528 Planarity : 0.004 0.058 600 Dihedral : 6.575 23.167 468 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.26 % Allowed : 7.58 % Favored : 91.16 % 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: -1.51 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.006 0.001 PHE E 346 TYR 0.012 0.002 TYR C 310 ARG 0.001 0.000 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 101 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.6941 (mttt) cc_final: 0.6657 (mtpt) REVERT: A 338 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7484 (mt-10) REVERT: A 340 LYS cc_start: 0.7641 (mttt) cc_final: 0.7423 (mttm) REVERT: A 348 ASP cc_start: 0.7460 (t0) cc_final: 0.7252 (t70) REVERT: A 349 ARG cc_start: 0.7202 (mtm180) cc_final: 0.6988 (mtm180) REVERT: A 351 GLN cc_start: 0.7170 (mt0) cc_final: 0.6676 (mp10) REVERT: A 369 LYS cc_start: 0.7428 (mtmt) cc_final: 0.6958 (mttp) REVERT: B 307 GLN cc_start: 0.7143 (tt0) cc_final: 0.6674 (mt0) REVERT: B 321 LYS cc_start: 0.7357 (mttt) cc_final: 0.7148 (mttp) REVERT: B 336 GLN cc_start: 0.7820 (mt0) cc_final: 0.7580 (mt0) REVERT: B 340 LYS cc_start: 0.7586 (mtpp) cc_final: 0.6658 (mtmm) REVERT: B 369 LYS cc_start: 0.7660 (tttt) cc_final: 0.7061 (ttmm) REVERT: B 375 LYS cc_start: 0.7210 (ttmt) cc_final: 0.6530 (tttm) REVERT: C 314 ASP cc_start: 0.7758 (t0) cc_final: 0.7457 (t0) REVERT: C 317 LYS cc_start: 0.7696 (mttt) cc_final: 0.7381 (mtpt) REVERT: C 340 LYS cc_start: 0.8610 (mttt) cc_final: 0.8319 (mmmm) REVERT: C 351 GLN cc_start: 0.7747 (mt0) cc_final: 0.7372 (mp10) REVERT: C 375 LYS cc_start: 0.8041 (ttmt) cc_final: 0.7797 (ttmt) REVERT: D 307 GLN cc_start: 0.7953 (tt0) cc_final: 0.7428 (mt0) REVERT: D 324 SER cc_start: 0.8238 (m) cc_final: 0.7878 (t) REVERT: D 336 GLN cc_start: 0.8245 (mt0) cc_final: 0.7935 (tt0) REVERT: D 347 LYS cc_start: 0.8322 (mptt) cc_final: 0.6659 (mtmm) REVERT: D 357 LEU cc_start: 0.7812 (tp) cc_final: 0.7600 (mp) REVERT: D 369 LYS cc_start: 0.8359 (tttt) cc_final: 0.7647 (ttmm) REVERT: D 375 LYS cc_start: 0.8378 (ttmt) cc_final: 0.7804 (tttp) REVERT: E 351 GLN cc_start: 0.7168 (mt0) cc_final: 0.6652 (mp10) REVERT: E 369 LYS cc_start: 0.7577 (mtmt) cc_final: 0.7105 (mttp) REVERT: E 372 GLU cc_start: 0.8238 (tt0) cc_final: 0.7991 (tt0) REVERT: F 307 GLN cc_start: 0.7220 (tt0) cc_final: 0.6639 (mt0) REVERT: F 311 LYS cc_start: 0.7883 (mttt) cc_final: 0.6555 (tppt) REVERT: F 336 GLN cc_start: 0.7633 (mt0) cc_final: 0.7302 (tt0) REVERT: F 340 LYS cc_start: 0.7637 (ttpp) cc_final: 0.6896 (mmpt) REVERT: F 358 ASP cc_start: 0.7809 (m-30) cc_final: 0.7409 (m-30) REVERT: F 375 LYS cc_start: 0.7661 (ttmt) cc_final: 0.7157 (tttm) outliers start: 5 outliers final: 5 residues processed: 98 average time/residue: 0.6799 time to fit residues: 73.4305 Evaluate side-chains 96 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 358 ASP 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: 5.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4499 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= 0.325 Angle : 0.557 4.084 4710 Z= 0.295 Chirality : 0.051 0.130 528 Planarity : 0.004 0.028 600 Dihedral : 5.794 23.784 468 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.53 % Allowed : 8.08 % 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: -1.34 (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 0.004 0.001 HIS A 330 PHE 0.006 0.001 PHE A 378 TYR 0.009 0.002 TYR C 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 96 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.571 Fit side-chains REVERT: A 314 ASP cc_start: 0.7610 (t0) cc_final: 0.7391 (t0) REVERT: A 317 LYS cc_start: 0.7243 (mttt) cc_final: 0.6873 (mtpt) REVERT: A 340 LYS cc_start: 0.7883 (mttt) cc_final: 0.7633 (mttm) REVERT: A 351 GLN cc_start: 0.7175 (mt0) cc_final: 0.6721 (mp10) REVERT: A 369 LYS cc_start: 0.7562 (mtmt) cc_final: 0.7032 (mttp) REVERT: B 307 GLN cc_start: 0.7547 (tt0) cc_final: 0.6879 (mt0) REVERT: B 321 LYS cc_start: 0.7517 (mttt) cc_final: 0.7315 (mttp) REVERT: B 340 LYS cc_start: 0.7642 (mtpp) cc_final: 0.6718 (mtmm) REVERT: B 342 GLU cc_start: 0.5978 (mp0) cc_final: 0.5735 (mp0) REVERT: B 369 LYS cc_start: 0.7721 (tttt) cc_final: 0.7033 (ttmm) REVERT: B 375 LYS cc_start: 0.7391 (ttmt) cc_final: 0.6761 (tttp) REVERT: C 314 ASP cc_start: 0.7750 (t0) cc_final: 0.7357 (t0) REVERT: C 317 LYS cc_start: 0.7808 (mttt) cc_final: 0.7484 (mtpt) REVERT: C 338 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7840 (mt-10) REVERT: C 340 LYS cc_start: 0.8629 (mttt) cc_final: 0.8429 (mttm) REVERT: C 375 LYS cc_start: 0.8293 (ttmt) cc_final: 0.8039 (ttmm) REVERT: D 307 GLN cc_start: 0.8051 (tt0) cc_final: 0.7425 (mt0) REVERT: D 324 SER cc_start: 0.8272 (m) cc_final: 0.7727 (t) REVERT: D 336 GLN cc_start: 0.8294 (mt0) cc_final: 0.8004 (tt0) REVERT: D 357 LEU cc_start: 0.7811 (tp) cc_final: 0.7578 (mp) REVERT: D 369 LYS cc_start: 0.8398 (tttt) cc_final: 0.7676 (ttmm) REVERT: D 375 LYS cc_start: 0.8441 (ttmt) cc_final: 0.7884 (tttp) REVERT: E 351 GLN cc_start: 0.7351 (mt0) cc_final: 0.6840 (mp10) REVERT: E 369 LYS cc_start: 0.7537 (mtmt) cc_final: 0.7040 (mttp) REVERT: F 307 GLN cc_start: 0.7443 (tt0) cc_final: 0.6852 (mt0) REVERT: F 311 LYS cc_start: 0.7933 (mttt) cc_final: 0.7676 (mtpt) REVERT: F 324 SER cc_start: 0.8591 (m) cc_final: 0.8252 (t) REVERT: F 336 GLN cc_start: 0.7727 (mt0) cc_final: 0.7492 (mt0) REVERT: F 340 LYS cc_start: 0.7539 (ttpp) cc_final: 0.6823 (mmtt) REVERT: F 358 ASP cc_start: 0.7994 (m-30) cc_final: 0.7628 (m-30) REVERT: F 375 LYS cc_start: 0.7783 (ttmt) cc_final: 0.7290 (tttm) outliers start: 10 outliers final: 6 residues processed: 89 average time/residue: 0.6555 time to fit residues: 65.1951 Evaluate side-chains 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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: 8.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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: 0.7580 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3522 Z= 0.263 Angle : 0.501 5.040 4710 Z= 0.262 Chirality : 0.050 0.121 528 Planarity : 0.003 0.024 600 Dihedral : 5.508 22.578 468 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.77 % Allowed : 9.34 % Favored : 88.89 % 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 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.004 0.001 PHE B 346 TYR 0.009 0.002 TYR C 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 88 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7758 (t0) cc_final: 0.7418 (t0) REVERT: A 317 LYS cc_start: 0.7287 (mttt) cc_final: 0.6826 (mtpt) REVERT: A 340 LYS cc_start: 0.7866 (mttt) cc_final: 0.7649 (mttm) REVERT: A 351 GLN cc_start: 0.7182 (mt0) cc_final: 0.6692 (mp10) REVERT: A 369 LYS cc_start: 0.7593 (mtmt) cc_final: 0.7003 (mttp) REVERT: B 340 LYS cc_start: 0.7567 (mtpp) cc_final: 0.6785 (mtmm) REVERT: B 375 LYS cc_start: 0.7405 (ttmt) cc_final: 0.6802 (tttp) REVERT: C 314 ASP cc_start: 0.7692 (t0) cc_final: 0.7217 (t0) REVERT: C 317 LYS cc_start: 0.7831 (mttt) cc_final: 0.7483 (mtpt) REVERT: C 338 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7815 (mt-10) REVERT: C 340 LYS cc_start: 0.8616 (mttt) cc_final: 0.8410 (mttm) REVERT: C 375 LYS cc_start: 0.8404 (ttmt) cc_final: 0.8146 (ttmm) REVERT: D 307 GLN cc_start: 0.8116 (tt0) cc_final: 0.7431 (mt0) REVERT: D 324 SER cc_start: 0.8439 (m) cc_final: 0.7880 (t) REVERT: D 336 GLN cc_start: 0.8290 (mt0) cc_final: 0.8004 (tt0) REVERT: D 369 LYS cc_start: 0.8356 (tttt) cc_final: 0.7658 (ttmm) REVERT: D 375 LYS cc_start: 0.8415 (ttmt) cc_final: 0.7884 (tttp) REVERT: E 340 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7595 (mtmt) REVERT: E 351 GLN cc_start: 0.7265 (mt0) cc_final: 0.6743 (mp10) REVERT: E 369 LYS cc_start: 0.7587 (mtmt) cc_final: 0.7111 (mttp) REVERT: F 307 GLN cc_start: 0.7462 (tt0) cc_final: 0.6834 (mt0) REVERT: F 311 LYS cc_start: 0.7983 (mttt) cc_final: 0.7697 (mtpt) REVERT: F 324 SER cc_start: 0.8527 (m) cc_final: 0.8249 (t) REVERT: F 336 GLN cc_start: 0.7791 (mt0) cc_final: 0.7583 (mt0) REVERT: F 340 LYS cc_start: 0.7554 (ttpp) cc_final: 0.6843 (mmtt) REVERT: F 358 ASP cc_start: 0.8000 (m-30) cc_final: 0.7598 (m-30) REVERT: F 375 LYS cc_start: 0.7794 (ttmt) cc_final: 0.7331 (tttm) outliers start: 7 outliers final: 6 residues processed: 84 average time/residue: 0.6638 time to fit residues: 62.2313 Evaluate side-chains 81 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 0.0770 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- 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: 0.7592 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 : 0.004 0.029 3522 Z= 0.240 Angle : 0.475 4.629 4710 Z= 0.247 Chirality : 0.050 0.130 528 Planarity : 0.003 0.023 600 Dihedral : 5.234 21.255 468 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.27 % Allowed : 9.09 % Favored : 88.64 % 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 (0.35), 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 0.002 0.001 HIS C 362 PHE 0.003 0.001 PHE C 378 TYR 0.006 0.001 TYR C 310 ARG 0.002 0.000 ARG A 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 91 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7750 (t0) cc_final: 0.7447 (t0) REVERT: A 317 LYS cc_start: 0.7290 (mttt) cc_final: 0.6819 (mtpt) REVERT: A 340 LYS cc_start: 0.7861 (mttt) cc_final: 0.7627 (mttm) REVERT: A 369 LYS cc_start: 0.7649 (mtmt) cc_final: 0.7064 (mttp) REVERT: A 370 LYS cc_start: 0.7706 (tttp) cc_final: 0.7251 (tttt) REVERT: B 340 LYS cc_start: 0.7700 (mtpp) cc_final: 0.6758 (mtmm) REVERT: B 375 LYS cc_start: 0.7484 (ttmt) cc_final: 0.6948 (tttm) REVERT: C 314 ASP cc_start: 0.7682 (t0) cc_final: 0.7217 (t0) REVERT: C 317 LYS cc_start: 0.7839 (mttt) cc_final: 0.7496 (mtpt) REVERT: C 338 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7767 (mt-10) REVERT: C 340 LYS cc_start: 0.8571 (mttt) cc_final: 0.8353 (mttm) REVERT: C 375 LYS cc_start: 0.8418 (ttmt) cc_final: 0.8148 (ttmm) REVERT: D 307 GLN cc_start: 0.8129 (tt0) cc_final: 0.7349 (mt0) REVERT: D 324 SER cc_start: 0.8432 (m) cc_final: 0.7847 (t) REVERT: D 336 GLN cc_start: 0.8301 (mt0) cc_final: 0.8006 (tt0) REVERT: D 369 LYS cc_start: 0.8363 (tttt) cc_final: 0.7839 (tttm) REVERT: D 375 LYS cc_start: 0.8457 (ttmt) cc_final: 0.7928 (tttp) REVERT: E 369 LYS cc_start: 0.7649 (mtmt) cc_final: 0.7141 (mttp) REVERT: F 307 GLN cc_start: 0.7444 (tt0) cc_final: 0.6811 (mt0) REVERT: F 311 LYS cc_start: 0.7970 (mttt) cc_final: 0.7667 (mtpt) REVERT: F 324 SER cc_start: 0.8545 (m) cc_final: 0.8255 (t) REVERT: F 340 LYS cc_start: 0.7599 (ttpp) cc_final: 0.6918 (mmtt) REVERT: F 358 ASP cc_start: 0.8033 (m-30) cc_final: 0.7656 (m-30) REVERT: F 375 LYS cc_start: 0.7762 (ttmt) cc_final: 0.7266 (tttm) outliers start: 9 outliers final: 7 residues processed: 86 average time/residue: 0.6361 time to fit residues: 61.3937 Evaluate side-chains 84 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 0.0970 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 overall best weight: 3.1984 ------------------------------------------------------------------------------- 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: 0.7614 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3522 Z= 0.308 Angle : 0.500 5.395 4710 Z= 0.260 Chirality : 0.049 0.123 528 Planarity : 0.003 0.024 600 Dihedral : 5.305 21.225 468 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.27 % Allowed : 10.10 % 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: -1.28 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.003 0.001 PHE A 346 TYR 0.005 0.001 TYR C 310 ARG 0.002 0.000 ARG E 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 82 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7719 (t0) cc_final: 0.7499 (t0) REVERT: A 317 LYS cc_start: 0.7334 (mttt) cc_final: 0.6847 (mtpt) REVERT: A 340 LYS cc_start: 0.7837 (mttt) cc_final: 0.7596 (mttm) REVERT: A 369 LYS cc_start: 0.7609 (mtmt) cc_final: 0.7034 (mttp) REVERT: B 340 LYS cc_start: 0.7695 (mtpp) cc_final: 0.6773 (mtmm) REVERT: B 375 LYS cc_start: 0.7505 (ttmt) cc_final: 0.6991 (tttm) REVERT: C 314 ASP cc_start: 0.7666 (t0) cc_final: 0.7181 (t0) REVERT: C 317 LYS cc_start: 0.7853 (mttt) cc_final: 0.7495 (mtpt) REVERT: C 338 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7781 (mt-10) REVERT: C 375 LYS cc_start: 0.8427 (ttmt) cc_final: 0.8152 (ttmm) REVERT: D 307 GLN cc_start: 0.8053 (tt0) cc_final: 0.7313 (mt0) REVERT: D 324 SER cc_start: 0.8455 (m) cc_final: 0.7862 (t) REVERT: D 336 GLN cc_start: 0.8311 (mt0) cc_final: 0.7988 (tt0) REVERT: D 369 LYS cc_start: 0.8359 (tttt) cc_final: 0.7868 (tttm) REVERT: D 375 LYS cc_start: 0.8484 (ttmt) cc_final: 0.7946 (tttp) REVERT: E 369 LYS cc_start: 0.7622 (mtmt) cc_final: 0.7131 (mttp) REVERT: E 375 LYS cc_start: 0.7763 (ttmt) cc_final: 0.7108 (ttmm) REVERT: F 307 GLN cc_start: 0.7433 (tt0) cc_final: 0.6707 (mt0) REVERT: F 311 LYS cc_start: 0.7999 (mttt) cc_final: 0.7675 (mtpt) REVERT: F 324 SER cc_start: 0.8545 (m) cc_final: 0.8253 (t) REVERT: F 340 LYS cc_start: 0.7567 (ttpp) cc_final: 0.6784 (mmtt) REVERT: F 358 ASP cc_start: 0.8057 (m-30) cc_final: 0.7647 (m-30) REVERT: F 375 LYS cc_start: 0.7803 (ttmt) cc_final: 0.7297 (tttm) outliers start: 9 outliers final: 8 residues processed: 78 average time/residue: 0.6248 time to fit residues: 54.6949 Evaluate side-chains 80 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- 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: 5.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN E 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.5790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 3522 Z= 0.472 Angle : 0.557 5.436 4710 Z= 0.292 Chirality : 0.049 0.127 528 Planarity : 0.004 0.023 600 Dihedral : 5.557 21.737 468 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.27 % Allowed : 11.62 % 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: -1.48 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.007 0.002 PHE E 346 TYR 0.005 0.001 TYR F 310 ARG 0.003 0.001 ARG E 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 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.625 Fit side-chains REVERT: A 314 ASP cc_start: 0.7623 (t0) cc_final: 0.7412 (t0) REVERT: A 317 LYS cc_start: 0.7390 (mttt) cc_final: 0.6964 (mtpt) REVERT: A 340 LYS cc_start: 0.7868 (mttt) cc_final: 0.7610 (mttm) REVERT: A 369 LYS cc_start: 0.7599 (mtmt) cc_final: 0.7046 (mttp) REVERT: A 370 LYS cc_start: 0.7901 (tttp) cc_final: 0.7657 (tttp) REVERT: B 340 LYS cc_start: 0.7692 (mtpp) cc_final: 0.6682 (mttm) REVERT: B 369 LYS cc_start: 0.7801 (tttt) cc_final: 0.7101 (ttmm) REVERT: B 375 LYS cc_start: 0.7612 (ttmt) cc_final: 0.7110 (tttm) REVERT: C 314 ASP cc_start: 0.7626 (t0) cc_final: 0.7047 (t0) REVERT: C 317 LYS cc_start: 0.7858 (mttt) cc_final: 0.7492 (mtpt) REVERT: C 338 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7705 (mt-10) REVERT: C 375 LYS cc_start: 0.8480 (ttmt) cc_final: 0.8186 (ttmm) REVERT: D 307 GLN cc_start: 0.8062 (tt0) cc_final: 0.7300 (mt0) REVERT: D 324 SER cc_start: 0.8447 (m) cc_final: 0.7890 (t) REVERT: D 336 GLN cc_start: 0.8329 (mt0) cc_final: 0.8046 (tt0) REVERT: D 369 LYS cc_start: 0.8389 (tttt) cc_final: 0.7908 (tttm) REVERT: D 375 LYS cc_start: 0.8497 (ttmt) cc_final: 0.7918 (tttp) REVERT: E 369 LYS cc_start: 0.7768 (mtmt) cc_final: 0.7268 (mttp) REVERT: E 375 LYS cc_start: 0.7831 (ttmt) cc_final: 0.7200 (ttmm) REVERT: F 311 LYS cc_start: 0.8030 (mttt) cc_final: 0.7697 (mtpt) REVERT: F 324 SER cc_start: 0.8551 (m) cc_final: 0.8280 (t) REVERT: F 340 LYS cc_start: 0.7592 (ttpp) cc_final: 0.6831 (mmtt) REVERT: F 347 LYS cc_start: 0.8035 (mmtm) cc_final: 0.7806 (mmtm) REVERT: F 358 ASP cc_start: 0.8078 (m-30) cc_final: 0.7614 (m-30) REVERT: F 375 LYS cc_start: 0.7828 (ttmt) cc_final: 0.7353 (tttm) outliers start: 9 outliers final: 9 residues processed: 81 average time/residue: 0.6209 time to fit residues: 56.5141 Evaluate side-chains 84 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 C residue 348 ASP 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: 2.9990 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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: 0.7623 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3522 Z= 0.212 Angle : 0.469 5.515 4710 Z= 0.242 Chirality : 0.050 0.121 528 Planarity : 0.003 0.025 600 Dihedral : 5.215 21.127 468 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 2.02 % Allowed : 11.87 % 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: -1.47 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 374 PHE 0.002 0.000 PHE C 378 TYR 0.005 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 83 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7572 (t0) cc_final: 0.7353 (t0) REVERT: A 317 LYS cc_start: 0.7353 (mttt) cc_final: 0.6933 (mtpt) REVERT: A 340 LYS cc_start: 0.7813 (mttt) cc_final: 0.7542 (mttm) REVERT: A 369 LYS cc_start: 0.7588 (mtmt) cc_final: 0.7023 (mttp) REVERT: A 370 LYS cc_start: 0.7829 (tttp) cc_final: 0.7604 (tttp) REVERT: B 340 LYS cc_start: 0.7670 (mtpp) cc_final: 0.6656 (mttm) REVERT: B 375 LYS cc_start: 0.7600 (ttmt) cc_final: 0.7078 (tttm) REVERT: C 314 ASP cc_start: 0.7612 (t0) cc_final: 0.7001 (t0) REVERT: C 317 LYS cc_start: 0.7826 (mttt) cc_final: 0.7468 (mtpt) REVERT: C 338 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7744 (mt-10) REVERT: C 375 LYS cc_start: 0.8414 (ttmt) cc_final: 0.8139 (ttmm) REVERT: D 307 GLN cc_start: 0.8060 (tt0) cc_final: 0.7298 (mt0) REVERT: D 324 SER cc_start: 0.8446 (m) cc_final: 0.7870 (t) REVERT: D 336 GLN cc_start: 0.8323 (mt0) cc_final: 0.8039 (tt0) REVERT: D 369 LYS cc_start: 0.8356 (tttt) cc_final: 0.7883 (tttm) REVERT: D 375 LYS cc_start: 0.8471 (ttmt) cc_final: 0.7926 (tttp) REVERT: E 369 LYS cc_start: 0.7690 (mtmt) cc_final: 0.7220 (mttp) REVERT: E 375 LYS cc_start: 0.7694 (ttmt) cc_final: 0.7031 (ttmm) REVERT: F 311 LYS cc_start: 0.8054 (mttt) cc_final: 0.7717 (mtpt) REVERT: F 324 SER cc_start: 0.8518 (m) cc_final: 0.8267 (t) REVERT: F 340 LYS cc_start: 0.7658 (ttpp) cc_final: 0.6909 (mmtt) REVERT: F 347 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7806 (mmtm) REVERT: F 358 ASP cc_start: 0.8085 (m-30) cc_final: 0.7616 (m-30) REVERT: F 375 LYS cc_start: 0.7790 (ttmt) cc_final: 0.7288 (tttm) outliers start: 8 outliers final: 8 residues processed: 80 average time/residue: 0.6172 time to fit residues: 55.4165 Evaluate side-chains 83 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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: 0.7626 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3522 Z= 0.255 Angle : 0.461 5.424 4710 Z= 0.237 Chirality : 0.049 0.121 528 Planarity : 0.003 0.024 600 Dihedral : 5.046 19.959 468 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.27 % Allowed : 11.62 % 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: -1.52 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 330 PHE 0.004 0.001 PHE C 378 TYR 0.004 0.001 TYR B 310 ARG 0.001 0.000 ARG F 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 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7546 (t0) cc_final: 0.7321 (t0) REVERT: A 317 LYS cc_start: 0.7349 (mttt) cc_final: 0.6931 (mtpt) REVERT: A 340 LYS cc_start: 0.7710 (mttt) cc_final: 0.7437 (mttm) REVERT: A 369 LYS cc_start: 0.7600 (mtmt) cc_final: 0.7043 (mttp) REVERT: A 370 LYS cc_start: 0.7834 (tttp) cc_final: 0.7599 (tttp) REVERT: B 340 LYS cc_start: 0.7673 (mtpp) cc_final: 0.6637 (mttm) REVERT: B 375 LYS cc_start: 0.7632 (ttmt) cc_final: 0.7112 (tttm) REVERT: C 314 ASP cc_start: 0.7624 (t0) cc_final: 0.7019 (t0) REVERT: C 317 LYS cc_start: 0.7846 (mttt) cc_final: 0.7478 (mtpt) REVERT: C 338 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7718 (mt-10) REVERT: C 342 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7333 (mt-10) REVERT: C 375 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8136 (ttmm) REVERT: D 307 GLN cc_start: 0.8068 (tt0) cc_final: 0.7296 (mt0) REVERT: D 324 SER cc_start: 0.8431 (m) cc_final: 0.7832 (t) REVERT: D 336 GLN cc_start: 0.8332 (mt0) cc_final: 0.8047 (tt0) REVERT: D 369 LYS cc_start: 0.8377 (tttt) cc_final: 0.7897 (tttm) REVERT: D 375 LYS cc_start: 0.8498 (ttmt) cc_final: 0.7938 (tttp) REVERT: E 369 LYS cc_start: 0.7675 (mtmt) cc_final: 0.7189 (mttp) REVERT: E 375 LYS cc_start: 0.7708 (ttmt) cc_final: 0.7051 (ttmm) REVERT: F 311 LYS cc_start: 0.8018 (mttt) cc_final: 0.7683 (mtpt) REVERT: F 324 SER cc_start: 0.8524 (m) cc_final: 0.8269 (t) REVERT: F 340 LYS cc_start: 0.7596 (ttpp) cc_final: 0.6818 (mmtt) REVERT: F 347 LYS cc_start: 0.8031 (mmtm) cc_final: 0.7802 (mmtm) REVERT: F 358 ASP cc_start: 0.8061 (m-30) cc_final: 0.7594 (m-30) REVERT: F 375 LYS cc_start: 0.7737 (ttmt) cc_final: 0.7252 (tttm) outliers start: 9 outliers final: 8 residues processed: 81 average time/residue: 0.6119 time to fit residues: 55.8017 Evaluate side-chains 84 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.7610 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3522 Z= 0.154 Angle : 0.433 5.531 4710 Z= 0.219 Chirality : 0.050 0.123 528 Planarity : 0.003 0.025 600 Dihedral : 4.782 19.062 468 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.02 % Allowed : 11.87 % 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: -1.49 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 362 PHE 0.002 0.000 PHE F 378 TYR 0.005 0.001 TYR B 310 ARG 0.001 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: 8 poor density : 77 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7544 (t0) cc_final: 0.7319 (t0) REVERT: A 317 LYS cc_start: 0.7342 (mttt) cc_final: 0.6920 (mtpt) REVERT: A 340 LYS cc_start: 0.7618 (mttt) cc_final: 0.7346 (mttm) REVERT: A 369 LYS cc_start: 0.7600 (mtmt) cc_final: 0.7040 (mttp) REVERT: A 370 LYS cc_start: 0.7871 (tttp) cc_final: 0.7658 (tttp) REVERT: B 340 LYS cc_start: 0.7651 (mtpp) cc_final: 0.6620 (mttm) REVERT: B 375 LYS cc_start: 0.7581 (ttmt) cc_final: 0.7073 (tttm) REVERT: C 314 ASP cc_start: 0.7633 (t0) cc_final: 0.6994 (t0) REVERT: C 317 LYS cc_start: 0.7813 (mttt) cc_final: 0.7459 (mtpt) REVERT: C 338 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7722 (mt-10) REVERT: C 342 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7383 (mt-10) REVERT: C 375 LYS cc_start: 0.8402 (ttmt) cc_final: 0.8123 (ttmm) REVERT: D 307 GLN cc_start: 0.8059 (tt0) cc_final: 0.7273 (mt0) REVERT: D 324 SER cc_start: 0.8432 (m) cc_final: 0.7783 (t) REVERT: D 336 GLN cc_start: 0.8321 (mt0) cc_final: 0.8039 (tt0) REVERT: D 369 LYS cc_start: 0.8351 (tttt) cc_final: 0.7869 (tttm) REVERT: D 375 LYS cc_start: 0.8496 (ttmt) cc_final: 0.7958 (tttp) REVERT: E 369 LYS cc_start: 0.7684 (mtmt) cc_final: 0.7187 (mttp) REVERT: E 375 LYS cc_start: 0.7643 (ttmt) cc_final: 0.7002 (ttmm) REVERT: F 311 LYS cc_start: 0.8042 (mttt) cc_final: 0.7707 (mtpt) REVERT: F 324 SER cc_start: 0.8474 (m) cc_final: 0.8236 (t) REVERT: F 340 LYS cc_start: 0.7644 (ttpp) cc_final: 0.6885 (mmtt) REVERT: F 358 ASP cc_start: 0.8077 (m-30) cc_final: 0.7630 (m-30) REVERT: F 375 LYS cc_start: 0.7720 (ttmt) cc_final: 0.7237 (tttm) outliers start: 8 outliers final: 8 residues processed: 83 average time/residue: 0.6494 time to fit residues: 60.9579 Evaluate side-chains 84 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.127367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.116570 restraints weight = 13831.376| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.69 r_work: 0.3695 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.6015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3522 Z= 0.270 Angle : 0.460 5.488 4710 Z= 0.235 Chirality : 0.050 0.164 528 Planarity : 0.003 0.024 600 Dihedral : 4.884 18.953 468 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.02 % Allowed : 12.12 % 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: -1.48 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (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 A 346 TYR 0.004 0.001 TYR B 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: 2966.40 seconds wall clock time: 52 minutes 46.88 seconds (3166.88 seconds total)