Starting phenix.real_space_refine on Sat Aug 3 05:25:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjj_18448/08_2024/8qjj_18448.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjj_18448/08_2024/8qjj_18448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjj_18448/08_2024/8qjj_18448.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjj_18448/08_2024/8qjj_18448.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjj_18448/08_2024/8qjj_18448.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjj_18448/08_2024/8qjj_18448.cif" } resolution = 3.35 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= 0.003 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 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 H 3588 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 314": "OD1" <-> "OD2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 314": "OD1" <-> "OD2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C PHE 346": "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 "C ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 314": "OD1" <-> "OD2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 314": "OD1" <-> "OD2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 372": "OE1" <-> "OE2" Residue "E ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 314": "OD1" <-> "OD2" Residue "F GLU 338": "OE1" <-> "OE2" 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 ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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: 7032 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 4.72, per 1000 atoms: 0.67 Number of scatterers: 7032 At special positions: 0 Unit cell: (151.616, 97.232, 37.904, 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 642 8.00 N 636 7.00 C 2160 6.00 H 3588 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: 5.24 Conformation dependent library (CDL) restraints added in 866.7 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 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, 44.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.561A pdb=" N VAL A 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N VAL C 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.739A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 318 removed outlier: 6.634A pdb=" N LYS A 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 321 through 322 removed outlier: 6.574A pdb=" N LYS A 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 325 through 330 removed outlier: 5.857A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN A 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 337 through 342 Processing sheet with id=AA7, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.438A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 350 through 357 removed outlier: 6.720A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N SER E 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY A 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.485A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 369 through 374 removed outlier: 6.451A pdb=" N ASN A 368 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ILE C 371 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N THR C 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU A 372 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLY A 367 " --> pdb=" O ASN E 368 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N LYS E 370 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (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: 6.583A pdb=" N VAL B 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL D 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE B 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN B 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N TYR F 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.666A pdb=" N VAL B 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 317 through 322 removed outlier: 6.546A pdb=" N LYS B 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N SER F 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N CYS F 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS B 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 325 through 330 removed outlier: 5.817A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY F 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN B 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.640A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N GLU D 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER B 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.478A pdb=" N ASP B 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 350 through 357 Processing sheet with id=AB9, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.497A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 369 through 374 removed outlier: 6.597A pdb=" N LYS B 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) 66 hydrogen bonds defined for protein. 198 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: 2.25 Time building geometry restraints manager: 5.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 3582 1.11 - 1.29: 570 1.29 - 1.46: 881 1.46 - 1.63: 2047 1.63 - 1.80: 6 Bond restraints: 7086 Sorted by residual: bond pdb=" CE2 TYR A 310 " pdb=" HE2 TYR A 310 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N ILE B 354 " pdb=" H ILE B 354 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N GLN C 351 " pdb=" H GLN C 351 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N ILE C 371 " pdb=" H ILE C 371 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" CD2 HIS D 374 " pdb=" HD2 HIS D 374 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.64e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 96.72 - 103.27: 22 103.27 - 109.82: 6051 109.82 - 116.37: 3208 116.37 - 122.92: 3011 122.92 - 129.47: 620 Bond angle restraints: 12912 Sorted by residual: angle pdb=" CA THR A 319 " pdb=" CB THR A 319 " pdb=" CG2 THR A 319 " ideal model delta sigma weight residual 110.50 119.20 -8.70 1.70e+00 3.46e-01 2.62e+01 angle pdb=" N SER A 316 " pdb=" CA SER A 316 " pdb=" C SER A 316 " ideal model delta sigma weight residual 110.43 116.97 -6.54 1.31e+00 5.83e-01 2.49e+01 angle pdb=" CA THR C 319 " pdb=" CB THR C 319 " pdb=" CG2 THR C 319 " ideal model delta sigma weight residual 110.50 118.44 -7.94 1.70e+00 3.46e-01 2.18e+01 angle pdb=" CA ASP F 345 " pdb=" CB ASP F 345 " pdb=" CG ASP F 345 " ideal model delta sigma weight residual 112.60 117.15 -4.55 1.00e+00 1.00e+00 2.07e+01 angle pdb=" CA ASP F 348 " pdb=" CB ASP F 348 " pdb=" CG ASP F 348 " ideal model delta sigma weight residual 112.60 117.13 -4.53 1.00e+00 1.00e+00 2.05e+01 ... (remaining 12907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.48: 2834 14.48 - 28.96: 198 28.96 - 43.44: 103 43.44 - 57.92: 61 57.92 - 72.41: 68 Dihedral angle restraints: 3264 sinusoidal: 1866 harmonic: 1398 Sorted by residual: dihedral pdb=" CA GLY A 365 " pdb=" C GLY A 365 " pdb=" N GLY A 366 " pdb=" CA GLY A 366 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA GLY F 365 " pdb=" C GLY F 365 " pdb=" N GLY F 366 " pdb=" CA GLY F 366 " 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 GLY B 365 " pdb=" C GLY B 365 " pdb=" N GLY B 366 " pdb=" CA GLY B 366 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 249 0.061 - 0.121: 163 0.121 - 0.181: 87 0.181 - 0.241: 18 0.241 - 0.301: 11 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS F 370 " pdb=" N LYS F 370 " pdb=" C LYS F 370 " pdb=" CB LYS F 370 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA ASP F 348 " pdb=" N ASP F 348 " pdb=" C ASP F 348 " pdb=" CB ASP F 348 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA LYS C 343 " pdb=" N LYS C 343 " pdb=" C LYS C 343 " pdb=" CB LYS C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 525 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 330 " 0.088 2.00e-02 2.50e+03 4.87e-02 5.34e+01 pdb=" CG HIS C 330 " -0.079 2.00e-02 2.50e+03 pdb=" ND1 HIS C 330 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS C 330 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 HIS C 330 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS C 330 " 0.019 2.00e-02 2.50e+03 pdb=" HD1 HIS C 330 " -0.017 2.00e-02 2.50e+03 pdb=" HD2 HIS C 330 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 HIS C 330 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 330 " -0.079 2.00e-02 2.50e+03 4.49e-02 4.53e+01 pdb=" CG HIS D 330 " 0.076 2.00e-02 2.50e+03 pdb=" ND1 HIS D 330 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 HIS D 330 " 0.044 2.00e-02 2.50e+03 pdb=" CE1 HIS D 330 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS D 330 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 HIS D 330 " 0.014 2.00e-02 2.50e+03 pdb=" HD2 HIS D 330 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 HIS D 330 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 374 " -0.034 2.00e-02 2.50e+03 6.28e-02 3.94e+01 pdb=" N LYS A 375 " 0.108 2.00e-02 2.50e+03 pdb=" CA LYS A 375 " -0.031 2.00e-02 2.50e+03 pdb=" H LYS A 375 " -0.043 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 531 2.19 - 2.79: 12402 2.79 - 3.39: 18577 3.39 - 4.00: 24104 4.00 - 4.60: 34365 Nonbonded interactions: 89979 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.583 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.595 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.630 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.631 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.659 2.450 ... (remaining 89974 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: 4.220 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 27.470 Find NCS groups from input model: 0.160 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 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 : 0.012 0.037 3498 Z= 0.790 Angle : 1.984 8.700 4680 Z= 1.309 Chirality : 0.097 0.301 528 Planarity : 0.011 0.061 594 Dihedral : 12.602 72.406 1344 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.004 HIS E 330 PHE 0.056 0.019 PHE F 346 TYR 0.057 0.017 TYR A 310 ARG 0.003 0.001 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 VAL cc_start: 0.7828 (t) cc_final: 0.6780 (t) REVERT: A 308 ILE cc_start: 0.7138 (mt) cc_final: 0.6647 (mp) REVERT: A 340 LYS cc_start: 0.8686 (ttpt) cc_final: 0.8080 (mtmt) REVERT: A 372 GLU cc_start: 0.7162 (tt0) cc_final: 0.5891 (mt-10) REVERT: B 340 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8160 (mttt) REVERT: B 372 GLU cc_start: 0.6598 (tt0) cc_final: 0.6313 (mt-10) REVERT: C 308 ILE cc_start: 0.7399 (mt) cc_final: 0.7109 (mp) REVERT: C 340 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8077 (mttt) REVERT: C 349 ARG cc_start: 0.8343 (mtt180) cc_final: 0.7197 (mmp-170) REVERT: C 370 LYS cc_start: 0.8030 (tttt) cc_final: 0.7158 (mttt) REVERT: D 340 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8076 (mttt) REVERT: D 349 ARG cc_start: 0.8501 (mtt180) cc_final: 0.7625 (mmp-170) REVERT: D 370 LYS cc_start: 0.8360 (tttt) cc_final: 0.7931 (mttt) REVERT: D 376 LEU cc_start: 0.7819 (tp) cc_final: 0.7422 (mt) REVERT: E 306 VAL cc_start: 0.6987 (t) cc_final: 0.6753 (t) REVERT: E 308 ILE cc_start: 0.6794 (mt) cc_final: 0.6466 (mt) REVERT: E 340 LYS cc_start: 0.8886 (ttpt) cc_final: 0.8344 (mttt) REVERT: E 349 ARG cc_start: 0.8120 (mtt180) cc_final: 0.6685 (pmt-80) REVERT: E 370 LYS cc_start: 0.7637 (tttt) cc_final: 0.7420 (ptpt) REVERT: E 372 GLU cc_start: 0.6815 (tt0) cc_final: 0.6087 (mp0) REVERT: F 340 LYS cc_start: 0.8836 (ttpt) cc_final: 0.8338 (mtmt) REVERT: F 370 LYS cc_start: 0.7598 (tttt) cc_final: 0.7047 (ptpt) REVERT: F 372 GLU cc_start: 0.6433 (tt0) cc_final: 0.5783 (mt-10) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.5869 time to fit residues: 94.7976 Evaluate side-chains 95 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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: 7.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 362 HIS B 362 HIS ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS D 362 HIS ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 HIS F 359 ASN F 362 HIS ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3498 Z= 0.207 Angle : 0.633 7.024 4680 Z= 0.333 Chirality : 0.053 0.151 528 Planarity : 0.003 0.023 594 Dihedral : 6.261 21.135 462 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.02 % Allowed : 11.11 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.26), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.20), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.014 0.002 PHE B 378 TYR 0.008 0.002 TYR C 310 ARG 0.003 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8654 (ttpt) cc_final: 0.8198 (mttt) REVERT: B 340 LYS cc_start: 0.8508 (ttpt) cc_final: 0.8062 (mttt) REVERT: B 347 LYS cc_start: 0.7859 (mttt) cc_final: 0.7641 (mttm) REVERT: B 372 GLU cc_start: 0.6623 (tt0) cc_final: 0.5898 (mt-10) REVERT: C 340 LYS cc_start: 0.8549 (ttpt) cc_final: 0.8049 (mttt) REVERT: C 349 ARG cc_start: 0.8403 (mtt180) cc_final: 0.7306 (mmp-170) REVERT: C 379 ARG cc_start: 0.4550 (tmm160) cc_final: 0.4215 (tmm160) REVERT: D 340 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8128 (mttp) REVERT: D 349 ARG cc_start: 0.8471 (mtt180) cc_final: 0.7459 (mmm160) REVERT: D 370 LYS cc_start: 0.8279 (tttt) cc_final: 0.8068 (mttt) REVERT: D 376 LEU cc_start: 0.7799 (tp) cc_final: 0.7365 (mt) REVERT: E 340 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8430 (mttt) REVERT: E 349 ARG cc_start: 0.8060 (mtt180) cc_final: 0.6615 (pmt-80) REVERT: E 370 LYS cc_start: 0.7683 (tttt) cc_final: 0.7011 (ptpt) REVERT: F 340 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8385 (mttt) REVERT: F 379 ARG cc_start: 0.4072 (pmt-80) cc_final: 0.3364 (mtm180) outliers start: 8 outliers final: 5 residues processed: 94 average time/residue: 0.5846 time to fit residues: 62.7081 Evaluate side-chains 89 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 342 GLU 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: 5.9990 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 ASN ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3498 Z= 0.270 Angle : 0.602 4.921 4680 Z= 0.322 Chirality : 0.053 0.150 528 Planarity : 0.003 0.019 594 Dihedral : 5.978 16.786 462 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.27 % Allowed : 12.88 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.26), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.20), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 362 PHE 0.008 0.002 PHE E 378 TYR 0.011 0.002 TYR C 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 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: 9 poor density : 92 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8637 (ttpt) cc_final: 0.8166 (mttt) REVERT: A 379 ARG cc_start: 0.5890 (mmt-90) cc_final: 0.5202 (tpp80) REVERT: B 340 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8050 (mttp) REVERT: B 347 LYS cc_start: 0.7504 (mttt) cc_final: 0.7255 (mttm) REVERT: B 348 ASP cc_start: 0.7434 (m-30) cc_final: 0.7195 (m-30) REVERT: B 372 GLU cc_start: 0.6884 (tt0) cc_final: 0.6492 (mp0) REVERT: C 340 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8022 (mttt) REVERT: C 349 ARG cc_start: 0.8459 (mtt180) cc_final: 0.7357 (mmp-170) REVERT: D 340 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8086 (mttp) REVERT: D 349 ARG cc_start: 0.8480 (mtt180) cc_final: 0.7498 (mmm160) REVERT: E 340 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8383 (mttt) REVERT: E 349 ARG cc_start: 0.8145 (mtt180) cc_final: 0.6695 (pmt-80) REVERT: E 370 LYS cc_start: 0.7668 (tttt) cc_final: 0.6990 (ptpt) REVERT: E 372 GLU cc_start: 0.6865 (tm-30) cc_final: 0.6636 (tm-30) REVERT: F 340 LYS cc_start: 0.8856 (ttpt) cc_final: 0.8392 (mtmt) REVERT: F 370 LYS cc_start: 0.7786 (tttt) cc_final: 0.7153 (mttt) REVERT: F 372 GLU cc_start: 0.6998 (tt0) cc_final: 0.6628 (mp0) outliers start: 9 outliers final: 8 residues processed: 95 average time/residue: 0.5651 time to fit residues: 60.8165 Evaluate side-chains 94 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.6241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3498 Z= 0.141 Angle : 0.499 3.968 4680 Z= 0.262 Chirality : 0.052 0.145 528 Planarity : 0.002 0.023 594 Dihedral : 5.275 14.620 462 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.27 % Allowed : 12.63 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.26), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.20), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.024 0.001 PHE B 378 TYR 0.007 0.002 TYR C 310 ARG 0.002 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 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: 9 poor density : 83 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8603 (ttpt) cc_final: 0.8135 (mttt) REVERT: B 372 GLU cc_start: 0.6698 (tt0) cc_final: 0.6374 (mp0) REVERT: C 307 GLN cc_start: 0.5459 (mp10) cc_final: 0.4891 (tp40) REVERT: C 308 ILE cc_start: 0.7834 (mp) cc_final: 0.7499 (mm) REVERT: C 340 LYS cc_start: 0.8537 (ttpt) cc_final: 0.8006 (mttt) REVERT: C 349 ARG cc_start: 0.8497 (mtt180) cc_final: 0.7367 (mmp-170) REVERT: D 340 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8049 (mttp) REVERT: D 349 ARG cc_start: 0.8505 (mtt180) cc_final: 0.7514 (mmm160) REVERT: D 372 GLU cc_start: 0.7689 (mp0) cc_final: 0.7407 (mp0) REVERT: E 340 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8398 (mttt) REVERT: E 349 ARG cc_start: 0.8118 (mtt180) cc_final: 0.6679 (pmt-80) REVERT: E 370 LYS cc_start: 0.7669 (tttt) cc_final: 0.6988 (ptpt) REVERT: E 372 GLU cc_start: 0.6719 (tm-30) cc_final: 0.6454 (tm-30) REVERT: F 340 LYS cc_start: 0.8825 (ttpt) cc_final: 0.8362 (mtmt) REVERT: F 370 LYS cc_start: 0.7865 (tttt) cc_final: 0.7251 (mttt) REVERT: F 372 GLU cc_start: 0.7153 (tt0) cc_final: 0.6766 (mp0) outliers start: 9 outliers final: 5 residues processed: 85 average time/residue: 0.5635 time to fit residues: 54.5567 Evaluate side-chains 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 340 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.6519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3498 Z= 0.279 Angle : 0.557 3.789 4680 Z= 0.297 Chirality : 0.052 0.145 528 Planarity : 0.003 0.021 594 Dihedral : 5.738 15.722 462 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.78 % Allowed : 12.88 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.26), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.20), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 362 PHE 0.015 0.002 PHE F 378 TYR 0.009 0.002 TYR C 310 ARG 0.002 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 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: 11 poor density : 82 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8133 (mttt) REVERT: B 340 LYS cc_start: 0.8534 (ttpt) cc_final: 0.7975 (mttp) REVERT: B 348 ASP cc_start: 0.7514 (m-30) cc_final: 0.7261 (m-30) REVERT: B 372 GLU cc_start: 0.6771 (tt0) cc_final: 0.6468 (mp0) REVERT: C 307 GLN cc_start: 0.5634 (mp10) cc_final: 0.5221 (tp40) REVERT: C 340 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8056 (mtmt) REVERT: C 349 ARG cc_start: 0.8416 (mtt180) cc_final: 0.7342 (mmp-170) REVERT: D 340 LYS cc_start: 0.8576 (mtpt) cc_final: 0.8037 (mttp) REVERT: D 349 ARG cc_start: 0.8506 (mtt180) cc_final: 0.7514 (mmm160) REVERT: D 372 GLU cc_start: 0.7855 (mp0) cc_final: 0.7590 (mp0) REVERT: E 340 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8413 (mttt) REVERT: E 349 ARG cc_start: 0.8198 (mtt180) cc_final: 0.6740 (pmt-80) REVERT: E 370 LYS cc_start: 0.7751 (tttt) cc_final: 0.6954 (mttt) REVERT: F 340 LYS cc_start: 0.8927 (ttpt) cc_final: 0.8368 (mtmt) REVERT: F 370 LYS cc_start: 0.7863 (tttt) cc_final: 0.7185 (mttt) REVERT: F 372 GLU cc_start: 0.7271 (tt0) cc_final: 0.6799 (mp0) outliers start: 11 outliers final: 6 residues processed: 85 average time/residue: 0.6142 time to fit residues: 58.9330 Evaluate side-chains 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.6702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3498 Z= 0.151 Angle : 0.491 3.603 4680 Z= 0.258 Chirality : 0.051 0.142 528 Planarity : 0.002 0.021 594 Dihedral : 5.096 14.555 462 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.02 % Allowed : 13.89 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.27), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.018 0.001 PHE B 378 TYR 0.006 0.001 TYR C 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.586 Fit side-chains REVERT: A 340 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8134 (mttt) REVERT: B 340 LYS cc_start: 0.8498 (mtpt) cc_final: 0.7990 (mttp) REVERT: B 372 GLU cc_start: 0.6702 (tt0) cc_final: 0.6375 (mp0) REVERT: C 307 GLN cc_start: 0.5715 (mp10) cc_final: 0.5290 (tp40) REVERT: C 340 LYS cc_start: 0.8526 (ttpt) cc_final: 0.8049 (mtmt) REVERT: C 349 ARG cc_start: 0.8429 (mtt180) cc_final: 0.7354 (mmp-170) REVERT: D 340 LYS cc_start: 0.8533 (mtpt) cc_final: 0.8014 (mttp) REVERT: D 349 ARG cc_start: 0.8550 (mtt180) cc_final: 0.7543 (mmm160) REVERT: D 372 GLU cc_start: 0.7906 (mp0) cc_final: 0.7642 (mp0) REVERT: E 340 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8411 (mttt) REVERT: E 349 ARG cc_start: 0.8154 (mtt180) cc_final: 0.6720 (pmt-80) REVERT: E 370 LYS cc_start: 0.7714 (tttt) cc_final: 0.7024 (ptpt) REVERT: E 372 GLU cc_start: 0.6934 (tm-30) cc_final: 0.6644 (tm-30) REVERT: F 340 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8343 (mtmt) REVERT: F 370 LYS cc_start: 0.7915 (tttt) cc_final: 0.7266 (mttt) REVERT: F 372 GLU cc_start: 0.7256 (tt0) cc_final: 0.6808 (mp0) outliers start: 8 outliers final: 6 residues processed: 81 average time/residue: 0.5989 time to fit residues: 54.9804 Evaluate side-chains 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.6826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3498 Z= 0.166 Angle : 0.481 3.442 4680 Z= 0.254 Chirality : 0.051 0.141 528 Planarity : 0.002 0.019 594 Dihedral : 4.996 14.022 462 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.27 % Allowed : 14.39 % Favored : 83.33 % 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: -1.96 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 362 PHE 0.018 0.002 PHE B 378 TYR 0.008 0.002 TYR C 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 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: 9 poor density : 80 time to evaluate : 0.542 Fit side-chains REVERT: A 340 LYS cc_start: 0.8627 (ttpt) cc_final: 0.8144 (mttt) REVERT: B 340 LYS cc_start: 0.8527 (mtpt) cc_final: 0.7955 (mttp) REVERT: B 372 GLU cc_start: 0.6665 (tt0) cc_final: 0.6349 (mp0) REVERT: C 307 GLN cc_start: 0.5756 (mp10) cc_final: 0.5363 (tp40) REVERT: C 340 LYS cc_start: 0.8526 (ttpt) cc_final: 0.8021 (mttt) REVERT: C 349 ARG cc_start: 0.8419 (mtt180) cc_final: 0.7359 (mmp-170) REVERT: D 340 LYS cc_start: 0.8535 (mtpt) cc_final: 0.7989 (mttp) REVERT: D 349 ARG cc_start: 0.8597 (mtt180) cc_final: 0.7603 (mmm160) REVERT: E 340 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8424 (mttt) REVERT: E 349 ARG cc_start: 0.8189 (mtt180) cc_final: 0.6711 (pmt-80) REVERT: E 370 LYS cc_start: 0.7761 (tttt) cc_final: 0.6957 (mttt) REVERT: E 372 GLU cc_start: 0.6844 (tm-30) cc_final: 0.6542 (tm-30) REVERT: F 340 LYS cc_start: 0.8944 (mtpt) cc_final: 0.8346 (mtmt) REVERT: F 370 LYS cc_start: 0.7925 (tttt) cc_final: 0.7182 (mttt) REVERT: F 372 GLU cc_start: 0.7280 (tt0) cc_final: 0.6886 (mp0) outliers start: 9 outliers final: 6 residues processed: 83 average time/residue: 0.5860 time to fit residues: 54.7350 Evaluate side-chains 84 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain F residue 342 GLU 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: 1.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.7014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3498 Z= 0.188 Angle : 0.493 3.580 4680 Z= 0.262 Chirality : 0.051 0.142 528 Planarity : 0.002 0.018 594 Dihedral : 5.051 13.865 462 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.77 % Allowed : 14.65 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.016 0.002 PHE B 378 TYR 0.007 0.002 TYR C 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8154 (mttt) REVERT: B 340 LYS cc_start: 0.8543 (mtpt) cc_final: 0.7964 (mttp) REVERT: B 372 GLU cc_start: 0.6662 (tt0) cc_final: 0.6380 (mp0) REVERT: C 307 GLN cc_start: 0.5796 (mp10) cc_final: 0.5405 (tp40) REVERT: C 340 LYS cc_start: 0.8529 (ttpt) cc_final: 0.8024 (mttt) REVERT: C 349 ARG cc_start: 0.8432 (mtt180) cc_final: 0.7372 (mmp-170) REVERT: D 340 LYS cc_start: 0.8546 (mtpt) cc_final: 0.7981 (mttp) REVERT: D 349 ARG cc_start: 0.8622 (mtt180) cc_final: 0.7607 (mmm160) REVERT: D 372 GLU cc_start: 0.7800 (mp0) cc_final: 0.7586 (mp0) REVERT: E 340 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8422 (mttt) REVERT: E 349 ARG cc_start: 0.8206 (mtt180) cc_final: 0.6746 (pmt-80) REVERT: E 370 LYS cc_start: 0.7757 (tttt) cc_final: 0.6993 (ptpt) REVERT: E 372 GLU cc_start: 0.6910 (tm-30) cc_final: 0.6599 (tm-30) REVERT: F 340 LYS cc_start: 0.8922 (mtpt) cc_final: 0.8325 (mtmt) REVERT: F 370 LYS cc_start: 0.7938 (tttt) cc_final: 0.7198 (mttt) REVERT: F 372 GLU cc_start: 0.7276 (tt0) cc_final: 0.6862 (mp0) outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 0.5980 time to fit residues: 53.7075 Evaluate side-chains 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.7037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3498 Z= 0.202 Angle : 0.504 3.702 4680 Z= 0.268 Chirality : 0.051 0.142 528 Planarity : 0.003 0.043 594 Dihedral : 5.153 13.713 462 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.52 % Allowed : 14.90 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.016 0.002 PHE B 378 TYR 0.007 0.002 TYR C 310 ARG 0.007 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8646 (ttpt) cc_final: 0.8157 (mttt) REVERT: B 340 LYS cc_start: 0.8519 (mtpt) cc_final: 0.7928 (mttp) REVERT: B 349 ARG cc_start: 0.8492 (mtm180) cc_final: 0.8250 (mtp-110) REVERT: B 372 GLU cc_start: 0.6606 (tt0) cc_final: 0.6333 (mp0) REVERT: C 307 GLN cc_start: 0.5880 (mp10) cc_final: 0.5436 (tp40) REVERT: C 340 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8028 (mttt) REVERT: C 349 ARG cc_start: 0.8416 (mtt180) cc_final: 0.7400 (mmp-170) REVERT: D 340 LYS cc_start: 0.8566 (mtpt) cc_final: 0.7973 (mttp) REVERT: D 349 ARG cc_start: 0.8635 (mtt180) cc_final: 0.7611 (mmm160) REVERT: D 372 GLU cc_start: 0.7817 (mp0) cc_final: 0.7601 (mp0) REVERT: E 340 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8433 (mttt) REVERT: E 349 ARG cc_start: 0.8225 (mtt180) cc_final: 0.6755 (pmt-80) REVERT: E 370 LYS cc_start: 0.7737 (tttt) cc_final: 0.6958 (ptpt) REVERT: E 372 GLU cc_start: 0.6913 (tm-30) cc_final: 0.6616 (tm-30) REVERT: F 340 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8319 (mtmt) REVERT: F 370 LYS cc_start: 0.7973 (tttt) cc_final: 0.7220 (mttt) REVERT: F 372 GLU cc_start: 0.7276 (tt0) cc_final: 0.6876 (mp0) outliers start: 6 outliers final: 5 residues processed: 82 average time/residue: 0.6160 time to fit residues: 56.7016 Evaluate side-chains 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 0.0670 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.7249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3498 Z= 0.116 Angle : 0.462 3.336 4680 Z= 0.243 Chirality : 0.051 0.136 528 Planarity : 0.003 0.036 594 Dihedral : 4.652 12.907 462 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.01 % Allowed : 15.66 % Favored : 83.33 % 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: -1.69 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.016 0.001 PHE B 378 TYR 0.015 0.002 TYR A 310 ARG 0.007 0.001 ARG F 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8606 (ttpt) cc_final: 0.8140 (mttt) REVERT: B 340 LYS cc_start: 0.8550 (mtpt) cc_final: 0.7985 (mttp) REVERT: B 349 ARG cc_start: 0.8474 (mtm180) cc_final: 0.8248 (mtp-110) REVERT: B 372 GLU cc_start: 0.6664 (tt0) cc_final: 0.6357 (mp0) REVERT: C 307 GLN cc_start: 0.5884 (mp10) cc_final: 0.5562 (tp-100) REVERT: C 340 LYS cc_start: 0.8508 (ttpt) cc_final: 0.8029 (mtmt) REVERT: C 349 ARG cc_start: 0.8435 (mtt180) cc_final: 0.7393 (mmp-170) REVERT: D 340 LYS cc_start: 0.8492 (mtpt) cc_final: 0.7955 (mttp) REVERT: D 349 ARG cc_start: 0.8647 (mtt180) cc_final: 0.7592 (mmm160) REVERT: D 372 GLU cc_start: 0.7782 (mp0) cc_final: 0.7577 (mp0) REVERT: E 340 LYS cc_start: 0.8825 (ttpt) cc_final: 0.8417 (mttt) REVERT: E 349 ARG cc_start: 0.8204 (mtt180) cc_final: 0.6738 (pmt-80) REVERT: E 370 LYS cc_start: 0.7737 (tttt) cc_final: 0.7000 (ptpt) REVERT: E 372 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6623 (tm-30) REVERT: F 340 LYS cc_start: 0.8913 (mtpt) cc_final: 0.8315 (mtmt) REVERT: F 370 LYS cc_start: 0.7971 (tttt) cc_final: 0.7248 (mttt) REVERT: F 372 GLU cc_start: 0.7237 (tt0) cc_final: 0.6868 (mp0) outliers start: 4 outliers final: 3 residues processed: 77 average time/residue: 0.6151 time to fit residues: 53.0639 Evaluate side-chains 77 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 368 ASN 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: 0.9980 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 0.0270 chunk 26 optimal weight: 0.0770 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.194162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.171931 restraints weight = 13028.349| |-----------------------------------------------------------------------------| r_work (start): 0.4529 rms_B_bonded: 2.36 r_work: 0.4449 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4364 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.4364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.7284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3498 Z= 0.114 Angle : 0.457 3.503 4680 Z= 0.241 Chirality : 0.051 0.134 528 Planarity : 0.003 0.038 594 Dihedral : 4.452 12.046 462 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.51 % Allowed : 15.91 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 330 PHE 0.016 0.002 PHE F 378 TYR 0.011 0.002 TYR A 310 ARG 0.006 0.001 ARG F 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2943.67 seconds wall clock time: 51 minutes 47.65 seconds (3107.65 seconds total)