Starting phenix.real_space_refine on Mon Mar 11 04:44:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjj_18448/03_2024/8qjj_18448.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjj_18448/03_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_18448/03_2024/8qjj_18448.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjj_18448/03_2024/8qjj_18448.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjj_18448/03_2024/8qjj_18448.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjj_18448/03_2024/8qjj_18448.pdb" } 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-5265/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: 3.78, per 1000 atoms: 0.54 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: 5.65 Conformation dependent library (CDL) restraints added in 682.7 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: 0.76 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: 2.28 Time building geometry restraints manager: 5.82 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 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.595 1.850 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.630 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.631 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.659 1.850 ... (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 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: 4.090 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: 11.680 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 27.300 Find NCS groups from input model: 0.330 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.430 ------------------------------------------------------------------------------- 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 : 0.538 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: 0.6149 time to fit residues: 99.2100 Evaluate side-chains 95 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 C 362 HIS D 362 HIS E 362 HIS F 362 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3498 Z= 0.199 Angle : 0.623 6.655 4680 Z= 0.329 Chirality : 0.051 0.148 528 Planarity : 0.003 0.023 594 Dihedral : 6.281 21.980 462 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.02 % Allowed : 11.62 % Favored : 86.36 % 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 (0.27), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.20), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 330 PHE 0.014 0.002 PHE B 378 TYR 0.007 0.001 TYR C 310 ARG 0.004 0.001 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 : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8699 (ttpt) cc_final: 0.8215 (mttt) REVERT: B 340 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8069 (mttp) REVERT: B 347 LYS cc_start: 0.7835 (mttt) cc_final: 0.7620 (mttm) REVERT: B 372 GLU cc_start: 0.6772 (tt0) cc_final: 0.6407 (mp0) REVERT: C 340 LYS cc_start: 0.8510 (ttpt) cc_final: 0.8042 (mttt) REVERT: C 349 ARG cc_start: 0.8381 (mtt180) cc_final: 0.7288 (mmp-170) REVERT: C 379 ARG cc_start: 0.4623 (tmm160) cc_final: 0.4282 (tmm160) REVERT: D 340 LYS cc_start: 0.8488 (ttpt) cc_final: 0.8149 (mttp) REVERT: D 349 ARG cc_start: 0.8488 (mtt180) cc_final: 0.7493 (mmm160) REVERT: D 370 LYS cc_start: 0.8285 (tttt) cc_final: 0.8079 (mttt) REVERT: D 376 LEU cc_start: 0.7808 (tp) cc_final: 0.7389 (mt) REVERT: E 340 LYS cc_start: 0.8831 (ttpt) cc_final: 0.8403 (mttt) REVERT: E 349 ARG cc_start: 0.8020 (mtt180) cc_final: 0.6529 (pmt-80) REVERT: E 370 LYS cc_start: 0.7749 (tttt) cc_final: 0.7015 (ptpt) REVERT: F 340 LYS cc_start: 0.8789 (ttpt) cc_final: 0.8386 (mttt) REVERT: F 372 GLU cc_start: 0.6775 (tt0) cc_final: 0.6449 (mp0) REVERT: F 379 ARG cc_start: 0.4020 (pmt-80) cc_final: 0.3323 (mtm180) outliers start: 8 outliers final: 5 residues processed: 94 average time/residue: 0.5437 time to fit residues: 57.9827 Evaluate side-chains 86 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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: 0.6980 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 359 ASN ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3498 Z= 0.154 Angle : 0.533 5.593 4680 Z= 0.280 Chirality : 0.051 0.145 528 Planarity : 0.002 0.026 594 Dihedral : 5.474 18.878 462 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.27 % Allowed : 13.38 % 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: -1.93 (0.27), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.005 0.001 PHE A 346 TYR 0.007 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 95 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8643 (ttpt) cc_final: 0.8157 (mttt) REVERT: A 378 PHE cc_start: 0.7207 (t80) cc_final: 0.6977 (t80) REVERT: B 340 LYS cc_start: 0.8489 (ttpt) cc_final: 0.8047 (mttp) REVERT: B 372 GLU cc_start: 0.6875 (tt0) cc_final: 0.6465 (mp0) REVERT: C 340 LYS cc_start: 0.8500 (ttpt) cc_final: 0.8014 (mttt) REVERT: C 349 ARG cc_start: 0.8463 (mtt180) cc_final: 0.7361 (mmp-170) REVERT: D 340 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8111 (mttp) REVERT: D 349 ARG cc_start: 0.8519 (mtt180) cc_final: 0.7525 (mmm160) REVERT: D 376 LEU cc_start: 0.7864 (tp) cc_final: 0.7333 (mt) REVERT: E 340 LYS cc_start: 0.8803 (ttpt) cc_final: 0.8380 (mttt) REVERT: E 349 ARG cc_start: 0.8049 (mtt180) cc_final: 0.6558 (pmt-80) REVERT: E 370 LYS cc_start: 0.7689 (tttt) cc_final: 0.7061 (ptpt) REVERT: F 340 LYS cc_start: 0.8797 (ttpt) cc_final: 0.8380 (mtmt) REVERT: F 372 GLU cc_start: 0.6879 (tt0) cc_final: 0.6554 (mp0) REVERT: F 379 ARG cc_start: 0.3827 (pmt-80) cc_final: 0.3528 (pmt170) outliers start: 9 outliers final: 7 residues processed: 89 average time/residue: 0.5837 time to fit residues: 58.5751 Evaluate side-chains 86 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 F residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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: 0.7694 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3498 Z= 0.201 Angle : 0.523 3.356 4680 Z= 0.278 Chirality : 0.052 0.144 528 Planarity : 0.003 0.021 594 Dihedral : 5.410 17.260 462 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.78 % Allowed : 12.37 % 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: -2.02 (0.27), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 362 PHE 0.029 0.003 PHE B 378 TYR 0.010 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 98 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8621 (ttpt) cc_final: 0.8117 (mttt) REVERT: B 340 LYS cc_start: 0.8516 (ttpt) cc_final: 0.7998 (mttp) REVERT: B 372 GLU cc_start: 0.6719 (tt0) cc_final: 0.6340 (mp0) REVERT: C 340 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8035 (mtmt) REVERT: C 349 ARG cc_start: 0.8473 (mtt180) cc_final: 0.7386 (mmp-170) REVERT: D 340 LYS cc_start: 0.8495 (ttpt) cc_final: 0.8026 (mttp) REVERT: D 349 ARG cc_start: 0.8490 (mtt180) cc_final: 0.7506 (mmm160) REVERT: E 340 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8371 (mttt) REVERT: E 349 ARG cc_start: 0.8163 (mtt180) cc_final: 0.6712 (pmt-80) REVERT: E 370 LYS cc_start: 0.7725 (tttt) cc_final: 0.7014 (ptpt) REVERT: F 340 LYS cc_start: 0.8845 (ttpt) cc_final: 0.8368 (mtmt) REVERT: F 370 LYS cc_start: 0.7998 (tttt) cc_final: 0.7089 (mttt) REVERT: F 372 GLU cc_start: 0.7262 (tt0) cc_final: 0.6854 (mp0) outliers start: 11 outliers final: 7 residues processed: 89 average time/residue: 0.5640 time to fit residues: 56.8613 Evaluate side-chains 93 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 368 ASN 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 340 LYS Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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: 0.7673 moved from start: 0.6426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3498 Z= 0.152 Angle : 0.481 3.714 4680 Z= 0.252 Chirality : 0.051 0.141 528 Planarity : 0.002 0.021 594 Dihedral : 5.017 15.290 462 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.78 % Allowed : 12.37 % 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: -1.86 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.005 0.001 PHE B 378 TYR 0.006 0.002 TYR C 310 ARG 0.003 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 94 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.637 Fit side-chains REVERT: A 340 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8121 (mttt) REVERT: B 340 LYS cc_start: 0.8516 (ttpt) cc_final: 0.8016 (mtmt) REVERT: B 372 GLU cc_start: 0.6660 (tt0) cc_final: 0.6286 (mp0) REVERT: C 308 ILE cc_start: 0.7542 (mt) cc_final: 0.7269 (mm) REVERT: C 340 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8025 (mtmt) REVERT: C 349 ARG cc_start: 0.8511 (mtt180) cc_final: 0.7346 (mmp-170) REVERT: D 340 LYS cc_start: 0.8492 (mtpt) cc_final: 0.8015 (mttp) REVERT: D 349 ARG cc_start: 0.8511 (mtt180) cc_final: 0.7561 (mmm160) REVERT: E 340 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8395 (mttt) REVERT: E 349 ARG cc_start: 0.8126 (mtt180) cc_final: 0.6704 (pmt-80) REVERT: E 370 LYS cc_start: 0.7733 (tttt) cc_final: 0.7075 (ptpt) REVERT: F 340 LYS cc_start: 0.8848 (ttpt) cc_final: 0.8343 (mtmt) REVERT: F 370 LYS cc_start: 0.8041 (tttt) cc_final: 0.7155 (mttt) REVERT: F 372 GLU cc_start: 0.7257 (tt0) cc_final: 0.6812 (mp0) outliers start: 11 outliers final: 7 residues processed: 84 average time/residue: 0.5849 time to fit residues: 55.5301 Evaluate side-chains 90 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain C residue 340 LYS 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 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: 4.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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: 0.7725 moved from start: 0.6641 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= 0.282 Angle : 0.545 3.688 4680 Z= 0.291 Chirality : 0.052 0.147 528 Planarity : 0.003 0.024 594 Dihedral : 5.523 15.824 462 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.29 % Allowed : 11.62 % 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: -2.02 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 362 PHE 0.014 0.002 PHE F 378 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** 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 98 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8104 (mttt) REVERT: B 340 LYS cc_start: 0.8536 (mtpt) cc_final: 0.7991 (mttp) REVERT: B 348 ASP cc_start: 0.7508 (m-30) cc_final: 0.7243 (m-30) REVERT: B 372 GLU cc_start: 0.6751 (tt0) cc_final: 0.6399 (mp0) REVERT: C 308 ILE cc_start: 0.7701 (mt) cc_final: 0.7438 (mm) REVERT: C 340 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8035 (mtmt) REVERT: C 349 ARG cc_start: 0.8452 (mtt180) cc_final: 0.7400 (mmp-170) REVERT: D 340 LYS cc_start: 0.8571 (mtpt) cc_final: 0.8014 (mttp) REVERT: D 349 ARG cc_start: 0.8547 (mtt180) cc_final: 0.7567 (mmm160) REVERT: E 340 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8408 (mttt) REVERT: E 349 ARG cc_start: 0.8144 (mtt180) cc_final: 0.6702 (pmt-80) REVERT: E 370 LYS cc_start: 0.7776 (tttt) cc_final: 0.7009 (ptpt) REVERT: F 340 LYS cc_start: 0.8920 (ttpt) cc_final: 0.8331 (mtmt) REVERT: F 372 GLU cc_start: 0.7294 (tt0) cc_final: 0.6820 (mp0) outliers start: 17 outliers final: 10 residues processed: 85 average time/residue: 0.5691 time to fit residues: 55.0177 Evaluate side-chains 92 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain C residue 305 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 324 SER 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: 9.9990 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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: 0.7690 moved from start: 0.6796 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= 0.159 Angle : 0.479 4.145 4680 Z= 0.252 Chirality : 0.051 0.142 528 Planarity : 0.002 0.019 594 Dihedral : 4.999 14.787 462 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.03 % Allowed : 13.38 % 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: -1.90 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.008 0.001 PHE A 378 TYR 0.007 0.001 TYR A 310 ARG 0.001 0.000 ARG E 379 *********************** 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 94 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8120 (mttt) REVERT: B 340 LYS cc_start: 0.8550 (mtpt) cc_final: 0.8009 (mttp) REVERT: B 372 GLU cc_start: 0.6701 (tt0) cc_final: 0.6339 (mp0) REVERT: C 308 ILE cc_start: 0.7689 (mt) cc_final: 0.7425 (mm) REVERT: C 340 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8028 (mtmt) REVERT: C 349 ARG cc_start: 0.8506 (mtt180) cc_final: 0.7391 (mmp-170) REVERT: D 340 LYS cc_start: 0.8544 (mtpt) cc_final: 0.7989 (mttp) REVERT: D 349 ARG cc_start: 0.8578 (mtt180) cc_final: 0.7579 (mmm160) REVERT: E 340 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8405 (mttt) REVERT: E 349 ARG cc_start: 0.8127 (mtt180) cc_final: 0.6694 (pmt-80) REVERT: E 370 LYS cc_start: 0.7782 (tttt) cc_final: 0.6973 (mttt) REVERT: F 340 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8333 (mtmt) REVERT: F 370 LYS cc_start: 0.8097 (tttt) cc_final: 0.7213 (mttt) REVERT: F 372 GLU cc_start: 0.7269 (tt0) cc_final: 0.6803 (mp0) outliers start: 12 outliers final: 8 residues processed: 84 average time/residue: 0.6052 time to fit residues: 57.3799 Evaluate side-chains 89 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 368 ASN 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.6899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3498 Z= 0.175 Angle : 0.480 3.777 4680 Z= 0.252 Chirality : 0.051 0.141 528 Planarity : 0.002 0.020 594 Dihedral : 4.929 14.535 462 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.78 % Allowed : 14.14 % Favored : 83.08 % 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: -1.88 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.015 0.002 PHE A 378 TYR 0.007 0.002 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** 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 89 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8092 (mttt) REVERT: B 340 LYS cc_start: 0.8574 (mtpt) cc_final: 0.7987 (mttp) REVERT: B 372 GLU cc_start: 0.6647 (tt0) cc_final: 0.6319 (mp0) REVERT: C 308 ILE cc_start: 0.7748 (mt) cc_final: 0.7480 (mm) REVERT: C 340 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8047 (mtmt) REVERT: C 349 ARG cc_start: 0.8498 (mtt180) cc_final: 0.7388 (mmp-170) REVERT: D 349 ARG cc_start: 0.8608 (mtt180) cc_final: 0.7601 (mmm160) REVERT: E 340 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8424 (mttt) REVERT: E 349 ARG cc_start: 0.8162 (mtt180) cc_final: 0.6723 (pmt-80) REVERT: E 370 LYS cc_start: 0.7739 (tttt) cc_final: 0.6937 (mttt) REVERT: F 340 LYS cc_start: 0.8908 (mtpt) cc_final: 0.8329 (mtmt) REVERT: F 370 LYS cc_start: 0.8077 (tttt) cc_final: 0.7199 (mttt) REVERT: F 372 GLU cc_start: 0.7249 (tt0) cc_final: 0.6807 (mp0) outliers start: 11 outliers final: 7 residues processed: 81 average time/residue: 0.5617 time to fit residues: 51.4725 Evaluate side-chains 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 340 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.7084 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= 0.147 Angle : 0.463 3.827 4680 Z= 0.243 Chirality : 0.051 0.139 528 Planarity : 0.002 0.018 594 Dihedral : 4.698 14.270 462 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.53 % Allowed : 14.39 % Favored : 83.08 % 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: -1.81 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.004 0.001 PHE E 378 TYR 0.007 0.001 TYR A 310 ARG 0.001 0.000 ARG E 379 *********************** 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 89 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8097 (mttt) REVERT: B 340 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8016 (mttp) REVERT: B 372 GLU cc_start: 0.6631 (tt0) cc_final: 0.6302 (mp0) REVERT: C 308 ILE cc_start: 0.7755 (mt) cc_final: 0.7484 (mm) REVERT: C 340 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8025 (mtmt) REVERT: C 349 ARG cc_start: 0.8502 (mtt180) cc_final: 0.7435 (mmp-170) REVERT: D 349 ARG cc_start: 0.8629 (mtt180) cc_final: 0.7624 (mmm160) REVERT: E 340 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8412 (mttt) REVERT: E 349 ARG cc_start: 0.8161 (mtt180) cc_final: 0.6714 (pmt-80) REVERT: E 370 LYS cc_start: 0.7723 (tttt) cc_final: 0.6924 (mttt) REVERT: F 340 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8313 (mtmt) REVERT: F 370 LYS cc_start: 0.8081 (tttt) cc_final: 0.7201 (mttt) REVERT: F 372 GLU cc_start: 0.7270 (tt0) cc_final: 0.6815 (mp0) outliers start: 10 outliers final: 6 residues processed: 81 average time/residue: 0.6298 time to fit residues: 57.4717 Evaluate side-chains 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 368 ASN 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 340 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3498 Z= 0.251 Angle : 0.516 3.600 4680 Z= 0.273 Chirality : 0.051 0.146 528 Planarity : 0.003 0.039 594 Dihedral : 5.135 14.651 462 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.27 % Allowed : 14.14 % 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: -2.01 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.016 0.002 PHE E 378 TYR 0.008 0.002 TYR C 310 ARG 0.008 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 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8104 (mttt) REVERT: B 340 LYS cc_start: 0.8573 (mtpt) cc_final: 0.7962 (mttp) REVERT: B 372 GLU cc_start: 0.6637 (tt0) cc_final: 0.6300 (mp0) REVERT: C 308 ILE cc_start: 0.7794 (mt) cc_final: 0.7525 (mm) REVERT: C 340 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8027 (mttt) REVERT: C 349 ARG cc_start: 0.8473 (mtt180) cc_final: 0.7379 (mmp-170) REVERT: D 340 LYS cc_start: 0.8568 (mtpt) cc_final: 0.7939 (mttp) REVERT: D 349 ARG cc_start: 0.8665 (mtt180) cc_final: 0.7620 (mmm160) REVERT: D 372 GLU cc_start: 0.7706 (mp0) cc_final: 0.7440 (mp0) REVERT: E 340 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8404 (mttt) REVERT: E 349 ARG cc_start: 0.8210 (mtt180) cc_final: 0.6766 (pmt-80) REVERT: F 340 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8307 (mtmt) REVERT: F 372 GLU cc_start: 0.7381 (tt0) cc_final: 0.6873 (mp0) outliers start: 9 outliers final: 5 residues processed: 79 average time/residue: 0.6006 time to fit residues: 53.4507 Evaluate side-chains 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 358 ASP 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 340 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.183686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.161231 restraints weight = 13538.501| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 2.28 r_work: 0.4333 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4248 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.7324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3498 Z= 0.190 Angle : 0.487 3.675 4680 Z= 0.256 Chirality : 0.051 0.140 528 Planarity : 0.003 0.026 594 Dihedral : 4.945 14.877 462 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.53 % Allowed : 14.14 % 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: -1.98 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.004 0.001 PHE C 346 TYR 0.007 0.002 TYR C 310 ARG 0.003 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2988.26 seconds wall clock time: 53 minutes 32.25 seconds (3212.25 seconds total)