Starting phenix.real_space_refine on Sat Aug 3 05:26:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9m_18286/08_2024/8q9m_18286.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9m_18286/08_2024/8q9m_18286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9m_18286/08_2024/8q9m_18286.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9m_18286/08_2024/8q9m_18286.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9m_18286/08_2024/8q9m_18286.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9m_18286/08_2024/8q9m_18286.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 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 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 PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 338": "OE1" <-> "OE2" Residue "G PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 372": "OE1" <-> "OE2" Residue "G PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E 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: "G" 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} Time building chain proxies: 4.20, per 1000 atoms: 0.60 Number of scatterers: 7032 At special positions: 0 Unit cell: (114.536, 118.656, 40.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 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: 4.65 Conformation dependent library (CDL) restraints added in 769.1 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 18 sheets defined 0.0% alpha, 50.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'G' and resid 306 through 310 removed outlier: 6.446A pdb=" N VAL A 306 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL G 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE A 308 " --> pdb=" O VAL G 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 313 through 314 removed outlier: 6.713A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 317 through 322 removed outlier: 6.368A pdb=" N VAL A 318 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LYS G 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER A 320 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N SER B 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR A 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N CYS B 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS A 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 325 through 330 removed outlier: 6.214A pdb=" N GLY A 326 " --> pdb=" O ASN G 327 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N HIS G 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 328 " --> pdb=" O HIS G 329 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY B 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN A 327 " --> pdb=" O GLY B 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 337 through 342 removed outlier: 6.519A pdb=" N GLU A 338 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N SER B 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS A 340 " --> pdb=" O SER B 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 345 through 346 removed outlier: 6.376A pdb=" N ASP A 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 350 through 357 removed outlier: 6.293A pdb=" N VAL A 350 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LYS G 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 352 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLY G 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE A 354 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU G 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER A 356 " --> pdb=" O LEU G 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 360 through 362 removed outlier: 6.429A pdb=" N THR A 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 369 through 377 removed outlier: 6.482A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.550A pdb=" N GLN C 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR E 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL C 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.755A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 322 removed outlier: 6.376A pdb=" N LYS C 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N SER E 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR C 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N CYS E 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS C 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 325 through 330 removed outlier: 6.108A pdb=" N GLY C 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N HIS D 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE C 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY E 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN C 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.501A pdb=" N GLU C 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N SER E 341 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS C 340 " --> pdb=" O SER E 341 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.347A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.325A pdb=" N VAL C 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LYS D 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER C 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N GLY D 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE C 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU D 357 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER C 356 " --> pdb=" O LEU D 357 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.460A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 369 through 377 removed outlier: 6.455A pdb=" N LYS C 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLU E 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE C 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N HIS E 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR C 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU E 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS C 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) 67 hydrogen bonds defined for protein. 201 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: 2.19 Time building geometry restraints manager: 4.96 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: 925 1.46 - 1.63: 2003 1.63 - 1.81: 6 Bond restraints: 7086 Sorted by residual: bond pdb=" NE2 GLN D 336 " pdb="HE22 GLN D 336 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ASP G 314 " pdb=" H ASP G 314 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLU D 372 " pdb=" H GLU D 372 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE A 354 " pdb=" H ILE A 354 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N SER D 356 " pdb=" H SER D 356 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 96.50 - 103.03: 17 103.03 - 109.55: 5473 109.55 - 116.08: 3760 116.08 - 122.60: 2961 122.60 - 129.12: 701 Bond angle restraints: 12912 Sorted by residual: angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.69 118.13 -7.44 1.33e+00 5.65e-01 3.13e+01 angle pdb=" CA ASP A 345 " pdb=" CB ASP A 345 " pdb=" CG ASP A 345 " ideal model delta sigma weight residual 112.60 117.48 -4.88 1.00e+00 1.00e+00 2.38e+01 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.69 116.99 -6.30 1.33e+00 5.65e-01 2.24e+01 angle pdb=" C GLY E 334 " pdb=" N GLY E 335 " pdb=" CA GLY E 335 " ideal model delta sigma weight residual 120.60 125.37 -4.77 1.01e+00 9.80e-01 2.23e+01 angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 110.69 116.71 -6.02 1.33e+00 5.65e-01 2.05e+01 ... (remaining 12907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.01: 2839 13.01 - 26.01: 210 26.01 - 39.02: 78 39.02 - 52.02: 50 52.02 - 65.03: 87 Dihedral angle restraints: 3264 sinusoidal: 1866 harmonic: 1398 Sorted by residual: dihedral pdb=" CA ILE D 360 " pdb=" C ILE D 360 " pdb=" N THR D 361 " pdb=" CA THR D 361 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA SER A 320 " pdb=" C SER A 320 " pdb=" N LYS A 321 " pdb=" CA LYS A 321 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ILE E 360 " pdb=" C ILE E 360 " pdb=" N THR E 361 " pdb=" CA THR E 361 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 288 0.056 - 0.112: 143 0.112 - 0.168: 65 0.168 - 0.223: 27 0.223 - 0.279: 5 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS D 347 " pdb=" N LYS D 347 " pdb=" C LYS D 347 " pdb=" CB LYS D 347 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA LYS D 343 " pdb=" N LYS D 343 " pdb=" C LYS D 343 " pdb=" CB LYS D 343 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA LYS G 347 " pdb=" N LYS G 347 " pdb=" C LYS G 347 " pdb=" CB LYS G 347 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 525 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 310 " -0.093 2.00e-02 2.50e+03 3.89e-02 4.54e+01 pdb=" CG TYR G 310 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR G 310 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR G 310 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR G 310 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR G 310 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR G 310 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR G 310 " -0.066 2.00e-02 2.50e+03 pdb=" HD1 TYR G 310 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR G 310 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 TYR G 310 " 0.020 2.00e-02 2.50e+03 pdb=" HE2 TYR G 310 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 327 " 0.035 2.00e-02 2.50e+03 5.23e-02 4.10e+01 pdb=" CG ASN C 327 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN C 327 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 327 " -0.097 2.00e-02 2.50e+03 pdb="HD21 ASN C 327 " 0.020 2.00e-02 2.50e+03 pdb="HD22 ASN C 327 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 379 " -0.156 9.50e-02 1.11e+02 6.58e-02 3.93e+01 pdb=" NE ARG A 379 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A 379 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 379 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 379 " 0.016 2.00e-02 2.50e+03 pdb="HH11 ARG A 379 " 0.080 2.00e-02 2.50e+03 pdb="HH12 ARG A 379 " -0.076 2.00e-02 2.50e+03 pdb="HH21 ARG A 379 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 379 " 0.035 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.28: 979 2.28 - 2.86: 14743 2.86 - 3.44: 17783 3.44 - 4.02: 24326 4.02 - 4.60: 33831 Nonbonded interactions: 91662 Sorted by model distance: nonbonded pdb=" O SER C 316 " pdb=" HG SER D 316 " model vdw 1.706 2.450 nonbonded pdb=" OD2 ASP B 314 " pdb=" HZ2 LYS B 370 " model vdw 1.726 2.450 nonbonded pdb=" OD2 ASP E 314 " pdb=" HZ2 LYS E 370 " model vdw 1.732 2.450 nonbonded pdb=" HG SER A 316 " pdb=" O SER B 316 " model vdw 1.740 2.450 nonbonded pdb=" O SER A 316 " pdb=" HG SER G 316 " model vdw 1.741 2.450 ... (remaining 91657 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 'G' } 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: 6.860 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 24.830 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.036 3498 Z= 0.727 Angle : 1.761 7.439 4680 Z= 1.164 Chirality : 0.086 0.279 528 Planarity : 0.009 0.055 594 Dihedral : 11.563 62.118 1344 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: -1.02 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.005 HIS C 330 PHE 0.036 0.010 PHE E 346 TYR 0.081 0.019 TYR G 310 ARG 0.005 0.001 ARG B 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 159 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.4992 (t0) cc_final: 0.3958 (t0) REVERT: A 316 SER cc_start: 0.6151 (t) cc_final: 0.5616 (p) REVERT: A 317 LYS cc_start: 0.6109 (ptmt) cc_final: 0.5845 (ptpp) REVERT: A 321 LYS cc_start: 0.7254 (ttmt) cc_final: 0.6968 (mttt) REVERT: A 369 LYS cc_start: 0.7384 (tttt) cc_final: 0.6915 (ttmt) REVERT: G 311 LYS cc_start: 0.5741 (mtmt) cc_final: 0.5175 (tppt) REVERT: G 321 LYS cc_start: 0.7366 (ttmt) cc_final: 0.7002 (mttt) REVERT: G 340 LYS cc_start: 0.8317 (mtpt) cc_final: 0.7865 (mttt) REVERT: G 343 LYS cc_start: 0.8990 (mttt) cc_final: 0.8699 (mttp) REVERT: G 345 ASP cc_start: 0.8167 (m-30) cc_final: 0.7904 (m-30) REVERT: G 349 ARG cc_start: 0.8173 (mtt180) cc_final: 0.6322 (mmp-170) REVERT: G 369 LYS cc_start: 0.7396 (tttt) cc_final: 0.6814 (mtmt) REVERT: G 375 LYS cc_start: 0.5138 (tttt) cc_final: 0.4906 (tttp) REVERT: B 311 LYS cc_start: 0.6266 (mtmt) cc_final: 0.5744 (mttt) REVERT: B 314 ASP cc_start: 0.5184 (t0) cc_final: 0.4670 (t0) REVERT: B 320 SER cc_start: 0.8248 (t) cc_final: 0.7873 (p) REVERT: B 321 LYS cc_start: 0.7739 (ttmt) cc_final: 0.7518 (mtmt) REVERT: B 342 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8276 (tt0) REVERT: B 347 LYS cc_start: 0.8617 (mttt) cc_final: 0.7736 (pptt) REVERT: B 369 LYS cc_start: 0.7960 (tttt) cc_final: 0.7623 (ttpt) REVERT: C 314 ASP cc_start: 0.4957 (t0) cc_final: 0.4309 (t0) REVERT: C 317 LYS cc_start: 0.6008 (ptmt) cc_final: 0.5743 (ptpp) REVERT: C 321 LYS cc_start: 0.7209 (ttmt) cc_final: 0.6935 (mtmt) REVERT: C 338 GLU cc_start: 0.8287 (tt0) cc_final: 0.8064 (tt0) REVERT: C 342 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7902 (mt-10) REVERT: C 369 LYS cc_start: 0.7385 (tttt) cc_final: 0.7010 (ttmt) REVERT: D 311 LYS cc_start: 0.6166 (mtmt) cc_final: 0.5365 (tppt) REVERT: D 314 ASP cc_start: 0.5909 (t0) cc_final: 0.5648 (t0) REVERT: D 315 LEU cc_start: 0.7022 (mp) cc_final: 0.6788 (mp) REVERT: D 321 LYS cc_start: 0.7126 (ttmt) cc_final: 0.6916 (mtmt) REVERT: D 340 LYS cc_start: 0.8416 (mtpt) cc_final: 0.8050 (mttt) REVERT: D 345 ASP cc_start: 0.8201 (m-30) cc_final: 0.8000 (m-30) REVERT: D 348 ASP cc_start: 0.8984 (t0) cc_final: 0.8762 (t70) REVERT: D 349 ARG cc_start: 0.8284 (mtt180) cc_final: 0.6267 (mmp-170) REVERT: E 307 GLN cc_start: 0.6439 (mt0) cc_final: 0.6200 (tt0) REVERT: E 311 LYS cc_start: 0.6198 (mtmt) cc_final: 0.5677 (mtpt) REVERT: E 314 ASP cc_start: 0.5037 (t0) cc_final: 0.4516 (t0) REVERT: E 317 LYS cc_start: 0.7079 (ptmt) cc_final: 0.6736 (mttt) REVERT: E 321 LYS cc_start: 0.7839 (ttmt) cc_final: 0.7453 (mttt) REVERT: E 338 GLU cc_start: 0.8427 (tt0) cc_final: 0.8176 (tt0) REVERT: E 342 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8232 (tt0) REVERT: E 347 LYS cc_start: 0.8539 (mttt) cc_final: 0.7768 (pptt) REVERT: E 369 LYS cc_start: 0.8182 (tttt) cc_final: 0.7908 (ttmt) REVERT: E 379 ARG cc_start: 0.5591 (mmt-90) cc_final: 0.3179 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 3.2260 time to fit residues: 523.4799 Evaluate side-chains 115 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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: 0.7980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN G 351 GLN B 307 GLN B 327 ASN D 307 GLN D 327 ASN E 351 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3211 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= 0.186 Angle : 0.543 4.238 4680 Z= 0.284 Chirality : 0.051 0.143 528 Planarity : 0.002 0.016 594 Dihedral : 6.220 18.175 462 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 13.13 % 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: -1.08 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.82 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.004 0.001 PHE A 346 TYR 0.008 0.001 TYR A 310 ARG 0.003 0.001 ARG C 349 *********************** 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 118 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.603 Fit side-chains REVERT: A 314 ASP cc_start: 0.5548 (t0) cc_final: 0.4602 (t0) REVERT: A 321 LYS cc_start: 0.7221 (ttmt) cc_final: 0.6755 (mttt) REVERT: A 340 LYS cc_start: 0.8422 (mtpt) cc_final: 0.8003 (mttt) REVERT: A 342 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7991 (mt-10) REVERT: A 369 LYS cc_start: 0.7595 (tttt) cc_final: 0.6908 (mttt) REVERT: G 311 LYS cc_start: 0.6063 (mtmt) cc_final: 0.5201 (tppt) REVERT: G 314 ASP cc_start: 0.6789 (t70) cc_final: 0.6469 (t0) REVERT: G 316 SER cc_start: 0.6351 (t) cc_final: 0.6071 (p) REVERT: G 321 LYS cc_start: 0.7281 (ttmt) cc_final: 0.6927 (mttt) REVERT: G 340 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7890 (mttt) REVERT: G 342 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8025 (mt-10) REVERT: G 343 LYS cc_start: 0.9027 (mttt) cc_final: 0.8711 (mttp) REVERT: G 349 ARG cc_start: 0.8207 (mtt180) cc_final: 0.6362 (mmp-170) REVERT: G 369 LYS cc_start: 0.7576 (tttt) cc_final: 0.7133 (mttt) REVERT: G 375 LYS cc_start: 0.5355 (tttt) cc_final: 0.5046 (tptt) REVERT: B 311 LYS cc_start: 0.6262 (mtmt) cc_final: 0.5743 (mttt) REVERT: B 314 ASP cc_start: 0.5340 (t0) cc_final: 0.4843 (t0) REVERT: B 320 SER cc_start: 0.8466 (t) cc_final: 0.8106 (p) REVERT: B 342 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8247 (tt0) REVERT: B 347 LYS cc_start: 0.8809 (mttt) cc_final: 0.7949 (pptt) REVERT: B 369 LYS cc_start: 0.7905 (tttt) cc_final: 0.7557 (tppt) REVERT: C 314 ASP cc_start: 0.5336 (t0) cc_final: 0.4877 (t0) REVERT: C 317 LYS cc_start: 0.6287 (ptmt) cc_final: 0.5864 (ptpp) REVERT: C 321 LYS cc_start: 0.7288 (ttmt) cc_final: 0.6780 (mttt) REVERT: C 338 GLU cc_start: 0.8278 (tt0) cc_final: 0.7916 (tt0) REVERT: C 342 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7947 (mt-10) REVERT: C 348 ASP cc_start: 0.8913 (t0) cc_final: 0.8544 (t70) REVERT: C 349 ARG cc_start: 0.7991 (mtt180) cc_final: 0.7446 (mtp85) REVERT: C 369 LYS cc_start: 0.7329 (tttt) cc_final: 0.7028 (ttmt) REVERT: D 311 LYS cc_start: 0.6358 (mtmt) cc_final: 0.5337 (tppt) REVERT: D 321 LYS cc_start: 0.7249 (ttmt) cc_final: 0.6849 (mttt) REVERT: D 340 LYS cc_start: 0.8479 (mtpt) cc_final: 0.8088 (mttt) REVERT: D 349 ARG cc_start: 0.8292 (mtt180) cc_final: 0.6288 (mmp-170) REVERT: E 311 LYS cc_start: 0.6229 (mtmt) cc_final: 0.5727 (mtpt) REVERT: E 314 ASP cc_start: 0.5534 (t0) cc_final: 0.5085 (t0) REVERT: E 317 LYS cc_start: 0.7257 (ptmt) cc_final: 0.6731 (mttt) REVERT: E 320 SER cc_start: 0.8439 (t) cc_final: 0.8141 (p) REVERT: E 338 GLU cc_start: 0.8361 (tt0) cc_final: 0.8109 (tt0) REVERT: E 342 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8258 (tt0) REVERT: E 347 LYS cc_start: 0.8675 (mttt) cc_final: 0.7862 (pptt) REVERT: E 369 LYS cc_start: 0.7914 (tttt) cc_final: 0.7678 (ttmt) REVERT: E 379 ARG cc_start: 0.5385 (mmt-90) cc_final: 0.3117 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 3.3101 time to fit residues: 398.4285 Evaluate side-chains 108 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 chunk 34 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 327 ASN C 351 GLN D 307 GLN E 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3775 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= 0.201 Angle : 0.521 4.083 4680 Z= 0.270 Chirality : 0.052 0.145 528 Planarity : 0.003 0.047 594 Dihedral : 5.373 16.186 462 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.77 % Allowed : 13.64 % Favored : 84.60 % 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: -1.32 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 329 PHE 0.007 0.001 PHE G 378 TYR 0.010 0.002 TYR A 310 ARG 0.003 0.001 ARG C 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 121 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.523 Fit side-chains REVERT: A 321 LYS cc_start: 0.7270 (ttmt) cc_final: 0.6804 (mttt) REVERT: A 340 LYS cc_start: 0.8427 (mtpt) cc_final: 0.7990 (mttt) REVERT: A 342 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8013 (tt0) REVERT: A 369 LYS cc_start: 0.7603 (tttt) cc_final: 0.6896 (mttt) REVERT: G 311 LYS cc_start: 0.6022 (mtmt) cc_final: 0.5053 (tppt) REVERT: G 314 ASP cc_start: 0.6975 (t70) cc_final: 0.6684 (t0) REVERT: G 321 LYS cc_start: 0.7348 (ttmt) cc_final: 0.7009 (mttt) REVERT: G 340 LYS cc_start: 0.8357 (mtpt) cc_final: 0.7885 (mttt) REVERT: G 342 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8083 (mt-10) REVERT: G 343 LYS cc_start: 0.9058 (mttt) cc_final: 0.8846 (mttp) REVERT: G 345 ASP cc_start: 0.8096 (m-30) cc_final: 0.7870 (t70) REVERT: G 349 ARG cc_start: 0.8327 (mtt180) cc_final: 0.6457 (mmp-170) REVERT: G 369 LYS cc_start: 0.7533 (tttt) cc_final: 0.7085 (mtmt) REVERT: G 375 LYS cc_start: 0.5382 (tttt) cc_final: 0.5051 (tptt) REVERT: B 311 LYS cc_start: 0.6258 (mtmt) cc_final: 0.5746 (mttt) REVERT: B 314 ASP cc_start: 0.5466 (t0) cc_final: 0.4878 (t0) REVERT: B 320 SER cc_start: 0.8352 (t) cc_final: 0.7880 (p) REVERT: B 342 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8240 (tt0) REVERT: B 347 LYS cc_start: 0.8777 (mttt) cc_final: 0.7917 (pptt) REVERT: B 369 LYS cc_start: 0.7912 (tttt) cc_final: 0.7582 (tppt) REVERT: B 375 LYS cc_start: 0.7161 (tttt) cc_final: 0.6863 (tttp) REVERT: C 314 ASP cc_start: 0.5313 (t0) cc_final: 0.4873 (t0) REVERT: C 317 LYS cc_start: 0.6329 (ptmt) cc_final: 0.5922 (ptpp) REVERT: C 321 LYS cc_start: 0.7355 (ttmt) cc_final: 0.7036 (mtmt) REVERT: C 338 GLU cc_start: 0.8261 (tt0) cc_final: 0.7904 (tt0) REVERT: C 342 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8001 (mt-10) REVERT: C 348 ASP cc_start: 0.8845 (t0) cc_final: 0.8596 (t70) REVERT: C 349 ARG cc_start: 0.8196 (mtt180) cc_final: 0.7844 (mtp85) REVERT: C 351 GLN cc_start: 0.8683 (mt0) cc_final: 0.8390 (mt0) REVERT: C 369 LYS cc_start: 0.7256 (tttt) cc_final: 0.6762 (mtmt) REVERT: D 311 LYS cc_start: 0.6237 (mtmt) cc_final: 0.5204 (tppt) REVERT: D 321 LYS cc_start: 0.7382 (ttmt) cc_final: 0.7015 (mttt) REVERT: D 340 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8055 (mttt) REVERT: D 349 ARG cc_start: 0.8379 (mtt180) cc_final: 0.6410 (mmp-170) REVERT: E 311 LYS cc_start: 0.6215 (mtmt) cc_final: 0.5759 (mtpt) REVERT: E 314 ASP cc_start: 0.5606 (t0) cc_final: 0.4987 (t0) REVERT: E 317 LYS cc_start: 0.7269 (ptmt) cc_final: 0.6731 (mttt) REVERT: E 320 SER cc_start: 0.8499 (t) cc_final: 0.8006 (p) REVERT: E 338 GLU cc_start: 0.8353 (tt0) cc_final: 0.8115 (tt0) REVERT: E 342 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8252 (tt0) REVERT: E 347 LYS cc_start: 0.8641 (mttt) cc_final: 0.7883 (pptt) REVERT: E 369 LYS cc_start: 0.7990 (tttt) cc_final: 0.7696 (ttmt) outliers start: 7 outliers final: 1 residues processed: 115 average time/residue: 3.3324 time to fit residues: 390.8787 Evaluate side-chains 104 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 307 GLN E 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3498 Z= 0.270 Angle : 0.525 4.258 4680 Z= 0.273 Chirality : 0.051 0.142 528 Planarity : 0.002 0.024 594 Dihedral : 5.247 15.754 462 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.26 % Allowed : 13.13 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 329 PHE 0.006 0.001 PHE G 378 TYR 0.012 0.003 TYR A 310 ARG 0.003 0.001 ARG G 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 107 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 0.599 Fit side-chains REVERT: A 321 LYS cc_start: 0.7295 (ttmt) cc_final: 0.6955 (mtpt) REVERT: A 340 LYS cc_start: 0.8435 (mtpt) cc_final: 0.7974 (mttt) REVERT: A 342 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8051 (tt0) REVERT: A 369 LYS cc_start: 0.7525 (tttt) cc_final: 0.6825 (mttt) REVERT: G 311 LYS cc_start: 0.5989 (mtmt) cc_final: 0.5139 (tppt) REVERT: G 321 LYS cc_start: 0.7271 (ttmt) cc_final: 0.6937 (mttt) REVERT: G 340 LYS cc_start: 0.8350 (mtpt) cc_final: 0.7874 (mttt) REVERT: G 342 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8069 (mt-10) REVERT: G 345 ASP cc_start: 0.8106 (m-30) cc_final: 0.7893 (t70) REVERT: G 349 ARG cc_start: 0.8337 (mtt180) cc_final: 0.6313 (mmp-170) REVERT: G 369 LYS cc_start: 0.7507 (tttt) cc_final: 0.7017 (mtmt) REVERT: B 311 LYS cc_start: 0.6267 (mtmt) cc_final: 0.5727 (mttt) REVERT: B 314 ASP cc_start: 0.5349 (t0) cc_final: 0.5001 (t0) REVERT: B 340 LYS cc_start: 0.8615 (mtpt) cc_final: 0.8006 (mttm) REVERT: B 342 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8228 (tt0) REVERT: B 347 LYS cc_start: 0.8760 (mttt) cc_final: 0.7876 (pptt) REVERT: B 369 LYS cc_start: 0.7975 (tttt) cc_final: 0.7614 (ttmt) REVERT: B 375 LYS cc_start: 0.7230 (tttt) cc_final: 0.7021 (tttm) REVERT: C 314 ASP cc_start: 0.5205 (t0) cc_final: 0.4898 (t0) REVERT: C 317 LYS cc_start: 0.6235 (ptmt) cc_final: 0.5846 (ptpp) REVERT: C 321 LYS cc_start: 0.7406 (ttmt) cc_final: 0.7090 (mtmt) REVERT: C 338 GLU cc_start: 0.8260 (tt0) cc_final: 0.7900 (tt0) REVERT: C 342 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8021 (mt-10) REVERT: C 348 ASP cc_start: 0.8816 (t0) cc_final: 0.8547 (t70) REVERT: C 349 ARG cc_start: 0.8308 (mtt180) cc_final: 0.7990 (mtp85) REVERT: C 369 LYS cc_start: 0.7287 (tttt) cc_final: 0.6763 (mtmt) REVERT: D 311 LYS cc_start: 0.6028 (mtmt) cc_final: 0.5142 (tppt) REVERT: D 321 LYS cc_start: 0.7357 (ttmt) cc_final: 0.7007 (mttt) REVERT: D 340 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8012 (mttt) REVERT: D 347 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8643 (mmtm) REVERT: D 349 ARG cc_start: 0.8343 (mtt180) cc_final: 0.6322 (mmp-170) REVERT: E 311 LYS cc_start: 0.6103 (mtmt) cc_final: 0.5621 (mtpt) REVERT: E 314 ASP cc_start: 0.5637 (t0) cc_final: 0.5045 (t0) REVERT: E 317 LYS cc_start: 0.7182 (ptmt) cc_final: 0.6709 (ptpp) REVERT: E 338 GLU cc_start: 0.8398 (tt0) cc_final: 0.8163 (tt0) REVERT: E 342 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8290 (tt0) REVERT: E 347 LYS cc_start: 0.8659 (mttt) cc_final: 0.7798 (pptt) REVERT: E 369 LYS cc_start: 0.8067 (tttt) cc_final: 0.7738 (ttmt) outliers start: 5 outliers final: 2 residues processed: 105 average time/residue: 3.5096 time to fit residues: 375.8116 Evaluate side-chains 98 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 351 GLN B 307 GLN D 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4270 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= 0.238 Angle : 0.510 4.178 4680 Z= 0.263 Chirality : 0.051 0.141 528 Planarity : 0.002 0.021 594 Dihedral : 5.025 14.423 462 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.26 % Allowed : 12.63 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 329 PHE 0.006 0.001 PHE A 378 TYR 0.011 0.002 TYR A 310 ARG 0.003 0.001 ARG A 349 *********************** 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 104 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7315 (ttmt) cc_final: 0.6987 (mtpt) REVERT: A 340 LYS cc_start: 0.8415 (mtpt) cc_final: 0.7964 (mttt) REVERT: A 342 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8055 (tt0) REVERT: A 369 LYS cc_start: 0.7540 (tttt) cc_final: 0.6874 (mttt) REVERT: G 311 LYS cc_start: 0.6005 (mtmt) cc_final: 0.5060 (tppt) REVERT: G 321 LYS cc_start: 0.7327 (ttmt) cc_final: 0.7020 (mttt) REVERT: G 340 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7848 (mttt) REVERT: G 342 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8107 (mt-10) REVERT: G 345 ASP cc_start: 0.8124 (m-30) cc_final: 0.7875 (t0) REVERT: G 349 ARG cc_start: 0.8369 (mtt180) cc_final: 0.6481 (mmp-170) REVERT: G 369 LYS cc_start: 0.7530 (tttt) cc_final: 0.7051 (mtmt) REVERT: B 311 LYS cc_start: 0.6242 (mtmt) cc_final: 0.5711 (mttt) REVERT: B 314 ASP cc_start: 0.5425 (t0) cc_final: 0.5000 (t0) REVERT: B 340 LYS cc_start: 0.8659 (mtpt) cc_final: 0.8030 (mttm) REVERT: B 342 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8244 (tt0) REVERT: B 347 LYS cc_start: 0.8759 (mttt) cc_final: 0.7846 (pptt) REVERT: B 349 ARG cc_start: 0.8208 (mtp85) cc_final: 0.7964 (mtt90) REVERT: B 369 LYS cc_start: 0.7933 (tttt) cc_final: 0.7590 (ttmt) REVERT: B 375 LYS cc_start: 0.7211 (tttt) cc_final: 0.7007 (tttm) REVERT: C 314 ASP cc_start: 0.5144 (t0) cc_final: 0.4839 (t0) REVERT: C 317 LYS cc_start: 0.6270 (ptmt) cc_final: 0.5864 (ptpp) REVERT: C 338 GLU cc_start: 0.8274 (tt0) cc_final: 0.7918 (tt0) REVERT: C 342 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8018 (mt-10) REVERT: C 348 ASP cc_start: 0.8801 (t0) cc_final: 0.8494 (t70) REVERT: C 349 ARG cc_start: 0.8329 (mtt180) cc_final: 0.7982 (mtp85) REVERT: C 369 LYS cc_start: 0.7286 (tttt) cc_final: 0.6755 (mtmt) REVERT: D 311 LYS cc_start: 0.6211 (mtmt) cc_final: 0.5265 (tppt) REVERT: D 321 LYS cc_start: 0.7384 (ttmt) cc_final: 0.7017 (mtpt) REVERT: D 340 LYS cc_start: 0.8455 (mtpt) cc_final: 0.7999 (mttt) REVERT: D 349 ARG cc_start: 0.8371 (mtt180) cc_final: 0.6359 (mmp-170) REVERT: E 311 LYS cc_start: 0.6111 (mtmt) cc_final: 0.5663 (mtpt) REVERT: E 314 ASP cc_start: 0.5754 (t0) cc_final: 0.5142 (t0) REVERT: E 317 LYS cc_start: 0.7189 (ptmt) cc_final: 0.6693 (ptpp) REVERT: E 338 GLU cc_start: 0.8359 (tt0) cc_final: 0.8121 (tt0) REVERT: E 342 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8295 (tt0) REVERT: E 347 LYS cc_start: 0.8673 (mttt) cc_final: 0.7815 (pptt) REVERT: E 369 LYS cc_start: 0.7976 (tttt) cc_final: 0.7704 (ttmt) outliers start: 5 outliers final: 3 residues processed: 101 average time/residue: 3.4555 time to fit residues: 356.3452 Evaluate side-chains 100 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.0370 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 overall best weight: 2.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4358 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= 0.244 Angle : 0.506 4.362 4680 Z= 0.260 Chirality : 0.050 0.141 528 Planarity : 0.002 0.023 594 Dihedral : 4.966 14.087 462 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.52 % Allowed : 13.64 % 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: -1.54 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 329 PHE 0.005 0.001 PHE A 378 TYR 0.010 0.002 TYR A 310 ARG 0.002 0.000 ARG G 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 102 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.599 Fit side-chains REVERT: A 321 LYS cc_start: 0.7281 (ttmt) cc_final: 0.6966 (mtpt) REVERT: A 340 LYS cc_start: 0.8409 (mtpt) cc_final: 0.7954 (mttt) REVERT: A 342 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8082 (tt0) REVERT: A 369 LYS cc_start: 0.7563 (tttt) cc_final: 0.6882 (mttt) REVERT: G 311 LYS cc_start: 0.5983 (mtmt) cc_final: 0.5081 (tppt) REVERT: G 321 LYS cc_start: 0.7273 (ttmt) cc_final: 0.6952 (mttt) REVERT: G 340 LYS cc_start: 0.8306 (mtpt) cc_final: 0.7825 (mttm) REVERT: G 342 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8108 (mt-10) REVERT: G 345 ASP cc_start: 0.8126 (m-30) cc_final: 0.7874 (t0) REVERT: G 349 ARG cc_start: 0.8328 (mtt180) cc_final: 0.6301 (mmp-170) REVERT: G 369 LYS cc_start: 0.7548 (tttt) cc_final: 0.7091 (mtmt) REVERT: B 311 LYS cc_start: 0.6196 (mtmt) cc_final: 0.5668 (mttt) REVERT: B 314 ASP cc_start: 0.5451 (t0) cc_final: 0.5026 (t0) REVERT: B 340 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8034 (mttm) REVERT: B 342 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8269 (tt0) REVERT: B 347 LYS cc_start: 0.8758 (mttt) cc_final: 0.7821 (pptt) REVERT: B 349 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7968 (mtt90) REVERT: B 369 LYS cc_start: 0.7950 (tttt) cc_final: 0.7636 (ttmt) REVERT: B 375 LYS cc_start: 0.7209 (tttt) cc_final: 0.7001 (tttm) REVERT: C 314 ASP cc_start: 0.5125 (t0) cc_final: 0.4801 (t0) REVERT: C 317 LYS cc_start: 0.6266 (ptmt) cc_final: 0.5856 (ptpp) REVERT: C 338 GLU cc_start: 0.8274 (tt0) cc_final: 0.7918 (tt0) REVERT: C 342 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8015 (mt-10) REVERT: C 348 ASP cc_start: 0.8779 (t0) cc_final: 0.8519 (t70) REVERT: C 349 ARG cc_start: 0.8292 (mtt180) cc_final: 0.7906 (mtp85) REVERT: C 369 LYS cc_start: 0.7352 (tttt) cc_final: 0.6782 (mtmt) REVERT: D 311 LYS cc_start: 0.6079 (mtmt) cc_final: 0.5153 (tppt) REVERT: D 340 LYS cc_start: 0.8431 (mtpt) cc_final: 0.7953 (mttt) REVERT: D 349 ARG cc_start: 0.8351 (mtt180) cc_final: 0.6358 (mmp-170) REVERT: E 311 LYS cc_start: 0.6085 (mtmt) cc_final: 0.5616 (mtpt) REVERT: E 314 ASP cc_start: 0.5716 (t0) cc_final: 0.5136 (t0) REVERT: E 317 LYS cc_start: 0.7184 (ptmt) cc_final: 0.6709 (ptpp) REVERT: E 338 GLU cc_start: 0.8364 (tt0) cc_final: 0.8128 (tt0) REVERT: E 342 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8283 (tt0) REVERT: E 347 LYS cc_start: 0.8675 (mttt) cc_final: 0.7787 (pptt) REVERT: E 349 ARG cc_start: 0.8516 (mtp85) cc_final: 0.8211 (mtp85) REVERT: E 369 LYS cc_start: 0.8015 (tttt) cc_final: 0.7710 (ttmt) outliers start: 6 outliers final: 3 residues processed: 99 average time/residue: 3.4286 time to fit residues: 346.5737 Evaluate side-chains 93 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3498 Z= 0.254 Angle : 0.515 5.557 4680 Z= 0.263 Chirality : 0.050 0.141 528 Planarity : 0.002 0.021 594 Dihedral : 4.934 14.212 462 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.52 % Allowed : 13.89 % Favored : 84.60 % 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: -1.56 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 329 PHE 0.005 0.001 PHE A 378 TYR 0.010 0.002 TYR A 310 ARG 0.003 0.000 ARG A 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 97 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.540 Fit side-chains REVERT: A 321 LYS cc_start: 0.7261 (ttmt) cc_final: 0.6978 (mtpt) REVERT: A 340 LYS cc_start: 0.8434 (mtpt) cc_final: 0.7954 (mttt) REVERT: A 342 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8088 (tt0) REVERT: A 349 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7872 (mtp180) REVERT: A 369 LYS cc_start: 0.7528 (tttt) cc_final: 0.6870 (mttt) REVERT: G 311 LYS cc_start: 0.5959 (mtmt) cc_final: 0.5094 (tppt) REVERT: G 321 LYS cc_start: 0.7325 (ttmt) cc_final: 0.7000 (mttt) REVERT: G 340 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7815 (mttm) REVERT: G 342 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8117 (mt-10) REVERT: G 345 ASP cc_start: 0.8112 (m-30) cc_final: 0.7886 (t0) REVERT: G 349 ARG cc_start: 0.8359 (mtt180) cc_final: 0.6472 (mmp-170) REVERT: G 369 LYS cc_start: 0.7559 (tttt) cc_final: 0.7088 (mtmt) REVERT: B 311 LYS cc_start: 0.6200 (mtmt) cc_final: 0.5673 (mttt) REVERT: B 314 ASP cc_start: 0.5465 (t0) cc_final: 0.5054 (t0) REVERT: B 340 LYS cc_start: 0.8652 (mtpt) cc_final: 0.8048 (mttm) REVERT: B 342 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8267 (tt0) REVERT: B 347 LYS cc_start: 0.8744 (mttt) cc_final: 0.7795 (pptt) REVERT: B 349 ARG cc_start: 0.8287 (mtp85) cc_final: 0.7983 (mtt90) REVERT: B 369 LYS cc_start: 0.7948 (tttt) cc_final: 0.7637 (ttmt) REVERT: B 375 LYS cc_start: 0.7211 (tttt) cc_final: 0.7003 (tttm) REVERT: C 314 ASP cc_start: 0.5133 (t0) cc_final: 0.4848 (t0) REVERT: C 317 LYS cc_start: 0.6272 (ptmt) cc_final: 0.5885 (ptpp) REVERT: C 338 GLU cc_start: 0.8289 (tt0) cc_final: 0.7932 (tt0) REVERT: C 342 GLU cc_start: 0.8495 (mt-10) cc_final: 0.7986 (mt-10) REVERT: C 348 ASP cc_start: 0.8793 (t0) cc_final: 0.8546 (t70) REVERT: C 349 ARG cc_start: 0.8322 (mtt180) cc_final: 0.7960 (mtp85) REVERT: C 369 LYS cc_start: 0.7393 (tttt) cc_final: 0.6833 (mtmt) REVERT: D 349 ARG cc_start: 0.8354 (mtt180) cc_final: 0.6361 (mmp-170) REVERT: E 311 LYS cc_start: 0.6086 (mtmt) cc_final: 0.5616 (mtpt) REVERT: E 314 ASP cc_start: 0.5715 (t0) cc_final: 0.5126 (t0) REVERT: E 317 LYS cc_start: 0.7201 (ptmt) cc_final: 0.6696 (ptpp) REVERT: E 338 GLU cc_start: 0.8351 (tt0) cc_final: 0.8115 (tt0) REVERT: E 342 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8283 (tt0) REVERT: E 347 LYS cc_start: 0.8680 (mttt) cc_final: 0.7790 (pptt) REVERT: E 349 ARG cc_start: 0.8529 (mtp85) cc_final: 0.8237 (mtp85) REVERT: E 369 LYS cc_start: 0.8055 (tttt) cc_final: 0.7739 (ttmt) outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 3.2943 time to fit residues: 312.7437 Evaluate side-chains 94 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN D 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4496 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= 0.224 Angle : 0.493 4.291 4680 Z= 0.253 Chirality : 0.050 0.139 528 Planarity : 0.002 0.020 594 Dihedral : 4.840 13.720 462 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.01 % Allowed : 14.39 % Favored : 84.60 % 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: -1.57 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 362 PHE 0.004 0.001 PHE A 378 TYR 0.009 0.002 TYR A 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 95 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.520 Fit side-chains REVERT: A 321 LYS cc_start: 0.7276 (ttmt) cc_final: 0.6980 (mtpt) REVERT: A 340 LYS cc_start: 0.8430 (mtpt) cc_final: 0.7937 (mttt) REVERT: A 342 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8102 (tt0) REVERT: A 369 LYS cc_start: 0.7531 (tttt) cc_final: 0.6896 (mttt) REVERT: G 311 LYS cc_start: 0.5982 (mtmt) cc_final: 0.5081 (tppt) REVERT: G 321 LYS cc_start: 0.7307 (ttmt) cc_final: 0.6970 (mttt) REVERT: G 340 LYS cc_start: 0.8278 (mtpt) cc_final: 0.7810 (mttm) REVERT: G 342 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8113 (mt-10) REVERT: G 345 ASP cc_start: 0.8123 (m-30) cc_final: 0.7894 (t70) REVERT: G 349 ARG cc_start: 0.8368 (mtt180) cc_final: 0.6413 (mmp-170) REVERT: G 369 LYS cc_start: 0.7568 (tttt) cc_final: 0.7078 (mtmt) REVERT: B 311 LYS cc_start: 0.6185 (mtmt) cc_final: 0.5657 (mttt) REVERT: B 314 ASP cc_start: 0.5496 (t0) cc_final: 0.5074 (t0) REVERT: B 340 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8045 (mttm) REVERT: B 342 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8260 (tt0) REVERT: B 347 LYS cc_start: 0.8733 (mttt) cc_final: 0.7772 (pptt) REVERT: B 349 ARG cc_start: 0.8282 (mtp85) cc_final: 0.7953 (mtt90) REVERT: B 369 LYS cc_start: 0.7926 (tttt) cc_final: 0.7586 (ttmt) REVERT: B 375 LYS cc_start: 0.7213 (tttt) cc_final: 0.7006 (tttm) REVERT: C 314 ASP cc_start: 0.5158 (t0) cc_final: 0.4828 (t0) REVERT: C 317 LYS cc_start: 0.6279 (ptmt) cc_final: 0.5887 (ptpp) REVERT: C 338 GLU cc_start: 0.8287 (tt0) cc_final: 0.7923 (tt0) REVERT: C 342 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8004 (mt-10) REVERT: C 348 ASP cc_start: 0.8788 (t0) cc_final: 0.8525 (t70) REVERT: C 349 ARG cc_start: 0.8313 (mtt180) cc_final: 0.7946 (mtp85) REVERT: C 369 LYS cc_start: 0.7390 (tttt) cc_final: 0.6832 (mtmt) REVERT: D 349 ARG cc_start: 0.8359 (mtt180) cc_final: 0.6373 (mmp-170) REVERT: E 311 LYS cc_start: 0.6083 (mtmt) cc_final: 0.5612 (mtpt) REVERT: E 314 ASP cc_start: 0.5741 (t0) cc_final: 0.5107 (t0) REVERT: E 317 LYS cc_start: 0.7192 (ptmt) cc_final: 0.6685 (ptpp) REVERT: E 338 GLU cc_start: 0.8330 (tt0) cc_final: 0.8066 (tt0) REVERT: E 342 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8282 (tt0) REVERT: E 347 LYS cc_start: 0.8674 (mttt) cc_final: 0.7779 (pptt) REVERT: E 349 ARG cc_start: 0.8517 (mtp85) cc_final: 0.8242 (mtp85) REVERT: E 369 LYS cc_start: 0.8033 (tttt) cc_final: 0.7738 (ttmt) outliers start: 4 outliers final: 3 residues processed: 93 average time/residue: 3.3617 time to fit residues: 319.1598 Evaluate side-chains 91 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 0.0270 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 351 GLN D 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4626 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= 0.138 Angle : 0.462 4.755 4680 Z= 0.234 Chirality : 0.051 0.134 528 Planarity : 0.002 0.014 594 Dihedral : 4.483 12.551 462 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.26 % Allowed : 14.14 % Favored : 84.60 % 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 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 362 PHE 0.002 0.000 PHE A 378 TYR 0.006 0.002 TYR C 310 ARG 0.002 0.000 ARG G 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 101 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.586 Fit side-chains REVERT: A 321 LYS cc_start: 0.7266 (ttmt) cc_final: 0.6975 (mtpt) REVERT: A 340 LYS cc_start: 0.8439 (mtpt) cc_final: 0.7964 (mttt) REVERT: A 342 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8041 (tt0) REVERT: A 349 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7873 (mtp180) REVERT: A 369 LYS cc_start: 0.7498 (tttt) cc_final: 0.6859 (mttt) REVERT: G 311 LYS cc_start: 0.6098 (mtmt) cc_final: 0.5097 (tppt) REVERT: G 321 LYS cc_start: 0.7268 (ttmt) cc_final: 0.6965 (mttt) REVERT: G 340 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7789 (mttm) REVERT: G 342 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8137 (mt-10) REVERT: G 345 ASP cc_start: 0.8130 (m-30) cc_final: 0.7879 (t0) REVERT: G 349 ARG cc_start: 0.8358 (mtt180) cc_final: 0.6380 (mmp-170) REVERT: G 369 LYS cc_start: 0.7634 (tttt) cc_final: 0.7152 (mtmt) REVERT: B 307 GLN cc_start: 0.6259 (mt0) cc_final: 0.5811 (tt0) REVERT: B 311 LYS cc_start: 0.6186 (mtmt) cc_final: 0.5678 (mttt) REVERT: B 314 ASP cc_start: 0.5650 (t0) cc_final: 0.5145 (t0) REVERT: B 340 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8016 (mttm) REVERT: B 342 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8239 (tt0) REVERT: B 347 LYS cc_start: 0.8742 (mttt) cc_final: 0.7737 (pptt) REVERT: B 349 ARG cc_start: 0.8258 (mtp85) cc_final: 0.7976 (mtt90) REVERT: B 369 LYS cc_start: 0.7843 (tttt) cc_final: 0.7513 (ttmt) REVERT: B 375 LYS cc_start: 0.7237 (tttt) cc_final: 0.6917 (tttp) REVERT: C 314 ASP cc_start: 0.5223 (t0) cc_final: 0.4831 (t0) REVERT: C 317 LYS cc_start: 0.6324 (ptmt) cc_final: 0.5914 (ptpp) REVERT: C 338 GLU cc_start: 0.8272 (tt0) cc_final: 0.7915 (tt0) REVERT: C 342 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8060 (mt-10) REVERT: C 348 ASP cc_start: 0.8760 (t0) cc_final: 0.8512 (t70) REVERT: C 349 ARG cc_start: 0.8324 (mtt180) cc_final: 0.8014 (mtp85) REVERT: C 351 GLN cc_start: 0.8664 (mt0) cc_final: 0.8364 (mt0) REVERT: C 369 LYS cc_start: 0.7416 (tttt) cc_final: 0.6817 (mtmt) REVERT: D 311 LYS cc_start: 0.6301 (mtmt) cc_final: 0.5282 (tppt) REVERT: D 342 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8177 (mt-10) REVERT: D 349 ARG cc_start: 0.8417 (mtt180) cc_final: 0.6462 (mmp-170) REVERT: E 311 LYS cc_start: 0.6095 (mtmt) cc_final: 0.5622 (mtpt) REVERT: E 314 ASP cc_start: 0.5884 (t0) cc_final: 0.5225 (t0) REVERT: E 317 LYS cc_start: 0.7227 (ptmt) cc_final: 0.6717 (ptpp) REVERT: E 338 GLU cc_start: 0.8298 (tt0) cc_final: 0.8043 (tt0) REVERT: E 342 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8289 (tt0) REVERT: E 347 LYS cc_start: 0.8686 (mttt) cc_final: 0.7788 (pptt) REVERT: E 349 ARG cc_start: 0.8498 (mtp85) cc_final: 0.8177 (mtt90) REVERT: E 369 LYS cc_start: 0.7789 (tttt) cc_final: 0.7491 (ttmt) outliers start: 5 outliers final: 3 residues processed: 98 average time/residue: 3.3747 time to fit residues: 337.7444 Evaluate side-chains 94 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.0170 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN G 351 GLN D 307 GLN D 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4678 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= 0.145 Angle : 0.457 4.714 4680 Z= 0.232 Chirality : 0.051 0.136 528 Planarity : 0.002 0.012 594 Dihedral : 4.331 11.642 462 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.01 % Allowed : 14.65 % 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: -1.48 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 362 PHE 0.003 0.001 PHE A 378 TYR 0.006 0.002 TYR A 310 ARG 0.002 0.000 ARG G 379 ********************** 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 97 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7271 (ttmt) cc_final: 0.6966 (mtpt) REVERT: A 340 LYS cc_start: 0.8435 (mtpt) cc_final: 0.7953 (mttt) REVERT: A 342 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8053 (tt0) REVERT: A 349 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7778 (mtp180) REVERT: A 369 LYS cc_start: 0.7429 (tttt) cc_final: 0.6812 (mttt) REVERT: G 311 LYS cc_start: 0.6097 (mtmt) cc_final: 0.5094 (tppt) REVERT: G 319 THR cc_start: 0.7776 (m) cc_final: 0.7290 (p) REVERT: G 321 LYS cc_start: 0.7252 (ttmt) cc_final: 0.6942 (mttt) REVERT: G 340 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7790 (mttm) REVERT: G 342 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8004 (tt0) REVERT: G 345 ASP cc_start: 0.8134 (m-30) cc_final: 0.7875 (t0) REVERT: G 351 GLN cc_start: 0.8848 (mt0) cc_final: 0.8585 (mt0) REVERT: G 369 LYS cc_start: 0.7647 (tttt) cc_final: 0.7159 (mtmt) REVERT: B 307 GLN cc_start: 0.6268 (mt0) cc_final: 0.5861 (tt0) REVERT: B 311 LYS cc_start: 0.6177 (mtmt) cc_final: 0.5666 (mttt) REVERT: B 314 ASP cc_start: 0.5680 (t0) cc_final: 0.5167 (t0) REVERT: B 340 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8027 (mttm) REVERT: B 342 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8203 (tt0) REVERT: B 347 LYS cc_start: 0.8747 (mttt) cc_final: 0.7736 (pptt) REVERT: B 349 ARG cc_start: 0.8329 (mtp85) cc_final: 0.8053 (mtt90) REVERT: B 369 LYS cc_start: 0.7868 (tttt) cc_final: 0.7541 (ttmt) REVERT: B 375 LYS cc_start: 0.7253 (tttt) cc_final: 0.6910 (tttp) REVERT: C 314 ASP cc_start: 0.5200 (t0) cc_final: 0.4844 (t0) REVERT: C 317 LYS cc_start: 0.6305 (ptmt) cc_final: 0.5896 (ptpp) REVERT: C 338 GLU cc_start: 0.8287 (tt0) cc_final: 0.7955 (tt0) REVERT: C 342 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8189 (mt-10) REVERT: C 348 ASP cc_start: 0.8757 (t0) cc_final: 0.8513 (t70) REVERT: C 349 ARG cc_start: 0.8334 (mtt180) cc_final: 0.8031 (mtp85) REVERT: C 351 GLN cc_start: 0.8670 (mt0) cc_final: 0.8370 (mt0) REVERT: C 369 LYS cc_start: 0.7451 (tttt) cc_final: 0.6859 (mtmt) REVERT: D 311 LYS cc_start: 0.6314 (mtmt) cc_final: 0.5291 (tppt) REVERT: D 342 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8157 (mt-10) REVERT: D 349 ARG cc_start: 0.8408 (mtt180) cc_final: 0.6447 (mmp-170) REVERT: E 311 LYS cc_start: 0.6089 (mtmt) cc_final: 0.5655 (mtpt) REVERT: E 314 ASP cc_start: 0.5899 (t0) cc_final: 0.5263 (t0) REVERT: E 317 LYS cc_start: 0.7229 (ptmt) cc_final: 0.6714 (ptpp) REVERT: E 338 GLU cc_start: 0.8301 (tt0) cc_final: 0.8050 (tt0) REVERT: E 342 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8290 (tt0) REVERT: E 347 LYS cc_start: 0.8701 (mttt) cc_final: 0.7803 (pptt) REVERT: E 349 ARG cc_start: 0.8497 (mtp85) cc_final: 0.8183 (mtt90) REVERT: E 369 LYS cc_start: 0.7819 (tttt) cc_final: 0.7518 (ttmt) outliers start: 4 outliers final: 3 residues processed: 94 average time/residue: 3.4023 time to fit residues: 326.3037 Evaluate side-chains 96 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN D 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.131979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.115950 restraints weight = 11656.426| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.44 r_work: 0.3680 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3498 Z= 0.182 Angle : 0.468 4.674 4680 Z= 0.239 Chirality : 0.050 0.137 528 Planarity : 0.002 0.013 594 Dihedral : 4.456 11.831 462 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.01 % Allowed : 14.65 % 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: -1.49 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 362 PHE 0.004 0.001 PHE A 378 TYR 0.008 0.002 TYR A 310 ARG 0.002 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6217.55 seconds wall clock time: 107 minutes 42.25 seconds (6462.25 seconds total)