Starting phenix.real_space_refine on Mon Mar 11 04:36:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9m_18286/03_2024/8q9m_18286.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9m_18286/03_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_18286/03_2024/8q9m_18286.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9m_18286/03_2024/8q9m_18286.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9m_18286/03_2024/8q9m_18286.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9m_18286/03_2024/8q9m_18286.pdb" } 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-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: "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: 3.57, per 1000 atoms: 0.51 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: 5.18 Conformation dependent library (CDL) restraints added in 662.1 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: 0.57 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: 2.17 Time building geometry restraints manager: 5.41 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 1.850 nonbonded pdb=" OD2 ASP B 314 " pdb=" HZ2 LYS B 370 " model vdw 1.726 1.850 nonbonded pdb=" OD2 ASP E 314 " pdb=" HZ2 LYS E 370 " model vdw 1.732 1.850 nonbonded pdb=" HG SER A 316 " pdb=" O SER B 316 " model vdw 1.740 1.850 nonbonded pdb=" O SER A 316 " pdb=" HG SER G 316 " model vdw 1.741 1.850 ... (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 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: 2.960 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: 11.760 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 25.040 Find NCS groups from input model: 0.310 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:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.970 ------------------------------------------------------------------------------- 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 : 0.568 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: 3.1738 time to fit residues: 515.0485 Evaluate side-chains 115 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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: 0.8980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.7804 moved from start: 0.3141 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= 0.192 Angle : 0.553 4.202 4680 Z= 0.288 Chirality : 0.049 0.133 528 Planarity : 0.002 0.016 594 Dihedral : 6.179 18.818 462 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 12.88 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.85 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 330 PHE 0.005 0.001 PHE A 346 TYR 0.008 0.002 TYR A 310 ARG 0.003 0.001 ARG A 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 119 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.638 Fit side-chains REVERT: A 314 ASP cc_start: 0.5401 (t0) cc_final: 0.4500 (t0) REVERT: A 321 LYS cc_start: 0.7149 (ttmt) cc_final: 0.6684 (mttt) REVERT: A 340 LYS cc_start: 0.8367 (mtpt) cc_final: 0.7930 (mttt) REVERT: A 342 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7976 (mt-10) REVERT: A 369 LYS cc_start: 0.7463 (tttt) cc_final: 0.6802 (mttt) REVERT: G 311 LYS cc_start: 0.6004 (mtmt) cc_final: 0.5237 (tppt) REVERT: G 314 ASP cc_start: 0.6673 (t70) cc_final: 0.6353 (t0) REVERT: G 321 LYS cc_start: 0.7155 (ttmt) cc_final: 0.6795 (mttt) REVERT: G 340 LYS cc_start: 0.8353 (mtpt) cc_final: 0.7895 (mttt) REVERT: G 342 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7997 (mt-10) REVERT: G 343 LYS cc_start: 0.9047 (mttt) cc_final: 0.8742 (mttp) REVERT: G 349 ARG cc_start: 0.8117 (mtt180) cc_final: 0.6288 (mmp-170) REVERT: G 369 LYS cc_start: 0.7426 (tttt) cc_final: 0.6976 (mttt) REVERT: G 375 LYS cc_start: 0.5296 (tttt) cc_final: 0.4987 (tptt) REVERT: B 311 LYS cc_start: 0.6255 (mtmt) cc_final: 0.5729 (mttt) REVERT: B 314 ASP cc_start: 0.4988 (t0) cc_final: 0.4707 (t0) REVERT: B 320 SER cc_start: 0.8477 (t) cc_final: 0.8057 (p) REVERT: B 342 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8253 (tt0) REVERT: B 347 LYS cc_start: 0.8789 (mttt) cc_final: 0.7940 (pptt) REVERT: B 369 LYS cc_start: 0.7986 (tttt) cc_final: 0.7632 (tppt) REVERT: C 317 LYS cc_start: 0.6179 (ptmt) cc_final: 0.5775 (ptpp) REVERT: C 321 LYS cc_start: 0.7206 (ttmt) cc_final: 0.6877 (mtmt) REVERT: C 338 GLU cc_start: 0.8208 (tt0) cc_final: 0.7871 (tt0) REVERT: C 342 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7935 (mt-10) REVERT: C 348 ASP cc_start: 0.8942 (t0) cc_final: 0.8693 (t70) REVERT: C 349 ARG cc_start: 0.7903 (mtt180) cc_final: 0.7611 (mtp85) REVERT: C 369 LYS cc_start: 0.7299 (tttt) cc_final: 0.6989 (ttmt) REVERT: D 311 LYS cc_start: 0.6355 (mtmt) cc_final: 0.5334 (tppt) REVERT: D 321 LYS cc_start: 0.7291 (ttmt) cc_final: 0.6890 (mttt) REVERT: D 340 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8078 (mttt) REVERT: D 345 ASP cc_start: 0.8111 (m-30) cc_final: 0.7905 (m-30) REVERT: D 349 ARG cc_start: 0.8210 (mtt180) cc_final: 0.6222 (mmp-170) REVERT: E 307 GLN cc_start: 0.6520 (mt0) cc_final: 0.6230 (tt0) REVERT: E 311 LYS cc_start: 0.6182 (mtmt) cc_final: 0.5689 (mtpt) REVERT: E 314 ASP cc_start: 0.4995 (t0) cc_final: 0.4617 (t0) REVERT: E 317 LYS cc_start: 0.7248 (ptmt) cc_final: 0.6642 (mttt) REVERT: E 320 SER cc_start: 0.8397 (t) cc_final: 0.8006 (p) REVERT: E 338 GLU cc_start: 0.8432 (tt0) cc_final: 0.8192 (tt0) REVERT: E 342 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8251 (tt0) REVERT: E 347 LYS cc_start: 0.8656 (mttt) cc_final: 0.7890 (pptt) REVERT: E 369 LYS cc_start: 0.8114 (tttt) cc_final: 0.7854 (ttmt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 3.3391 time to fit residues: 405.5156 Evaluate side-chains 107 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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: 5.9990 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 0.0010 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- 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 C 327 ASN D 307 GLN E 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3751 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= 0.285 Angle : 0.554 3.988 4680 Z= 0.287 Chirality : 0.050 0.139 528 Planarity : 0.003 0.046 594 Dihedral : 5.552 16.724 462 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.52 % Allowed : 13.38 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 329 PHE 0.008 0.002 PHE G 378 TYR 0.013 0.003 TYR A 310 ARG 0.004 0.001 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 114 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7208 (ttmt) cc_final: 0.6872 (mtpt) REVERT: A 340 LYS cc_start: 0.8416 (mtpt) cc_final: 0.7945 (mttt) REVERT: A 342 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8011 (tt0) REVERT: A 369 LYS cc_start: 0.7495 (tttt) cc_final: 0.6853 (mttt) REVERT: G 311 LYS cc_start: 0.5951 (mtmt) cc_final: 0.5174 (tppt) REVERT: G 321 LYS cc_start: 0.7136 (ttmt) cc_final: 0.6785 (mttt) REVERT: G 340 LYS cc_start: 0.8357 (mtpt) cc_final: 0.7877 (mttt) REVERT: G 342 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8040 (mt-10) REVERT: G 343 LYS cc_start: 0.9076 (mttt) cc_final: 0.8871 (mttp) REVERT: G 345 ASP cc_start: 0.8072 (m-30) cc_final: 0.7838 (t70) REVERT: G 349 ARG cc_start: 0.8237 (mtt180) cc_final: 0.6354 (mmp-170) REVERT: G 351 GLN cc_start: 0.8674 (mt0) cc_final: 0.8454 (mt0) REVERT: G 369 LYS cc_start: 0.7417 (tttt) cc_final: 0.6964 (mtmt) REVERT: B 311 LYS cc_start: 0.6296 (mtmt) cc_final: 0.5773 (mttt) REVERT: B 314 ASP cc_start: 0.5006 (t0) cc_final: 0.4455 (t0) REVERT: B 342 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8279 (tt0) REVERT: B 347 LYS cc_start: 0.8706 (mttt) cc_final: 0.7858 (pptt) REVERT: B 369 LYS cc_start: 0.7987 (tttt) cc_final: 0.7644 (ttpt) REVERT: B 375 LYS cc_start: 0.7223 (tttt) cc_final: 0.7014 (tttm) REVERT: C 314 ASP cc_start: 0.5125 (t0) cc_final: 0.4477 (t0) REVERT: C 317 LYS cc_start: 0.6192 (ptmt) cc_final: 0.5799 (ptpp) REVERT: C 321 LYS cc_start: 0.7407 (ttmt) cc_final: 0.7064 (mtmt) REVERT: C 338 GLU cc_start: 0.8237 (tt0) cc_final: 0.7870 (tt0) REVERT: C 342 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7992 (mt-10) REVERT: C 348 ASP cc_start: 0.8881 (t0) cc_final: 0.8668 (t70) REVERT: C 349 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7920 (mtp180) REVERT: C 369 LYS cc_start: 0.7242 (tttt) cc_final: 0.6716 (mtmt) REVERT: D 311 LYS cc_start: 0.6138 (mtmt) cc_final: 0.5235 (tppt) REVERT: D 321 LYS cc_start: 0.7398 (ttmt) cc_final: 0.7082 (mtmt) REVERT: D 340 LYS cc_start: 0.8449 (mtpt) cc_final: 0.8019 (mttt) REVERT: D 347 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8680 (mmtm) REVERT: D 349 ARG cc_start: 0.8313 (mtt180) cc_final: 0.6300 (mmp-170) REVERT: E 311 LYS cc_start: 0.6090 (mtmt) cc_final: 0.5608 (mtpt) REVERT: E 314 ASP cc_start: 0.5193 (t0) cc_final: 0.4824 (t0) REVERT: E 317 LYS cc_start: 0.7234 (ptmt) cc_final: 0.6644 (mttt) REVERT: E 338 GLU cc_start: 0.8429 (tt0) cc_final: 0.8187 (tt0) REVERT: E 342 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8270 (tt0) REVERT: E 347 LYS cc_start: 0.8651 (mttt) cc_final: 0.7925 (pptt) REVERT: E 369 LYS cc_start: 0.8125 (tttt) cc_final: 0.7831 (ttmt) outliers start: 6 outliers final: 2 residues processed: 109 average time/residue: 3.5973 time to fit residues: 399.7698 Evaluate side-chains 102 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 348 ASP 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: 0.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 0.2980 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 307 GLN B 368 ASN D 307 GLN E 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4081 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= 0.309 Angle : 0.541 4.296 4680 Z= 0.281 Chirality : 0.050 0.139 528 Planarity : 0.003 0.024 594 Dihedral : 5.363 15.236 462 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 1.42 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: -1.55 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 329 PHE 0.007 0.001 PHE A 378 TYR 0.012 0.003 TYR A 310 ARG 0.006 0.001 ARG G 349 *********************** 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 103 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.602 Fit side-chains REVERT: A 321 LYS cc_start: 0.7228 (ttmt) cc_final: 0.6885 (mtpt) REVERT: A 340 LYS cc_start: 0.8398 (mtpt) cc_final: 0.7918 (mttt) REVERT: A 342 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8037 (tt0) REVERT: A 369 LYS cc_start: 0.7464 (tttt) cc_final: 0.6851 (mttt) REVERT: G 311 LYS cc_start: 0.5902 (mtmt) cc_final: 0.5075 (tppt) REVERT: G 321 LYS cc_start: 0.7217 (ttmt) cc_final: 0.6815 (mttt) REVERT: G 340 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7846 (mttt) REVERT: G 342 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8062 (mt-10) REVERT: G 345 ASP cc_start: 0.8074 (m-30) cc_final: 0.7852 (t70) REVERT: G 349 ARG cc_start: 0.8275 (mtt180) cc_final: 0.6333 (mmp-170) REVERT: G 369 LYS cc_start: 0.7395 (tttt) cc_final: 0.6935 (mtmt) REVERT: B 311 LYS cc_start: 0.6265 (mtmt) cc_final: 0.5724 (mttt) REVERT: B 340 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8049 (mttm) REVERT: B 342 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8289 (tt0) REVERT: B 347 LYS cc_start: 0.8723 (mttt) cc_final: 0.7858 (pptt) REVERT: B 369 LYS cc_start: 0.8012 (tttt) cc_final: 0.7667 (ttmt) REVERT: B 375 LYS cc_start: 0.7266 (tttt) cc_final: 0.7062 (tttm) REVERT: C 317 LYS cc_start: 0.6189 (ptmt) cc_final: 0.5823 (ptpp) REVERT: C 338 GLU cc_start: 0.8231 (tt0) cc_final: 0.7859 (tt0) REVERT: C 342 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7985 (mt-10) REVERT: C 348 ASP cc_start: 0.8873 (t0) cc_final: 0.8671 (t70) REVERT: C 349 ARG cc_start: 0.8207 (mtt180) cc_final: 0.7969 (mtp180) REVERT: C 369 LYS cc_start: 0.7259 (tttt) cc_final: 0.6753 (mtmt) REVERT: D 311 LYS cc_start: 0.6103 (mtmt) cc_final: 0.5172 (tppt) REVERT: D 321 LYS cc_start: 0.7398 (ttmt) cc_final: 0.7039 (mtpt) REVERT: D 340 LYS cc_start: 0.8450 (mtpt) cc_final: 0.8002 (mttt) REVERT: D 347 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8653 (mmtm) REVERT: D 349 ARG cc_start: 0.8306 (mtt180) cc_final: 0.6258 (mmp-170) REVERT: E 311 LYS cc_start: 0.6091 (mtmt) cc_final: 0.5631 (mtpt) REVERT: E 314 ASP cc_start: 0.5256 (t0) cc_final: 0.4762 (t0) REVERT: E 317 LYS cc_start: 0.7214 (ptmt) cc_final: 0.6719 (ptpp) REVERT: E 338 GLU cc_start: 0.8405 (tt0) cc_final: 0.8164 (tt0) REVERT: E 342 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8268 (tt0) REVERT: E 347 LYS cc_start: 0.8660 (mttt) cc_final: 0.7828 (pptt) REVERT: E 369 LYS cc_start: 0.8107 (tttt) cc_final: 0.7784 (ttmt) outliers start: 4 outliers final: 1 residues processed: 101 average time/residue: 3.3967 time to fit residues: 350.1117 Evaluate side-chains 95 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 0.0000 chunk 8 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN G 351 GLN B 307 GLN C 307 GLN D 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3498 Z= 0.158 Angle : 0.484 4.281 4680 Z= 0.245 Chirality : 0.050 0.128 528 Planarity : 0.002 0.021 594 Dihedral : 4.879 13.399 462 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.76 % Allowed : 15.15 % 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: -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 0.002 0.001 HIS E 362 PHE 0.003 0.001 PHE A 378 TYR 0.006 0.002 TYR C 310 ARG 0.003 0.000 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 103 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 0.653 Fit side-chains REVERT: A 321 LYS cc_start: 0.7169 (ttmt) cc_final: 0.6888 (mtpt) REVERT: A 340 LYS cc_start: 0.8367 (mtpt) cc_final: 0.7897 (mttt) REVERT: A 342 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8047 (tt0) REVERT: A 369 LYS cc_start: 0.7518 (tttt) cc_final: 0.6852 (mttt) REVERT: G 311 LYS cc_start: 0.5957 (mtmt) cc_final: 0.5034 (tppt) REVERT: G 321 LYS cc_start: 0.7106 (ttmt) cc_final: 0.6715 (mttt) REVERT: G 340 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7808 (mttt) REVERT: G 342 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8092 (mt-10) REVERT: G 345 ASP cc_start: 0.8067 (m-30) cc_final: 0.7849 (t0) REVERT: G 349 ARG cc_start: 0.8299 (mtt180) cc_final: 0.6366 (mmp-170) REVERT: G 351 GLN cc_start: 0.8693 (mt0) cc_final: 0.8462 (mt0) REVERT: G 369 LYS cc_start: 0.7482 (tttt) cc_final: 0.7006 (mtmt) REVERT: B 311 LYS cc_start: 0.6207 (mtmt) cc_final: 0.5685 (mttt) REVERT: B 340 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8041 (mttm) REVERT: B 342 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8217 (tt0) REVERT: B 347 LYS cc_start: 0.8712 (mttt) cc_final: 0.7866 (pptt) REVERT: B 369 LYS cc_start: 0.7939 (tttt) cc_final: 0.7615 (ttmt) REVERT: B 375 LYS cc_start: 0.7310 (tttt) cc_final: 0.7074 (tttm) REVERT: C 317 LYS cc_start: 0.6217 (ptmt) cc_final: 0.5834 (ptpp) REVERT: C 338 GLU cc_start: 0.8208 (tt0) cc_final: 0.7825 (tt0) REVERT: C 342 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8039 (mt-10) REVERT: C 369 LYS cc_start: 0.7276 (tttt) cc_final: 0.6771 (mtmt) REVERT: D 311 LYS cc_start: 0.6334 (mtmt) cc_final: 0.5306 (tppt) REVERT: D 321 LYS cc_start: 0.7360 (ttmt) cc_final: 0.7004 (mtpt) REVERT: D 340 LYS cc_start: 0.8414 (mtpt) cc_final: 0.7979 (mttt) REVERT: D 342 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8172 (mt-10) REVERT: D 349 ARG cc_start: 0.8291 (mtt180) cc_final: 0.6288 (mmp-170) REVERT: E 311 LYS cc_start: 0.6030 (mtmt) cc_final: 0.5571 (mtpt) REVERT: E 314 ASP cc_start: 0.5227 (t0) cc_final: 0.4795 (t0) REVERT: E 317 LYS cc_start: 0.7224 (ptmt) cc_final: 0.6734 (ptpp) REVERT: E 338 GLU cc_start: 0.8395 (tt0) cc_final: 0.8130 (tt0) REVERT: E 342 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8277 (tt0) REVERT: E 347 LYS cc_start: 0.8635 (mttt) cc_final: 0.7835 (pptt) REVERT: E 369 LYS cc_start: 0.8011 (tttt) cc_final: 0.7710 (ttmt) outliers start: 3 outliers final: 1 residues processed: 102 average time/residue: 3.4633 time to fit residues: 360.3042 Evaluate side-chains 99 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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: 3.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 D 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 3498 Z= 0.321 Angle : 0.522 4.117 4680 Z= 0.272 Chirality : 0.050 0.141 528 Planarity : 0.003 0.032 594 Dihedral : 5.109 14.617 462 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.26 % Allowed : 14.65 % 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: -1.55 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (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 A 378 TYR 0.013 0.003 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: 5 poor density : 97 time to evaluate : 0.540 Fit side-chains REVERT: A 321 LYS cc_start: 0.7156 (ttmt) cc_final: 0.6877 (mtpt) REVERT: A 340 LYS cc_start: 0.8381 (mtpt) cc_final: 0.7901 (mttt) REVERT: A 342 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8058 (tt0) REVERT: A 369 LYS cc_start: 0.7458 (tttt) cc_final: 0.6833 (mttt) REVERT: G 311 LYS cc_start: 0.5908 (mtmt) cc_final: 0.5114 (tppt) REVERT: G 321 LYS cc_start: 0.7199 (ttmt) cc_final: 0.6786 (mttt) REVERT: G 340 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7814 (mttm) REVERT: G 342 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8088 (mt-10) REVERT: G 345 ASP cc_start: 0.8076 (m-30) cc_final: 0.7842 (t0) REVERT: G 349 ARG cc_start: 0.8267 (mtt180) cc_final: 0.6331 (mmp-170) REVERT: G 369 LYS cc_start: 0.7418 (tttt) cc_final: 0.6939 (mtmt) REVERT: B 311 LYS cc_start: 0.6202 (mtmt) cc_final: 0.5668 (mttt) REVERT: B 340 LYS cc_start: 0.8673 (mtpt) cc_final: 0.8068 (mttm) REVERT: B 342 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8248 (tt0) REVERT: B 347 LYS cc_start: 0.8734 (mttt) cc_final: 0.7835 (pptt) REVERT: B 369 LYS cc_start: 0.8039 (tttt) cc_final: 0.7716 (ttmt) REVERT: B 375 LYS cc_start: 0.7279 (tttt) cc_final: 0.7076 (tttm) REVERT: C 317 LYS cc_start: 0.6207 (ptmt) cc_final: 0.5827 (ptpp) REVERT: C 338 GLU cc_start: 0.8217 (tt0) cc_final: 0.7844 (tt0) REVERT: C 342 GLU cc_start: 0.8505 (mt-10) cc_final: 0.7994 (mt-10) REVERT: C 369 LYS cc_start: 0.7360 (tttt) cc_final: 0.6808 (mtmt) REVERT: D 311 LYS cc_start: 0.6038 (mtmt) cc_final: 0.5143 (tppt) REVERT: D 340 LYS cc_start: 0.8427 (mtpt) cc_final: 0.7959 (mttt) REVERT: D 349 ARG cc_start: 0.8295 (mtt180) cc_final: 0.6203 (mmp-170) REVERT: E 311 LYS cc_start: 0.6081 (mtmt) cc_final: 0.5631 (mtpt) REVERT: E 314 ASP cc_start: 0.5201 (t0) cc_final: 0.4797 (t0) REVERT: E 317 LYS cc_start: 0.7216 (ptmt) cc_final: 0.6707 (ptpp) REVERT: E 338 GLU cc_start: 0.8392 (tt0) cc_final: 0.8148 (tt0) REVERT: E 342 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8270 (tt0) REVERT: E 347 LYS cc_start: 0.8674 (mttt) cc_final: 0.7805 (pptt) REVERT: E 369 LYS cc_start: 0.8097 (tttt) cc_final: 0.7781 (ttmt) outliers start: 5 outliers final: 2 residues processed: 99 average time/residue: 3.5002 time to fit residues: 353.4002 Evaluate side-chains 89 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain E residue 345 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 C 307 GLN D 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3498 Z= 0.332 Angle : 0.538 5.041 4680 Z= 0.278 Chirality : 0.050 0.140 528 Planarity : 0.003 0.030 594 Dihedral : 5.136 14.860 462 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.76 % Allowed : 14.90 % 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: -1.61 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.006 0.001 PHE A 378 TYR 0.012 0.003 TYR A 310 ARG 0.003 0.001 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 89 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.523 Fit side-chains REVERT: A 321 LYS cc_start: 0.7188 (ttmt) cc_final: 0.6895 (mtpt) REVERT: A 340 LYS cc_start: 0.8398 (mtpt) cc_final: 0.7890 (mttt) REVERT: A 342 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8070 (tt0) REVERT: A 349 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7913 (mtp180) REVERT: A 369 LYS cc_start: 0.7469 (tttt) cc_final: 0.6887 (mttt) REVERT: G 311 LYS cc_start: 0.5945 (mtmt) cc_final: 0.5166 (tppt) REVERT: G 321 LYS cc_start: 0.7243 (ttmt) cc_final: 0.6822 (mttt) REVERT: G 340 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7777 (mttm) REVERT: G 342 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8086 (mt-10) REVERT: G 345 ASP cc_start: 0.8082 (m-30) cc_final: 0.7840 (t0) REVERT: G 349 ARG cc_start: 0.8262 (mtt180) cc_final: 0.6338 (mmp-170) REVERT: G 369 LYS cc_start: 0.7469 (tttt) cc_final: 0.6995 (mtmt) REVERT: B 311 LYS cc_start: 0.6193 (mtmt) cc_final: 0.5668 (mttt) REVERT: B 340 LYS cc_start: 0.8677 (mtpt) cc_final: 0.8083 (mttm) REVERT: B 342 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8276 (tt0) REVERT: B 347 LYS cc_start: 0.8724 (mttt) cc_final: 0.7812 (pptt) REVERT: B 369 LYS cc_start: 0.8029 (tttt) cc_final: 0.7718 (ttmt) REVERT: B 375 LYS cc_start: 0.7289 (tttt) cc_final: 0.7045 (tttm) REVERT: C 317 LYS cc_start: 0.6199 (ptmt) cc_final: 0.5821 (ptpp) REVERT: C 338 GLU cc_start: 0.8219 (tt0) cc_final: 0.7852 (tt0) REVERT: C 342 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8007 (mt-10) REVERT: C 369 LYS cc_start: 0.7448 (tttt) cc_final: 0.6914 (mtmt) REVERT: D 349 ARG cc_start: 0.8300 (mtt180) cc_final: 0.6220 (mmp-170) REVERT: E 311 LYS cc_start: 0.6065 (mtmt) cc_final: 0.5612 (mtpt) REVERT: E 314 ASP cc_start: 0.5121 (t0) cc_final: 0.4738 (t0) REVERT: E 317 LYS cc_start: 0.7232 (ptmt) cc_final: 0.6717 (ptpp) REVERT: E 338 GLU cc_start: 0.8404 (tt0) cc_final: 0.8158 (tt0) REVERT: E 342 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8264 (tt0) REVERT: E 347 LYS cc_start: 0.8675 (mttt) cc_final: 0.7789 (pptt) REVERT: E 369 LYS cc_start: 0.8088 (tttt) cc_final: 0.7811 (ttmt) outliers start: 3 outliers final: 2 residues processed: 87 average time/residue: 3.6892 time to fit residues: 327.4341 Evaluate side-chains 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain E residue 345 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 C 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4488 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= 0.179 Angle : 0.481 4.625 4680 Z= 0.245 Chirality : 0.050 0.129 528 Planarity : 0.002 0.023 594 Dihedral : 4.809 13.526 462 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.76 % Allowed : 15.40 % Favored : 83.84 % 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 (0.33), 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 0.001 HIS C 362 PHE 0.003 0.001 PHE A 378 TYR 0.007 0.002 TYR B 310 ARG 0.002 0.000 ARG G 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: 3 poor density : 86 time to evaluate : 0.593 Fit side-chains REVERT: A 321 LYS cc_start: 0.7198 (ttmt) cc_final: 0.6903 (mtpt) REVERT: A 340 LYS cc_start: 0.8379 (mtpt) cc_final: 0.7878 (mttt) REVERT: A 342 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8080 (tt0) REVERT: A 369 LYS cc_start: 0.7466 (tttt) cc_final: 0.6878 (mttt) REVERT: G 311 LYS cc_start: 0.6001 (mtmt) cc_final: 0.5164 (tppt) REVERT: G 321 LYS cc_start: 0.7167 (ttmt) cc_final: 0.6791 (mttt) REVERT: G 340 LYS cc_start: 0.8223 (mtpt) cc_final: 0.7743 (mttm) REVERT: G 342 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8087 (mt-10) REVERT: G 345 ASP cc_start: 0.8068 (m-30) cc_final: 0.7848 (t0) REVERT: G 349 ARG cc_start: 0.8298 (mtt180) cc_final: 0.6336 (mmp-170) REVERT: G 369 LYS cc_start: 0.7496 (tttt) cc_final: 0.7007 (mtmt) REVERT: B 311 LYS cc_start: 0.6198 (mtmt) cc_final: 0.5669 (mttt) REVERT: B 340 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8068 (mttm) REVERT: B 342 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8250 (tt0) REVERT: B 347 LYS cc_start: 0.8701 (mttt) cc_final: 0.7805 (pptt) REVERT: B 369 LYS cc_start: 0.7971 (tttt) cc_final: 0.7669 (ttmt) REVERT: B 375 LYS cc_start: 0.7322 (tttt) cc_final: 0.7082 (tttm) REVERT: C 317 LYS cc_start: 0.6218 (ptmt) cc_final: 0.5825 (ptpp) REVERT: C 338 GLU cc_start: 0.8220 (tt0) cc_final: 0.7852 (tt0) REVERT: C 342 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8049 (mt-10) REVERT: C 369 LYS cc_start: 0.7453 (tttt) cc_final: 0.6916 (mtmt) REVERT: D 342 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8178 (mt-10) REVERT: D 345 ASP cc_start: 0.8068 (m-30) cc_final: 0.7794 (t70) REVERT: D 349 ARG cc_start: 0.8281 (mtt180) cc_final: 0.6236 (mmp-170) REVERT: E 311 LYS cc_start: 0.6007 (mtmt) cc_final: 0.5545 (mtpt) REVERT: E 314 ASP cc_start: 0.5227 (t0) cc_final: 0.4788 (t0) REVERT: E 317 LYS cc_start: 0.7215 (ptmt) cc_final: 0.6697 (ptpp) REVERT: E 338 GLU cc_start: 0.8405 (tt0) cc_final: 0.8156 (tt0) REVERT: E 342 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8286 (tt0) REVERT: E 347 LYS cc_start: 0.8646 (mttt) cc_final: 0.7781 (pptt) REVERT: E 369 LYS cc_start: 0.8029 (tttt) cc_final: 0.7716 (ttmt) outliers start: 3 outliers final: 3 residues processed: 88 average time/residue: 3.2599 time to fit residues: 293.1627 Evaluate side-chains 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 349 ARG Chi-restraints excluded: chain D 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: 1.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 C 307 GLN D 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4527 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= 0.209 Angle : 0.482 4.436 4680 Z= 0.247 Chirality : 0.050 0.136 528 Planarity : 0.002 0.018 594 Dihedral : 4.769 13.561 462 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.01 % Allowed : 15.40 % 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: -1.56 (0.33), 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 0.001 HIS D 374 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 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 91 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.602 Fit side-chains REVERT: A 321 LYS cc_start: 0.7214 (ttmt) cc_final: 0.6907 (mtpt) REVERT: A 340 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7879 (mttt) REVERT: A 342 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8061 (tt0) REVERT: A 369 LYS cc_start: 0.7468 (tttt) cc_final: 0.6864 (mttt) REVERT: G 311 LYS cc_start: 0.6004 (mtmt) cc_final: 0.5164 (tppt) REVERT: G 321 LYS cc_start: 0.7175 (ttmt) cc_final: 0.6780 (mttt) REVERT: G 340 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7743 (mttm) REVERT: G 342 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8084 (mt-10) REVERT: G 345 ASP cc_start: 0.8066 (m-30) cc_final: 0.7849 (t0) REVERT: G 349 ARG cc_start: 0.8307 (mtt180) cc_final: 0.6372 (mmp-170) REVERT: G 369 LYS cc_start: 0.7454 (tttt) cc_final: 0.6948 (mtmt) REVERT: B 311 LYS cc_start: 0.6200 (mtmt) cc_final: 0.5670 (mttt) REVERT: B 340 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8076 (mttm) REVERT: B 342 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8247 (tt0) REVERT: B 347 LYS cc_start: 0.8705 (mttt) cc_final: 0.7798 (pptt) REVERT: B 369 LYS cc_start: 0.8017 (tttt) cc_final: 0.7716 (ttmt) REVERT: B 375 LYS cc_start: 0.7291 (tttt) cc_final: 0.7049 (tttm) REVERT: C 317 LYS cc_start: 0.6233 (ptmt) cc_final: 0.5840 (ptpp) REVERT: C 338 GLU cc_start: 0.8223 (tt0) cc_final: 0.7849 (tt0) REVERT: C 342 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8065 (mt-10) REVERT: C 369 LYS cc_start: 0.7430 (tttt) cc_final: 0.6896 (mtmt) REVERT: D 342 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8172 (mt-10) REVERT: D 345 ASP cc_start: 0.8060 (m-30) cc_final: 0.7786 (t70) REVERT: D 349 ARG cc_start: 0.8277 (mtt180) cc_final: 0.6246 (mmp-170) REVERT: E 311 LYS cc_start: 0.6025 (mtmt) cc_final: 0.5566 (mtpt) REVERT: E 314 ASP cc_start: 0.5219 (t0) cc_final: 0.4770 (t0) REVERT: E 317 LYS cc_start: 0.7226 (ptmt) cc_final: 0.6705 (ptpp) REVERT: E 338 GLU cc_start: 0.8410 (tt0) cc_final: 0.8143 (tt0) REVERT: E 342 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8286 (tt0) REVERT: E 347 LYS cc_start: 0.8644 (mttt) cc_final: 0.7758 (pptt) REVERT: E 369 LYS cc_start: 0.8061 (tttt) cc_final: 0.7763 (ttmt) outliers start: 4 outliers final: 1 residues processed: 89 average time/residue: 3.2623 time to fit residues: 296.6711 Evaluate side-chains 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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: 0.8980 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 C 307 GLN D 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4559 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= 0.171 Angle : 0.470 4.798 4680 Z= 0.239 Chirality : 0.050 0.130 528 Planarity : 0.002 0.027 594 Dihedral : 4.634 13.088 462 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.51 % Allowed : 16.16 % 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: -1.56 (0.33), 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 0.001 HIS C 362 PHE 0.003 0.001 PHE A 378 TYR 0.007 0.002 TYR A 310 ARG 0.003 0.000 ARG A 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 88 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.615 Fit side-chains REVERT: A 340 LYS cc_start: 0.8385 (mtpt) cc_final: 0.7875 (mttt) REVERT: A 342 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8067 (tt0) REVERT: A 349 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7883 (mtt180) REVERT: A 369 LYS cc_start: 0.7476 (tttt) cc_final: 0.6879 (mttt) REVERT: G 311 LYS cc_start: 0.5973 (mtmt) cc_final: 0.5098 (tppt) REVERT: G 321 LYS cc_start: 0.7176 (ttmt) cc_final: 0.6775 (mttt) REVERT: G 340 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7731 (mttm) REVERT: G 342 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8075 (mt-10) REVERT: G 345 ASP cc_start: 0.8062 (m-30) cc_final: 0.7848 (t0) REVERT: G 349 ARG cc_start: 0.8243 (mtt180) cc_final: 0.6212 (mmp-170) REVERT: G 369 LYS cc_start: 0.7500 (tttt) cc_final: 0.7008 (mtmt) REVERT: B 307 GLN cc_start: 0.6213 (mt0) cc_final: 0.5792 (tt0) REVERT: B 311 LYS cc_start: 0.6196 (mtmt) cc_final: 0.5674 (mttt) REVERT: B 340 LYS cc_start: 0.8665 (mtpt) cc_final: 0.8071 (mttm) REVERT: B 342 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8263 (tt0) REVERT: B 347 LYS cc_start: 0.8709 (mttt) cc_final: 0.7811 (pptt) REVERT: B 369 LYS cc_start: 0.7992 (tttt) cc_final: 0.7679 (ttmt) REVERT: B 375 LYS cc_start: 0.7282 (tttt) cc_final: 0.7049 (tttm) REVERT: C 317 LYS cc_start: 0.6252 (ptmt) cc_final: 0.5853 (ptpp) REVERT: C 338 GLU cc_start: 0.8224 (tt0) cc_final: 0.7851 (tt0) REVERT: C 342 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8067 (mt-10) REVERT: C 369 LYS cc_start: 0.7431 (tttt) cc_final: 0.6897 (mtmt) REVERT: D 342 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8188 (mt-10) REVERT: D 345 ASP cc_start: 0.8065 (m-30) cc_final: 0.7803 (t70) REVERT: D 349 ARG cc_start: 0.8287 (mtt180) cc_final: 0.6248 (mmp-170) REVERT: E 311 LYS cc_start: 0.6016 (mtmt) cc_final: 0.5565 (mtpt) REVERT: E 314 ASP cc_start: 0.5235 (t0) cc_final: 0.4762 (t0) REVERT: E 317 LYS cc_start: 0.7193 (ptmt) cc_final: 0.6689 (ptpp) REVERT: E 338 GLU cc_start: 0.8426 (tt0) cc_final: 0.8161 (tt0) REVERT: E 342 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8281 (tt0) REVERT: E 347 LYS cc_start: 0.8639 (mttt) cc_final: 0.7760 (pptt) REVERT: E 369 LYS cc_start: 0.7975 (tttt) cc_final: 0.7676 (ttmt) outliers start: 2 outliers final: 1 residues processed: 87 average time/residue: 3.3085 time to fit residues: 294.0148 Evaluate side-chains 86 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 0.0470 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.126737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.109780 restraints weight = 11981.987| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.52 r_work: 0.3599 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.4602 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= 0.166 Angle : 0.484 6.446 4680 Z= 0.242 Chirality : 0.050 0.130 528 Planarity : 0.002 0.019 594 Dihedral : 4.529 12.776 462 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.01 % Allowed : 15.91 % 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: -1.56 (0.33), 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 0.001 HIS C 362 PHE 0.003 0.001 PHE A 378 TYR 0.007 0.002 TYR A 310 ARG 0.002 0.000 ARG G 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6011.78 seconds wall clock time: 105 minutes 12.38 seconds (6312.38 seconds total)