Starting phenix.real_space_refine on Tue Feb 13 04:08:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8caq_16532/02_2024/8caq_16532.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8caq_16532/02_2024/8caq_16532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8caq_16532/02_2024/8caq_16532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8caq_16532/02_2024/8caq_16532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8caq_16532/02_2024/8caq_16532.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8caq_16532/02_2024/8caq_16532.pdb" } resolution = 2.3 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= 0.001 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: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 1800 2.51 5 N 530 2.21 5 O 535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 314": "OD1" <-> "OD2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 379": "NH1" <-> "NH2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 314": "OD1" <-> "OD2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 379": "NH1" <-> "NH2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 314": "OD1" <-> "OD2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 379": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 2870 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 1.99, per 1000 atoms: 0.69 Number of scatterers: 2870 At special positions: 0 Unit cell: (139.256, 119.48, 32.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 535 8.00 N 530 7.00 C 1800 6.00 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: 0.97 Conformation dependent library (CDL) restraints added in 548.5 milliseconds 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 56.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.367A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.822A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 322 removed outlier: 6.403A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N SER B 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR A 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N CYS B 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS A 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 325 through 330 removed outlier: 8.567A pdb=" N LEU A 325 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N ILE B 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN A 327 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS B 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS A 329 " --> pdb=" O HIS B 330 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY A 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN E 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 346 removed outlier: 6.861A pdb=" N LEU A 344 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP B 345 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE A 346 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU E 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LYS A 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N PHE E 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 357 removed outlier: 6.411A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N SER B 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY A 355 " --> pdb=" O SER B 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.229A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 369 through 378 removed outlier: 6.825A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AB1, first strand: chain 'C' and resid 313 through 314 Processing sheet with id=AB2, first strand: chain 'C' and resid 317 through 322 Processing sheet with id=AB3, first strand: chain 'C' and resid 325 through 330 removed outlier: 6.806A pdb=" N GLY C 326 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN D 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 337 through 346 removed outlier: 6.316A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLU D 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER C 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU D 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LYS C 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N PHE D 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 350 through 357 Processing sheet with id=AB6, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.229A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 369 through 378 66 hydrogen bonds defined for protein. 198 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.64 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 681 1.34 - 1.46: 697 1.46 - 1.57: 1532 1.57 - 1.69: 0 1.69 - 1.81: 5 Bond restraints: 2915 Sorted by residual: bond pdb=" CG HIS C 362 " pdb=" CD2 HIS C 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.44e+00 bond pdb=" CG HIS A 362 " pdb=" CD2 HIS A 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.44e+00 bond pdb=" CG HIS B 362 " pdb=" CD2 HIS B 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.43e+00 bond pdb=" CG HIS D 362 " pdb=" CD2 HIS D 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.42e+00 bond pdb=" CG HIS E 362 " pdb=" CD2 HIS E 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.39e+00 ... (remaining 2910 not shown) Histogram of bond angle deviations from ideal: 102.32 - 108.21: 223 108.21 - 114.09: 1557 114.09 - 119.97: 989 119.97 - 125.85: 1091 125.85 - 131.73: 40 Bond angle restraints: 3900 Sorted by residual: angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 110.42 116.53 -6.11 1.49e+00 4.50e-01 1.68e+01 angle pdb=" N GLY B 326 " pdb=" CA GLY B 326 " pdb=" C GLY B 326 " ideal model delta sigma weight residual 110.42 116.52 -6.10 1.49e+00 4.50e-01 1.68e+01 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.42 116.52 -6.10 1.49e+00 4.50e-01 1.67e+01 angle pdb=" N GLY E 326 " pdb=" CA GLY E 326 " pdb=" C GLY E 326 " ideal model delta sigma weight residual 110.42 116.51 -6.09 1.49e+00 4.50e-01 1.67e+01 angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.42 116.51 -6.09 1.49e+00 4.50e-01 1.67e+01 ... (remaining 3895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 1645 15.14 - 30.28: 95 30.28 - 45.42: 25 45.42 - 60.55: 10 60.55 - 75.69: 5 Dihedral angle restraints: 1780 sinusoidal: 745 harmonic: 1035 Sorted by residual: dihedral pdb=" CA GLY B 335 " pdb=" C GLY B 335 " pdb=" N GLN B 336 " pdb=" CA GLN B 336 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLY E 335 " pdb=" C GLY E 335 " pdb=" N GLN E 336 " pdb=" CA GLN E 336 " ideal model delta harmonic sigma weight residual 180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLY A 335 " pdb=" C GLY A 335 " pdb=" N GLN A 336 " pdb=" CA GLN A 336 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 1777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 163 0.043 - 0.085: 173 0.085 - 0.127: 79 0.127 - 0.169: 20 0.169 - 0.212: 5 Chirality restraints: 440 Sorted by residual: chirality pdb=" CA LYS B 369 " pdb=" N LYS B 369 " pdb=" C LYS B 369 " pdb=" CB LYS B 369 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LYS E 369 " pdb=" N LYS E 369 " pdb=" C LYS E 369 " pdb=" CB LYS E 369 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LYS D 369 " pdb=" N LYS D 369 " pdb=" C LYS D 369 " pdb=" CB LYS D 369 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 437 not shown) Planarity restraints: 495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " 0.017 2.00e-02 2.50e+03 1.13e-02 2.56e+00 pdb=" CG TYR D 310 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.017 2.00e-02 2.50e+03 1.13e-02 2.55e+00 pdb=" CG TYR A 310 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.017 2.00e-02 2.50e+03 1.13e-02 2.54e+00 pdb=" CG TYR C 310 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.004 2.00e-02 2.50e+03 ... (remaining 492 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.06: 1590 3.06 - 3.52: 2604 3.52 - 3.98: 4241 3.98 - 4.44: 4342 4.44 - 4.90: 8817 Nonbonded interactions: 21594 Sorted by model distance: nonbonded pdb=" N ASP B 348 " pdb=" O ASP B 348 " model vdw 2.606 2.496 nonbonded pdb=" N ASP A 348 " pdb=" O ASP A 348 " model vdw 2.606 2.496 nonbonded pdb=" N ASP C 348 " pdb=" O ASP C 348 " model vdw 2.607 2.496 nonbonded pdb=" N ASP D 348 " pdb=" O ASP D 348 " model vdw 2.607 2.496 nonbonded pdb=" N ASP E 348 " pdb=" O ASP E 348 " model vdw 2.607 2.496 ... (remaining 21589 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' } 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: 2.810 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: 0.000 Extract box with map and model: 12.780 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.320 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 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:10.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 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 : 0.007 0.042 2915 Z= 0.497 Angle : 1.178 6.107 3900 Z= 0.758 Chirality : 0.071 0.212 440 Planarity : 0.007 0.031 495 Dihedral : 12.141 75.692 1120 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.52 % Allowed : 3.03 % Favored : 95.45 % 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: -3.61 (0.31), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.24), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS E 362 PHE 0.008 0.003 PHE B 378 TYR 0.026 0.007 TYR D 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 0.370 Fit side-chains REVERT: B 349 ARG cc_start: 0.9009 (mtt180) cc_final: 0.6996 (pmt-80) REVERT: B 379 ARG cc_start: 0.8324 (mtt180) cc_final: 0.7517 (pmt170) REVERT: C 349 ARG cc_start: 0.9022 (mtt180) cc_final: 0.7029 (pmt170) REVERT: C 379 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7436 (pmt170) REVERT: D 311 LYS cc_start: 0.8725 (mtmt) cc_final: 0.8389 (mmtt) REVERT: D 349 ARG cc_start: 0.8992 (mtt180) cc_final: 0.7199 (mmm160) REVERT: E 307 GLN cc_start: 0.8274 (tt0) cc_final: 0.7991 (mt0) REVERT: E 311 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8461 (mmtt) REVERT: E 349 ARG cc_start: 0.8975 (mtt180) cc_final: 0.7581 (mmp-170) outliers start: 5 outliers final: 0 residues processed: 110 average time/residue: 1.5464 time to fit residues: 173.2055 Evaluate side-chains 71 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 0.0770 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 351 GLN C 351 GLN C 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2915 Z= 0.155 Angle : 0.550 6.256 3900 Z= 0.268 Chirality : 0.048 0.124 440 Planarity : 0.004 0.025 495 Dihedral : 5.030 15.383 385 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.73 % Allowed : 13.33 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 362 PHE 0.004 0.001 PHE A 346 TYR 0.008 0.002 TYR C 310 ARG 0.003 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.307 Fit side-chains REVERT: A 338 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: B 338 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8554 (tm-30) REVERT: B 348 ASP cc_start: 0.9086 (t0) cc_final: 0.7859 (p0) REVERT: B 349 ARG cc_start: 0.8975 (mtt180) cc_final: 0.6858 (pmt-80) REVERT: B 379 ARG cc_start: 0.8299 (mtt180) cc_final: 0.7645 (pmt170) REVERT: C 349 ARG cc_start: 0.9018 (mtt180) cc_final: 0.6958 (pmt170) REVERT: C 379 ARG cc_start: 0.8290 (mtt180) cc_final: 0.7456 (pmt170) REVERT: D 307 GLN cc_start: 0.8365 (tt0) cc_final: 0.8094 (mt0) REVERT: D 349 ARG cc_start: 0.9028 (mtt180) cc_final: 0.7208 (mmm160) REVERT: D 379 ARG cc_start: 0.4545 (OUTLIER) cc_final: 0.3526 (mmt180) REVERT: E 307 GLN cc_start: 0.8149 (tt0) cc_final: 0.7830 (mt0) REVERT: E 349 ARG cc_start: 0.9028 (mtt180) cc_final: 0.7424 (mmm160) REVERT: E 379 ARG cc_start: 0.4691 (OUTLIER) cc_final: 0.3530 (mmt180) outliers start: 9 outliers final: 1 residues processed: 82 average time/residue: 1.3702 time to fit residues: 114.7189 Evaluate side-chains 70 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 0.1980 chunk 31 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 327 ASN C 307 GLN C 351 GLN E 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2915 Z= 0.277 Angle : 0.564 5.059 3900 Z= 0.287 Chirality : 0.049 0.132 440 Planarity : 0.003 0.021 495 Dihedral : 4.844 15.540 385 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.73 % Allowed : 13.94 % 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: -2.30 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.006 0.001 PHE E 346 TYR 0.015 0.004 TYR E 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.364 Fit side-chains REVERT: A 338 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: B 314 ASP cc_start: 0.8807 (t70) cc_final: 0.8599 (t0) REVERT: B 348 ASP cc_start: 0.9120 (t0) cc_final: 0.7884 (p0) REVERT: B 349 ARG cc_start: 0.8990 (mtt180) cc_final: 0.6871 (pmt-80) REVERT: B 379 ARG cc_start: 0.8433 (mtt180) cc_final: 0.7674 (pmt170) REVERT: C 349 ARG cc_start: 0.9037 (mtt180) cc_final: 0.6954 (pmt170) REVERT: C 379 ARG cc_start: 0.8352 (mtt180) cc_final: 0.7482 (pmt170) REVERT: D 349 ARG cc_start: 0.9023 (mtt180) cc_final: 0.7210 (mmm160) REVERT: D 379 ARG cc_start: 0.4541 (OUTLIER) cc_final: 0.3376 (mmt180) REVERT: E 349 ARG cc_start: 0.9036 (mtt180) cc_final: 0.7417 (mmm160) REVERT: E 379 ARG cc_start: 0.4531 (OUTLIER) cc_final: 0.3313 (mmt180) outliers start: 9 outliers final: 0 residues processed: 75 average time/residue: 1.3759 time to fit residues: 105.3927 Evaluate side-chains 71 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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 C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2915 Z= 0.310 Angle : 0.571 4.795 3900 Z= 0.288 Chirality : 0.049 0.134 440 Planarity : 0.003 0.019 495 Dihedral : 4.861 15.729 385 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.12 % Allowed : 15.15 % Favored : 82.73 % 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: -2.11 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 330 PHE 0.005 0.001 PHE E 346 TYR 0.014 0.003 TYR C 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.365 Fit side-chains REVERT: A 338 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8471 (tt0) REVERT: B 314 ASP cc_start: 0.8774 (t70) cc_final: 0.8522 (t0) REVERT: B 348 ASP cc_start: 0.9121 (t0) cc_final: 0.7915 (p0) REVERT: B 349 ARG cc_start: 0.8993 (mtt180) cc_final: 0.6888 (pmt-80) REVERT: B 379 ARG cc_start: 0.8418 (mtt180) cc_final: 0.7677 (pmt170) REVERT: C 349 ARG cc_start: 0.9039 (mtt180) cc_final: 0.6990 (pmt170) REVERT: C 379 ARG cc_start: 0.8371 (mtt180) cc_final: 0.7501 (pmt170) REVERT: D 349 ARG cc_start: 0.9012 (mtt180) cc_final: 0.7194 (mmm160) REVERT: D 379 ARG cc_start: 0.4700 (OUTLIER) cc_final: 0.3549 (mmt180) REVERT: E 349 ARG cc_start: 0.9030 (mtt180) cc_final: 0.7403 (mmm160) REVERT: E 379 ARG cc_start: 0.4573 (OUTLIER) cc_final: 0.3364 (mmt180) outliers start: 7 outliers final: 0 residues processed: 74 average time/residue: 1.4529 time to fit residues: 109.6648 Evaluate side-chains 71 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 33 optimal weight: 0.0050 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 368 ASN C 307 GLN C 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2915 Z= 0.152 Angle : 0.504 4.581 3900 Z= 0.249 Chirality : 0.048 0.124 440 Planarity : 0.002 0.015 495 Dihedral : 4.554 15.128 385 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.82 % Allowed : 16.06 % Favored : 82.12 % 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: -2.01 (0.37), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 374 PHE 0.004 0.001 PHE A 346 TYR 0.008 0.002 TYR E 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.364 Fit side-chains REVERT: A 338 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: B 348 ASP cc_start: 0.9106 (t0) cc_final: 0.7896 (p0) REVERT: B 349 ARG cc_start: 0.8993 (mtt180) cc_final: 0.6836 (pmt-80) REVERT: B 379 ARG cc_start: 0.8409 (mtt180) cc_final: 0.7752 (pmt170) REVERT: C 349 ARG cc_start: 0.9022 (mtt180) cc_final: 0.7002 (pmt170) REVERT: C 379 ARG cc_start: 0.8321 (mtt180) cc_final: 0.7532 (pmt170) REVERT: D 307 GLN cc_start: 0.8382 (tt0) cc_final: 0.8114 (mt0) REVERT: D 349 ARG cc_start: 0.9004 (mtt180) cc_final: 0.7215 (mmm160) REVERT: D 379 ARG cc_start: 0.4676 (OUTLIER) cc_final: 0.3532 (mmt180) REVERT: E 349 ARG cc_start: 0.9022 (mtt180) cc_final: 0.7370 (mmm160) REVERT: E 379 ARG cc_start: 0.4246 (OUTLIER) cc_final: 0.3103 (mmt180) outliers start: 6 outliers final: 0 residues processed: 75 average time/residue: 1.4473 time to fit residues: 110.8122 Evaluate side-chains 73 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 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 C 307 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2915 Z= 0.263 Angle : 0.551 4.861 3900 Z= 0.278 Chirality : 0.049 0.131 440 Planarity : 0.003 0.014 495 Dihedral : 4.659 14.935 385 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.82 % Allowed : 17.27 % Favored : 80.91 % 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: -1.95 (0.37), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 330 PHE 0.005 0.001 PHE E 346 TYR 0.014 0.003 TYR E 310 ARG 0.004 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.396 Fit side-chains REVERT: A 338 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8500 (tt0) REVERT: B 348 ASP cc_start: 0.9108 (t0) cc_final: 0.7901 (p0) REVERT: B 349 ARG cc_start: 0.8998 (mtt180) cc_final: 0.6877 (pmt-80) REVERT: B 379 ARG cc_start: 0.8310 (mtt180) cc_final: 0.7763 (pmt170) REVERT: C 349 ARG cc_start: 0.9030 (mtt180) cc_final: 0.7022 (pmt-80) REVERT: C 379 ARG cc_start: 0.8361 (mtt180) cc_final: 0.7567 (pmt170) REVERT: D 349 ARG cc_start: 0.8999 (mtt180) cc_final: 0.7208 (mmm160) REVERT: D 379 ARG cc_start: 0.4648 (OUTLIER) cc_final: 0.3526 (mmt180) REVERT: E 349 ARG cc_start: 0.9014 (mtt180) cc_final: 0.7361 (mmm160) REVERT: E 379 ARG cc_start: 0.4229 (OUTLIER) cc_final: 0.3078 (mmt180) outliers start: 6 outliers final: 0 residues processed: 76 average time/residue: 1.4667 time to fit residues: 113.6736 Evaluate side-chains 76 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 2915 Z= 0.390 Angle : 0.605 5.531 3900 Z= 0.310 Chirality : 0.050 0.135 440 Planarity : 0.003 0.014 495 Dihedral : 4.922 15.814 385 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.12 % Allowed : 16.36 % Favored : 81.52 % 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: -1.95 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 330 PHE 0.006 0.001 PHE D 378 TYR 0.018 0.004 TYR E 310 ARG 0.003 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.346 Fit side-chains REVERT: A 338 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8480 (tt0) REVERT: B 349 ARG cc_start: 0.9002 (mtt180) cc_final: 0.6940 (pmt-80) REVERT: B 379 ARG cc_start: 0.8343 (mtt180) cc_final: 0.7755 (pmt170) REVERT: C 349 ARG cc_start: 0.9042 (mtt180) cc_final: 0.7012 (pmt170) REVERT: C 379 ARG cc_start: 0.8449 (mtt180) cc_final: 0.7567 (pmt170) REVERT: D 349 ARG cc_start: 0.8995 (mtt180) cc_final: 0.7185 (mmm160) REVERT: D 379 ARG cc_start: 0.4657 (OUTLIER) cc_final: 0.3509 (mmt180) REVERT: E 349 ARG cc_start: 0.9019 (mtt180) cc_final: 0.7359 (mmm160) REVERT: E 379 ARG cc_start: 0.4219 (OUTLIER) cc_final: 0.3030 (mmt180) outliers start: 7 outliers final: 1 residues processed: 75 average time/residue: 1.4767 time to fit residues: 112.9266 Evaluate side-chains 77 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 18 optimal weight: 0.3980 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 28 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 362 HIS C 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2915 Z= 0.338 Angle : 0.600 6.353 3900 Z= 0.304 Chirality : 0.050 0.132 440 Planarity : 0.002 0.012 495 Dihedral : 4.916 16.102 385 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.52 % Allowed : 18.18 % Favored : 80.30 % 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: -1.89 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 330 PHE 0.005 0.001 PHE E 346 TYR 0.015 0.003 TYR D 310 ARG 0.003 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.380 Fit side-chains REVERT: A 338 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: B 348 ASP cc_start: 0.9115 (t0) cc_final: 0.7945 (p0) REVERT: B 349 ARG cc_start: 0.9000 (mtt180) cc_final: 0.7015 (pmt-80) REVERT: B 379 ARG cc_start: 0.8322 (mtt180) cc_final: 0.7753 (pmt170) REVERT: C 349 ARG cc_start: 0.9051 (mtt180) cc_final: 0.7021 (pmt170) REVERT: C 379 ARG cc_start: 0.8462 (mtt180) cc_final: 0.7561 (pmt170) REVERT: D 349 ARG cc_start: 0.8996 (mtt180) cc_final: 0.7191 (mmm160) REVERT: D 379 ARG cc_start: 0.4264 (OUTLIER) cc_final: 0.3172 (mmt180) REVERT: E 349 ARG cc_start: 0.9020 (mtt180) cc_final: 0.7355 (mmm160) REVERT: E 379 ARG cc_start: 0.4225 (OUTLIER) cc_final: 0.3108 (mmt180) outliers start: 5 outliers final: 0 residues processed: 76 average time/residue: 1.4132 time to fit residues: 109.6041 Evaluate side-chains 76 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 2915 Z= 0.532 Angle : 0.666 5.970 3900 Z= 0.344 Chirality : 0.053 0.139 440 Planarity : 0.003 0.017 495 Dihedral : 5.199 16.665 385 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.12 % Allowed : 17.88 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.009 0.002 PHE D 378 TYR 0.022 0.005 TYR E 310 ARG 0.004 0.001 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.318 Fit side-chains REVERT: A 338 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: B 349 ARG cc_start: 0.9015 (mtt180) cc_final: 0.6879 (pmt-80) REVERT: B 379 ARG cc_start: 0.8304 (mtt180) cc_final: 0.7703 (pmt170) REVERT: C 349 ARG cc_start: 0.9068 (mtt180) cc_final: 0.7048 (pmt170) REVERT: C 379 ARG cc_start: 0.8482 (mtt180) cc_final: 0.7570 (pmt170) REVERT: D 349 ARG cc_start: 0.9004 (mtt180) cc_final: 0.7161 (mmm160) REVERT: D 379 ARG cc_start: 0.4254 (OUTLIER) cc_final: 0.3128 (mmt180) REVERT: E 349 ARG cc_start: 0.9005 (mtt180) cc_final: 0.7333 (mmm160) REVERT: E 379 ARG cc_start: 0.4021 (OUTLIER) cc_final: 0.2927 (mmt180) outliers start: 7 outliers final: 1 residues processed: 78 average time/residue: 1.4364 time to fit residues: 114.2945 Evaluate side-chains 80 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 20 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 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 C 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2915 Z= 0.210 Angle : 0.603 7.310 3900 Z= 0.295 Chirality : 0.049 0.125 440 Planarity : 0.002 0.015 495 Dihedral : 4.840 16.447 385 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.21 % Allowed : 19.39 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 362 PHE 0.004 0.001 PHE A 346 TYR 0.007 0.002 TYR E 310 ARG 0.003 0.001 ARG A 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.332 Fit side-chains REVERT: A 338 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8516 (tt0) REVERT: B 348 ASP cc_start: 0.9110 (t0) cc_final: 0.7913 (p0) REVERT: B 349 ARG cc_start: 0.8983 (mtt180) cc_final: 0.6872 (pmt-80) REVERT: B 379 ARG cc_start: 0.8338 (mtt180) cc_final: 0.7828 (pmt170) REVERT: C 349 ARG cc_start: 0.9037 (mtt180) cc_final: 0.7028 (pmt-80) REVERT: C 379 ARG cc_start: 0.8457 (mtt180) cc_final: 0.7567 (pmt170) REVERT: D 349 ARG cc_start: 0.8987 (mtt180) cc_final: 0.7206 (mmm160) REVERT: E 349 ARG cc_start: 0.9016 (mtt180) cc_final: 0.7386 (mmm160) REVERT: E 379 ARG cc_start: 0.3917 (OUTLIER) cc_final: 0.2912 (mmt180) outliers start: 4 outliers final: 1 residues processed: 75 average time/residue: 1.4779 time to fit residues: 113.0739 Evaluate side-chains 74 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.6902 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.104421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.094673 restraints weight = 4518.308| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.98 r_work: 0.3683 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2915 Z= 0.198 Angle : 0.568 6.331 3900 Z= 0.277 Chirality : 0.049 0.129 440 Planarity : 0.002 0.018 495 Dihedral : 4.726 15.314 385 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.91 % Allowed : 19.39 % Favored : 79.70 % 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: -1.83 (0.37), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 362 PHE 0.004 0.001 PHE A 346 TYR 0.009 0.002 TYR E 310 ARG 0.003 0.000 ARG A 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2289.90 seconds wall clock time: 41 minutes 6.49 seconds (2466.49 seconds total)