Starting phenix.real_space_refine on Tue Feb 11 01:13:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8r_18258/02_2025/8q8r_18258.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8r_18258/02_2025/8q8r_18258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q8r_18258/02_2025/8q8r_18258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8r_18258/02_2025/8q8r_18258.map" model { file = "/net/cci-nas-00/data/ceres_data/8q8r_18258/02_2025/8q8r_18258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8r_18258/02_2025/8q8r_18258.cif" } resolution = 2.1 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2172 2.51 5 N 642 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3468 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "D" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 3.28, per 1000 atoms: 0.95 Number of scatterers: 3468 At special positions: 0 Unit cell: (87.967, 150.489, 36.35, 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 6 16.00 O 648 8.00 N 642 7.00 C 2172 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 - 3.00 Amino acid : True - 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: 0.89 Conformation dependent library (CDL) restraints added in 404.0 milliseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 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, 51.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.740A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 321 removed outlier: 6.342A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330 removed outlier: 6.976A pdb=" N GLY D 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN A 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 removed outlier: 6.543A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 347 removed outlier: 6.172A pdb=" N LYS A 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE D 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP A 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 356 removed outlier: 6.755A pdb=" N SER D 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL B 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LYS D 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER B 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N GLY D 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ILE B 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.595A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N HIS D 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 378 removed outlier: 6.520A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N GLU D 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE A 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N HIS D 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR A 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU D 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS A 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N PHE D 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR A 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.543A pdb=" N ILE C 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE E 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314 Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 321 removed outlier: 6.353A pdb=" N VAL C 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N LYS E 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER C 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL E 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N LYS F 321 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER E 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 325 through 330 removed outlier: 5.764A pdb=" N GLY C 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N HIS E 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLY E 326 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N HIS F 329 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE E 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.535A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LYS E 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LYS F 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL E 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 343 through 347 Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 356 removed outlier: 6.358A pdb=" N VAL C 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LYS E 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER C 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N GLY E 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ILE C 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL E 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LYS F 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER E 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N GLY F 355 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ILE E 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.570A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N HIS E 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN E 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N HIS F 362 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR E 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 369 through 378 68 hydrogen bonds defined for protein. 204 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: 0.82 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 950 1.33 - 1.45: 455 1.45 - 1.57: 2111 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3522 Sorted by residual: bond pdb=" CZ ARG C 379 " pdb=" NH2 ARG C 379 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.10e+00 bond pdb=" CZ ARG B 379 " pdb=" NH2 ARG B 379 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.89e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.47e+00 bond pdb=" CZ ARG D 379 " pdb=" NH2 ARG D 379 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.25e+00 bond pdb=" CZ ARG F 379 " pdb=" NH2 ARG F 379 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.22e+00 ... (remaining 3517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 3165 1.68 - 3.36: 1208 3.36 - 5.03: 283 5.03 - 6.71: 47 6.71 - 8.39: 7 Bond angle restraints: 4710 Sorted by residual: angle pdb=" CB HIS B 374 " pdb=" CG HIS B 374 " pdb=" CD2 HIS B 374 " ideal model delta sigma weight residual 131.20 125.16 6.04 1.30e+00 5.92e-01 2.16e+01 angle pdb=" CB HIS E 362 " pdb=" CG HIS E 362 " pdb=" CD2 HIS E 362 " ideal model delta sigma weight residual 131.20 125.18 6.02 1.30e+00 5.92e-01 2.14e+01 angle pdb=" CB HIS A 362 " pdb=" CG HIS A 362 " pdb=" CD2 HIS A 362 " ideal model delta sigma weight residual 131.20 125.19 6.01 1.30e+00 5.92e-01 2.13e+01 angle pdb=" C LEU B 357 " pdb=" CA LEU B 357 " pdb=" CB LEU B 357 " ideal model delta sigma weight residual 111.74 119.08 -7.34 1.59e+00 3.96e-01 2.13e+01 angle pdb=" OE1 GLN D 336 " pdb=" CD GLN D 336 " pdb=" NE2 GLN D 336 " ideal model delta sigma weight residual 122.60 117.99 4.61 1.00e+00 1.00e+00 2.13e+01 ... (remaining 4705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.49: 1949 13.49 - 26.98: 150 26.98 - 40.47: 28 40.47 - 53.96: 7 53.96 - 67.45: 8 Dihedral angle restraints: 2142 sinusoidal: 894 harmonic: 1248 Sorted by residual: dihedral pdb=" N ARG C 349 " pdb=" C ARG C 349 " pdb=" CA ARG C 349 " pdb=" CB ARG C 349 " ideal model delta harmonic sigma weight residual 122.80 135.29 -12.49 0 2.50e+00 1.60e-01 2.49e+01 dihedral pdb=" C ARG C 349 " pdb=" N ARG C 349 " pdb=" CA ARG C 349 " pdb=" CB ARG C 349 " ideal model delta harmonic sigma weight residual -122.60 -135.07 12.47 0 2.50e+00 1.60e-01 2.49e+01 dihedral pdb=" N ARG B 349 " pdb=" C ARG B 349 " pdb=" CA ARG B 349 " pdb=" CB ARG B 349 " ideal model delta harmonic sigma weight residual 122.80 134.85 -12.05 0 2.50e+00 1.60e-01 2.32e+01 ... (remaining 2139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 380 0.092 - 0.184: 124 0.184 - 0.275: 16 0.275 - 0.367: 2 0.367 - 0.459: 6 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA ARG C 349 " pdb=" N ARG C 349 " pdb=" C ARG C 349 " pdb=" CB ARG C 349 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" CA ARG B 349 " pdb=" N ARG B 349 " pdb=" C ARG B 349 " pdb=" CB ARG B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" CA GLU D 372 " pdb=" N GLU D 372 " pdb=" C GLU D 372 " pdb=" CB GLU D 372 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.59e+00 ... (remaining 525 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " 0.082 2.00e-02 2.50e+03 4.57e-02 4.17e+01 pdb=" CG TYR D 310 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 378 " -0.064 2.00e-02 2.50e+03 4.81e-02 4.06e+01 pdb=" CG PHE E 378 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 PHE E 378 " 0.051 2.00e-02 2.50e+03 pdb=" CD2 PHE E 378 " 0.069 2.00e-02 2.50e+03 pdb=" CE1 PHE E 378 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE E 378 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE E 378 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " -0.073 2.00e-02 2.50e+03 4.31e-02 3.72e+01 pdb=" CG TYR E 310 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.033 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " -0.074 2.00e-02 2.50e+03 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.98: 1551 2.98 - 3.46: 2879 3.46 - 3.94: 5435 3.94 - 4.42: 5766 4.42 - 4.90: 10964 Nonbonded interactions: 26595 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.505 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.517 3.040 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.519 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.521 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.532 3.040 ... (remaining 26590 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.690 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 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 0.037 3522 Z= 0.769 Angle : 1.820 8.390 4710 Z= 1.198 Chirality : 0.098 0.459 528 Planarity : 0.013 0.122 600 Dihedral : 11.112 67.450 1350 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 1.52 % 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: -1.41 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.005 HIS E 330 PHE 0.069 0.022 PHE E 378 TYR 0.082 0.027 TYR D 310 ARG 0.004 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.389 Fit side-chains REVERT: A 373 THR cc_start: 0.8478 (m) cc_final: 0.7846 (p) REVERT: B 314 ASP cc_start: 0.8131 (t0) cc_final: 0.7899 (t0) REVERT: B 315 LEU cc_start: 0.8638 (mp) cc_final: 0.8346 (mm) REVERT: B 370 LYS cc_start: 0.8283 (tttp) cc_final: 0.7660 (tttp) REVERT: B 373 THR cc_start: 0.8466 (m) cc_final: 0.8177 (p) REVERT: B 375 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7546 (tttt) REVERT: C 373 THR cc_start: 0.8502 (m) cc_final: 0.8236 (p) REVERT: D 373 THR cc_start: 0.8470 (m) cc_final: 0.7991 (p) REVERT: E 373 THR cc_start: 0.8517 (m) cc_final: 0.7994 (p) REVERT: F 336 GLN cc_start: 0.8580 (tp40) cc_final: 0.8244 (mt0) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 1.3141 time to fit residues: 244.6791 Evaluate side-chains 105 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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: 4.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.153447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.125842 restraints weight = 3251.646| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.48 r_work: 0.3738 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3522 Z= 0.284 Angle : 0.787 9.932 4710 Z= 0.383 Chirality : 0.054 0.172 528 Planarity : 0.004 0.025 600 Dihedral : 6.400 18.063 468 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 5.30 % Allowed : 16.67 % Favored : 78.03 % 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: -1.38 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 329 PHE 0.008 0.002 PHE C 378 TYR 0.011 0.002 TYR D 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.456 Fit side-chains REVERT: A 311 LYS cc_start: 0.8269 (mttt) cc_final: 0.7666 (mmpt) REVERT: A 373 THR cc_start: 0.8814 (m) cc_final: 0.8490 (p) REVERT: B 372 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7460 (mt-10) REVERT: B 375 LYS cc_start: 0.8303 (ttmt) cc_final: 0.8017 (tttt) REVERT: B 379 ARG cc_start: 0.6045 (mtm180) cc_final: 0.5796 (mpp-170) REVERT: C 342 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7072 (mp0) REVERT: C 372 GLU cc_start: 0.8104 (tt0) cc_final: 0.7778 (mm-30) REVERT: C 375 LYS cc_start: 0.8350 (ttmt) cc_final: 0.8084 (tttt) REVERT: E 347 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7398 (mtmm) REVERT: E 372 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7833 (mm-30) outliers start: 21 outliers final: 9 residues processed: 132 average time/residue: 1.2387 time to fit residues: 167.7088 Evaluate side-chains 121 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 369 LYS Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.151359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.124150 restraints weight = 3213.297| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.46 r_work: 0.3710 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 3522 Z= 0.388 Angle : 0.812 10.713 4710 Z= 0.400 Chirality : 0.056 0.238 528 Planarity : 0.004 0.027 600 Dihedral : 6.365 18.019 468 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 6.31 % Allowed : 16.92 % Favored : 76.77 % 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: -1.65 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 329 PHE 0.009 0.002 PHE C 378 TYR 0.012 0.003 TYR D 310 ARG 0.003 0.001 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7569 (tt0) cc_final: 0.7145 (tt0) REVERT: A 373 THR cc_start: 0.8823 (m) cc_final: 0.8536 (p) REVERT: B 375 LYS cc_start: 0.8316 (ttmt) cc_final: 0.8034 (tttt) REVERT: C 342 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7127 (mp0) REVERT: C 372 GLU cc_start: 0.8060 (tt0) cc_final: 0.7787 (mm-30) REVERT: E 343 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7810 (mmmt) REVERT: E 347 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7384 (mtmm) REVERT: F 343 LYS cc_start: 0.8270 (mmtt) cc_final: 0.7771 (mtpm) outliers start: 25 outliers final: 15 residues processed: 128 average time/residue: 1.3951 time to fit residues: 182.8289 Evaluate side-chains 129 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 369 LYS Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 C 351 GLN F 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.152310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.126523 restraints weight = 3336.701| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.38 r_work: 0.3704 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 3522 Z= 0.360 Angle : 0.764 10.496 4710 Z= 0.377 Chirality : 0.055 0.228 528 Planarity : 0.004 0.026 600 Dihedral : 6.235 17.963 468 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 7.83 % Allowed : 15.15 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 329 PHE 0.009 0.002 PHE C 378 TYR 0.011 0.002 TYR D 310 ARG 0.003 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7541 (tt0) cc_final: 0.7176 (tt0) REVERT: A 373 THR cc_start: 0.8804 (m) cc_final: 0.8544 (p) REVERT: B 375 LYS cc_start: 0.8275 (ttmt) cc_final: 0.8031 (tttt) REVERT: C 372 GLU cc_start: 0.8012 (tt0) cc_final: 0.7769 (mm-30) REVERT: C 375 LYS cc_start: 0.8312 (ttmt) cc_final: 0.8104 (tttt) REVERT: E 343 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7813 (mmmt) REVERT: E 347 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7394 (mtmm) REVERT: F 343 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7858 (mtpm) outliers start: 31 outliers final: 19 residues processed: 130 average time/residue: 1.3470 time to fit residues: 179.2417 Evaluate side-chains 124 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 369 LYS Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 C 351 GLN F 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.150344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.124498 restraints weight = 3346.706| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.42 r_work: 0.3719 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 3522 Z= 0.333 Angle : 0.746 10.111 4710 Z= 0.367 Chirality : 0.055 0.211 528 Planarity : 0.004 0.026 600 Dihedral : 6.141 17.692 468 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 8.59 % Allowed : 15.40 % Favored : 76.01 % 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: -1.67 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 329 PHE 0.011 0.002 PHE E 378 TYR 0.010 0.002 TYR D 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7538 (tt0) cc_final: 0.7098 (tt0) REVERT: B 375 LYS cc_start: 0.8321 (ttmt) cc_final: 0.8004 (tttt) REVERT: C 372 GLU cc_start: 0.8055 (tt0) cc_final: 0.7822 (mm-30) REVERT: C 375 LYS cc_start: 0.8370 (ttmt) cc_final: 0.8119 (tttt) REVERT: E 343 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7801 (mmmt) REVERT: F 343 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7816 (mtpm) outliers start: 34 outliers final: 20 residues processed: 127 average time/residue: 1.3455 time to fit residues: 174.9367 Evaluate side-chains 127 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 369 LYS Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN C 351 GLN F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.153065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.127378 restraints weight = 3366.403| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.38 r_work: 0.3720 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3522 Z= 0.282 Angle : 0.707 9.367 4710 Z= 0.343 Chirality : 0.053 0.189 528 Planarity : 0.004 0.026 600 Dihedral : 5.989 16.637 468 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 7.83 % Allowed : 16.67 % Favored : 75.51 % 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: -1.65 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 329 PHE 0.011 0.002 PHE D 378 TYR 0.010 0.002 TYR D 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.437 Fit side-chains REVERT: A 307 GLN cc_start: 0.7556 (tt0) cc_final: 0.7137 (tt0) REVERT: B 372 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: B 375 LYS cc_start: 0.8348 (ttmt) cc_final: 0.8078 (tttt) REVERT: B 379 ARG cc_start: 0.6125 (mtm180) cc_final: 0.5690 (mtm110) REVERT: C 372 GLU cc_start: 0.8009 (tt0) cc_final: 0.7766 (mm-30) REVERT: F 343 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7972 (mtpm) outliers start: 31 outliers final: 18 residues processed: 126 average time/residue: 1.3145 time to fit residues: 169.6595 Evaluate side-chains 131 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 369 LYS Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 5 optimal weight: 0.0970 chunk 32 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN C 351 GLN F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.151509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.124290 restraints weight = 3241.125| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.47 r_work: 0.3704 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3522 Z= 0.338 Angle : 0.747 10.311 4710 Z= 0.367 Chirality : 0.056 0.219 528 Planarity : 0.004 0.026 600 Dihedral : 6.080 17.689 468 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 8.08 % Allowed : 16.67 % Favored : 75.25 % 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: -1.71 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 329 PHE 0.008 0.002 PHE F 378 TYR 0.010 0.002 TYR D 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.396 Fit side-chains REVERT: A 307 GLN cc_start: 0.7546 (tt0) cc_final: 0.7132 (tt0) REVERT: A 343 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7867 (mtpm) REVERT: B 375 LYS cc_start: 0.8347 (ttmt) cc_final: 0.8031 (tttt) REVERT: B 379 ARG cc_start: 0.6210 (mtm180) cc_final: 0.5868 (mtm110) REVERT: C 372 GLU cc_start: 0.8054 (tt0) cc_final: 0.7819 (mm-30) REVERT: F 343 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7956 (mtpm) outliers start: 32 outliers final: 21 residues processed: 123 average time/residue: 1.2589 time to fit residues: 158.8165 Evaluate side-chains 129 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 369 LYS Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN C 351 GLN F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.153022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.125973 restraints weight = 3226.441| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.46 r_work: 0.3728 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3522 Z= 0.228 Angle : 0.680 9.673 4710 Z= 0.326 Chirality : 0.053 0.170 528 Planarity : 0.003 0.025 600 Dihedral : 5.811 16.203 468 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 5.30 % Allowed : 19.95 % Favored : 74.75 % 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: -1.65 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 362 PHE 0.015 0.002 PHE D 378 TYR 0.009 0.002 TYR D 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.445 Fit side-chains REVERT: A 307 GLN cc_start: 0.7536 (tt0) cc_final: 0.7120 (tt0) REVERT: B 375 LYS cc_start: 0.8358 (ttmt) cc_final: 0.8076 (tttt) REVERT: B 379 ARG cc_start: 0.6203 (mtm180) cc_final: 0.5735 (mtm110) REVERT: C 340 LYS cc_start: 0.8207 (mttp) cc_final: 0.8003 (mmtt) REVERT: C 372 GLU cc_start: 0.8015 (tt0) cc_final: 0.7766 (mm-30) REVERT: C 375 LYS cc_start: 0.8345 (ttmt) cc_final: 0.8091 (tttt) REVERT: E 373 THR cc_start: 0.8724 (m) cc_final: 0.8377 (p) REVERT: F 343 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7972 (mtpm) outliers start: 21 outliers final: 15 residues processed: 125 average time/residue: 1.3707 time to fit residues: 175.4510 Evaluate side-chains 118 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN C 351 GLN F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.152138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.124990 restraints weight = 3191.685| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.45 r_work: 0.3712 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3522 Z= 0.298 Angle : 0.724 10.362 4710 Z= 0.351 Chirality : 0.055 0.201 528 Planarity : 0.004 0.025 600 Dihedral : 5.944 16.860 468 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 5.56 % Allowed : 19.44 % Favored : 75.00 % 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: -1.68 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 329 PHE 0.006 0.002 PHE A 346 TYR 0.010 0.002 TYR D 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.425 Fit side-chains REVERT: A 307 GLN cc_start: 0.7552 (tt0) cc_final: 0.7141 (tt0) REVERT: A 311 LYS cc_start: 0.8311 (mttt) cc_final: 0.7769 (mmpt) REVERT: B 375 LYS cc_start: 0.8324 (ttmt) cc_final: 0.8054 (tttt) REVERT: B 379 ARG cc_start: 0.6144 (mtm180) cc_final: 0.5765 (mtm110) REVERT: C 372 GLU cc_start: 0.8015 (tt0) cc_final: 0.7774 (mm-30) REVERT: C 375 LYS cc_start: 0.8336 (ttmt) cc_final: 0.8097 (tttt) REVERT: F 343 LYS cc_start: 0.8243 (mmtt) cc_final: 0.7975 (mtpm) outliers start: 22 outliers final: 17 residues processed: 118 average time/residue: 1.2926 time to fit residues: 156.4213 Evaluate side-chains 120 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 369 LYS Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 40 optimal weight: 0.4980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN C 351 GLN F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.155941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.129191 restraints weight = 3244.406| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.46 r_work: 0.3773 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3522 Z= 0.170 Angle : 0.646 9.265 4710 Z= 0.303 Chirality : 0.052 0.176 528 Planarity : 0.003 0.023 600 Dihedral : 5.534 15.571 468 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.78 % Allowed : 22.47 % Favored : 74.75 % 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: -1.63 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.017 0.002 PHE D 378 TYR 0.008 0.001 TYR D 310 ARG 0.001 0.000 ARG F 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.461 Fit side-chains REVERT: A 307 GLN cc_start: 0.7521 (tt0) cc_final: 0.7111 (tt0) REVERT: B 375 LYS cc_start: 0.8357 (ttmt) cc_final: 0.8057 (tttt) REVERT: B 379 ARG cc_start: 0.6158 (mtm180) cc_final: 0.5846 (mtm110) REVERT: C 372 GLU cc_start: 0.8022 (tt0) cc_final: 0.7775 (mm-30) REVERT: C 375 LYS cc_start: 0.8341 (ttmt) cc_final: 0.8072 (tttt) REVERT: D 378 PHE cc_start: 0.7782 (t80) cc_final: 0.7574 (t80) REVERT: E 373 THR cc_start: 0.8706 (m) cc_final: 0.8323 (p) REVERT: F 319 THR cc_start: 0.8281 (m) cc_final: 0.7981 (p) REVERT: F 343 LYS cc_start: 0.8241 (mmtt) cc_final: 0.7971 (mtpm) outliers start: 11 outliers final: 10 residues processed: 115 average time/residue: 1.2518 time to fit residues: 147.8719 Evaluate side-chains 112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.154721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.127737 restraints weight = 3238.910| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.46 r_work: 0.3752 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3522 Z= 0.209 Angle : 0.664 9.567 4710 Z= 0.314 Chirality : 0.053 0.183 528 Planarity : 0.003 0.024 600 Dihedral : 5.637 15.960 468 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.03 % Allowed : 23.48 % Favored : 73.48 % 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: -1.59 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 362 PHE 0.017 0.002 PHE D 378 TYR 0.008 0.002 TYR D 310 ARG 0.002 0.000 ARG D 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4599.48 seconds wall clock time: 81 minutes 45.42 seconds (4905.42 seconds total)