Starting phenix.real_space_refine on Mon Sep 23 17:17:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p66_13219/09_2024/7p66_13219.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p66_13219/09_2024/7p66_13219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p66_13219/09_2024/7p66_13219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p66_13219/09_2024/7p66_13219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p66_13219/09_2024/7p66_13219.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p66_13219/09_2024/7p66_13219.cif" } resolution = 3.0 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= 0.004 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 10 5.16 5 C 2530 2.51 5 N 760 2.21 5 O 760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4060 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Restraints were copied for chains: C, B, E, D Time building chain proxies: 2.76, per 1000 atoms: 0.68 Number of scatterers: 4060 At special positions: 0 Unit cell: (109.25, 92, 46, 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 10 16.00 O 760 8.00 N 760 7.00 C 2530 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: 0.94 Conformation dependent library (CDL) restraints added in 500.9 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 930 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 44.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 284 removed outlier: 6.877A pdb=" N GLN C 276 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE B 277 " --> pdb=" O GLN C 276 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE C 278 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN B 279 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS C 280 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS B 281 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN A 276 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASN B 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE A 278 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LYS B 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N LYS A 280 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ASP B 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N LEU A 282 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N GLN A 276 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N ASN D 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N ILE A 278 " --> pdb=" O ASN D 279 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N LYS D 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LYS A 280 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ASP D 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 282 " --> pdb=" O ASP D 283 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N GLN D 276 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 10.315A pdb=" N ASN E 279 " --> pdb=" O GLN D 276 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N ILE D 278 " --> pdb=" O ASN E 279 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N LYS E 281 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LYS D 280 " --> pdb=" O LYS E 281 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ASP E 283 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU D 282 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 287 through 290 removed outlier: 6.333A pdb=" N VAL A 287 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N LYS D 290 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER A 289 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL D 287 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LYS E 290 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER D 289 " --> pdb=" O LYS E 290 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 297 through 298 removed outlier: 6.690A pdb=" N ILE A 297 " --> pdb=" O LYS D 298 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE D 297 " --> pdb=" O LYS E 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.531A pdb=" N GLN A 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TYR D 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL A 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN D 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYR E 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.804A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.334A pdb=" N VAL A 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LYS D 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N SER A 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL D 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LYS E 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N SER D 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.420A pdb=" N ILE A 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE D 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 337 through 345 removed outlier: 6.542A pdb=" N GLU B 338 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N SER C 341 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LYS B 340 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LYS C 343 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU B 342 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ASP C 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 344 " --> pdb=" O ASP C 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 348 through 350 removed outlier: 6.995A pdb=" N ASP B 348 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASP A 348 " --> pdb=" O ARG B 349 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 355 through 362 removed outlier: 6.929A pdb=" N SER B 356 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU C 357 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP B 358 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN C 359 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER A 356 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU B 357 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP A 358 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASN B 359 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLY A 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ASP D 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N LEU A 357 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N ILE D 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN A 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N HIS D 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N THR A 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N GLY D 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N ASP E 358 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N LEU D 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N ILE E 360 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN D 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N HIS E 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR D 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 369 through 373 removed outlier: 6.932A pdb=" N LYS B 370 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS A 370 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N GLU D 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE A 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS D 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLU E 372 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE D 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 376 through 377 removed outlier: 6.958A pdb=" N THR A 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 80 hydrogen bonds defined for protein. 240 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: 1.03 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1355 1.34 - 1.46: 632 1.46 - 1.58: 2118 1.58 - 1.69: 0 1.69 - 1.81: 10 Bond restraints: 4115 Sorted by residual: bond pdb=" N SER B 352 " pdb=" CA SER B 352 " ideal model delta sigma weight residual 1.455 1.491 -0.037 1.27e-02 6.20e+03 8.31e+00 bond pdb=" N SER A 352 " pdb=" CA SER A 352 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 8.15e+00 bond pdb=" N SER D 352 " pdb=" CA SER D 352 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 8.13e+00 bond pdb=" N SER E 352 " pdb=" CA SER E 352 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 8.13e+00 bond pdb=" N SER C 352 " pdb=" CA SER C 352 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 8.07e+00 ... (remaining 4110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 4961 0.92 - 1.84: 344 1.84 - 2.77: 120 2.77 - 3.69: 55 3.69 - 4.61: 15 Bond angle restraints: 5495 Sorted by residual: angle pdb=" N GLN A 351 " pdb=" CA GLN A 351 " pdb=" C GLN A 351 " ideal model delta sigma weight residual 112.30 107.69 4.61 1.36e+00 5.41e-01 1.15e+01 angle pdb=" N GLN C 351 " pdb=" CA GLN C 351 " pdb=" C GLN C 351 " ideal model delta sigma weight residual 112.30 107.70 4.60 1.36e+00 5.41e-01 1.14e+01 angle pdb=" N GLN E 351 " pdb=" CA GLN E 351 " pdb=" C GLN E 351 " ideal model delta sigma weight residual 112.30 107.70 4.60 1.36e+00 5.41e-01 1.14e+01 angle pdb=" N GLN B 351 " pdb=" CA GLN B 351 " pdb=" C GLN B 351 " ideal model delta sigma weight residual 112.30 107.72 4.58 1.36e+00 5.41e-01 1.13e+01 angle pdb=" N GLN D 351 " pdb=" CA GLN D 351 " pdb=" C GLN D 351 " ideal model delta sigma weight residual 112.30 107.72 4.58 1.36e+00 5.41e-01 1.13e+01 ... (remaining 5490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.40: 2160 11.40 - 22.79: 235 22.79 - 34.18: 95 34.18 - 45.58: 20 45.58 - 56.97: 15 Dihedral angle restraints: 2525 sinusoidal: 1055 harmonic: 1470 Sorted by residual: dihedral pdb=" CA ASP D 358 " pdb=" CB ASP D 358 " pdb=" CG ASP D 358 " pdb=" OD1 ASP D 358 " ideal model delta sinusoidal sigma weight residual -30.00 -82.26 52.26 1 2.00e+01 2.50e-03 9.31e+00 dihedral pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " pdb=" CG ASP E 358 " pdb=" OD1 ASP E 358 " ideal model delta sinusoidal sigma weight residual -30.00 -82.23 52.23 1 2.00e+01 2.50e-03 9.30e+00 dihedral pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " pdb=" OD1 ASP A 358 " ideal model delta sinusoidal sigma weight residual -30.00 -82.22 52.22 1 2.00e+01 2.50e-03 9.30e+00 ... (remaining 2522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 417 0.041 - 0.082: 83 0.082 - 0.122: 91 0.122 - 0.163: 9 0.163 - 0.204: 15 Chirality restraints: 615 Sorted by residual: chirality pdb=" CB ILE C 360 " pdb=" CA ILE C 360 " pdb=" CG1 ILE C 360 " pdb=" CG2 ILE C 360 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE E 360 " pdb=" CA ILE E 360 " pdb=" CG1 ILE E 360 " pdb=" CG2 ILE E 360 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB ILE D 360 " pdb=" CA ILE D 360 " pdb=" CG1 ILE D 360 " pdb=" CG2 ILE D 360 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 612 not shown) Planarity restraints: 705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 349 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C ARG C 349 " -0.035 2.00e-02 2.50e+03 pdb=" O ARG C 349 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL C 350 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 349 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C ARG A 349 " -0.035 2.00e-02 2.50e+03 pdb=" O ARG A 349 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A 350 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 349 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C ARG D 349 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG D 349 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL D 350 " 0.012 2.00e-02 2.50e+03 ... (remaining 702 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1398 2.89 - 3.39: 3508 3.39 - 3.90: 6963 3.90 - 4.40: 7450 4.40 - 4.90: 15049 Nonbonded interactions: 34368 Sorted by model distance: nonbonded pdb=" OG SER C 289 " pdb=" OG SER C 320 " model vdw 2.388 3.040 nonbonded pdb=" OG SER A 289 " pdb=" OG SER A 320 " model vdw 2.389 3.040 nonbonded pdb=" OG SER D 289 " pdb=" OG SER D 320 " model vdw 2.389 3.040 nonbonded pdb=" OG SER B 289 " pdb=" OG SER B 320 " model vdw 2.389 3.040 nonbonded pdb=" OG SER E 289 " pdb=" OG SER E 320 " model vdw 2.389 3.040 ... (remaining 34363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.800 Find NCS groups from input model: 0.130 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:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 0.004 0.037 4115 Z= 0.238 Angle : 0.661 4.610 5495 Z= 0.423 Chirality : 0.059 0.204 615 Planarity : 0.004 0.020 705 Dihedral : 12.126 56.974 1595 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: -2.50 (0.29), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.014 0.002 PHE E 346 TYR 0.004 0.001 TYR A 310 ARG 0.002 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.485 Fit side-chains REVERT: A 372 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7381 (mm-30) REVERT: B 310 TYR cc_start: 0.7964 (t80) cc_final: 0.7753 (t80) REVERT: B 372 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7579 (mm-30) REVERT: D 315 LEU cc_start: 0.9184 (mp) cc_final: 0.8967 (mt) REVERT: D 372 GLU cc_start: 0.7459 (mm-30) cc_final: 0.6859 (mm-30) REVERT: E 372 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7062 (mm-30) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.8110 time to fit residues: 92.8444 Evaluate side-chains 84 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 20 optimal weight: 0.0770 chunk 39 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 overall best weight: 3.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS B 288 GLN B 296 ASN B 351 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS C 296 ASN C 351 GLN C 374 HIS D 296 ASN D 351 GLN D 374 HIS E 288 GLN E 296 ASN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN E 368 ASN E 374 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 4115 Z= 0.493 Angle : 0.666 7.380 5495 Z= 0.341 Chirality : 0.052 0.143 615 Planarity : 0.004 0.032 705 Dihedral : 5.418 18.989 550 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.30 % Allowed : 9.68 % Favored : 86.02 % 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: -2.51 (0.29), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 362 PHE 0.021 0.004 PHE D 346 TYR 0.012 0.002 TYR D 310 ARG 0.003 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 0.587 Fit side-chains REVERT: A 274 LYS cc_start: 0.7486 (mtmt) cc_final: 0.7238 (mtpp) REVERT: A 315 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8946 (mt) REVERT: B 274 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7764 (ptmt) REVERT: B 286 ASN cc_start: 0.9076 (t0) cc_final: 0.8868 (t0) REVERT: B 305 SER cc_start: 0.9231 (p) cc_final: 0.8926 (p) REVERT: C 379 ARG cc_start: 0.6846 (tpt-90) cc_final: 0.6405 (mmp-170) REVERT: D 315 LEU cc_start: 0.9187 (mp) cc_final: 0.8978 (mt) REVERT: D 345 ASP cc_start: 0.6478 (m-30) cc_final: 0.6057 (m-30) REVERT: E 379 ARG cc_start: 0.7234 (tpt-90) cc_final: 0.6077 (pmt170) outliers start: 20 outliers final: 5 residues processed: 99 average time/residue: 0.9488 time to fit residues: 97.9042 Evaluate side-chains 88 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN B 288 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN C 307 GLN E 288 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4115 Z= 0.262 Angle : 0.553 5.830 5495 Z= 0.282 Chirality : 0.050 0.145 615 Planarity : 0.004 0.031 705 Dihedral : 4.917 15.868 550 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.37 % Allowed : 16.34 % Favored : 81.29 % 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: -2.60 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.017 0.003 PHE E 346 TYR 0.009 0.001 TYR E 310 ARG 0.002 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.531 Fit side-chains REVERT: A 274 LYS cc_start: 0.7542 (mtmt) cc_final: 0.7200 (mtpp) REVERT: A 315 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8939 (mt) REVERT: B 379 ARG cc_start: 0.6327 (tpt-90) cc_final: 0.5942 (tmt-80) REVERT: C 379 ARG cc_start: 0.6828 (tpt-90) cc_final: 0.6426 (mmp-170) REVERT: D 345 ASP cc_start: 0.6236 (m-30) cc_final: 0.5974 (m-30) REVERT: E 379 ARG cc_start: 0.6931 (tpt-90) cc_final: 0.6182 (ppt90) outliers start: 11 outliers final: 5 residues processed: 84 average time/residue: 0.8487 time to fit residues: 74.9293 Evaluate side-chains 81 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 279 ASN C 288 GLN D 276 GLN E 276 GLN E 288 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4115 Z= 0.154 Angle : 0.503 6.991 5495 Z= 0.253 Chirality : 0.049 0.141 615 Planarity : 0.003 0.027 705 Dihedral : 4.599 15.419 550 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.58 % Allowed : 16.13 % Favored : 81.29 % 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: -2.63 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS C 362 PHE 0.016 0.003 PHE D 346 TYR 0.008 0.001 TYR C 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.445 Fit side-chains REVERT: A 286 ASN cc_start: 0.9105 (t0) cc_final: 0.8898 (t0) REVERT: A 315 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8981 (mt) REVERT: B 379 ARG cc_start: 0.6387 (tpt-90) cc_final: 0.6137 (tmt-80) REVERT: C 379 ARG cc_start: 0.6884 (tpt-90) cc_final: 0.6626 (mmp-170) REVERT: D 315 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8803 (mt) REVERT: E 372 GLU cc_start: 0.7830 (mp0) cc_final: 0.7528 (mp0) REVERT: E 379 ARG cc_start: 0.6840 (tpt-90) cc_final: 0.6238 (pmt-80) outliers start: 12 outliers final: 3 residues processed: 90 average time/residue: 0.8694 time to fit residues: 81.8104 Evaluate side-chains 88 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN C 288 GLN D 276 GLN E 276 GLN E 288 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 4115 Z= 0.447 Angle : 0.624 7.063 5495 Z= 0.319 Chirality : 0.052 0.164 615 Planarity : 0.004 0.036 705 Dihedral : 5.163 17.443 550 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.52 % Allowed : 16.99 % Favored : 78.49 % 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: -2.79 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.21), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.020 0.003 PHE D 346 TYR 0.014 0.003 TYR C 310 ARG 0.003 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 0.489 Fit side-chains REVERT: A 315 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8959 (mt) REVERT: C 274 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7784 (ptmt) REVERT: C 379 ARG cc_start: 0.7002 (tpt-90) cc_final: 0.6439 (tpm170) REVERT: D 315 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8719 (mp) REVERT: E 372 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: E 379 ARG cc_start: 0.6969 (tpt-90) cc_final: 0.6497 (pmt170) outliers start: 21 outliers final: 8 residues processed: 88 average time/residue: 0.8742 time to fit residues: 80.4433 Evaluate side-chains 88 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 372 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN D 276 GLN E 276 GLN E 288 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4115 Z= 0.298 Angle : 0.569 7.123 5495 Z= 0.288 Chirality : 0.050 0.146 615 Planarity : 0.004 0.035 705 Dihedral : 4.967 16.926 550 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.66 % Allowed : 18.71 % Favored : 77.63 % 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: -2.81 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.21), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.019 0.003 PHE D 346 TYR 0.011 0.002 TYR C 310 ARG 0.003 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.447 Fit side-chains REVERT: A 315 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9007 (mt) REVERT: C 379 ARG cc_start: 0.6894 (tpt-90) cc_final: 0.6424 (tpm170) REVERT: D 274 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7554 (ttpt) REVERT: D 315 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8789 (mt) REVERT: E 372 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: E 379 ARG cc_start: 0.6690 (tpt-90) cc_final: 0.6475 (pmt-80) outliers start: 17 outliers final: 7 residues processed: 86 average time/residue: 0.9363 time to fit residues: 84.0294 Evaluate side-chains 84 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 372 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 0.0030 chunk 48 optimal weight: 0.1980 chunk 30 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 351 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN C 279 ASN C 288 GLN ** D 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 GLN E 288 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4115 Z= 0.136 Angle : 0.524 6.740 5495 Z= 0.263 Chirality : 0.049 0.139 615 Planarity : 0.003 0.029 705 Dihedral : 4.551 15.440 550 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.58 % Allowed : 19.14 % Favored : 78.28 % 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: -2.73 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 362 PHE 0.016 0.002 PHE D 346 TYR 0.007 0.001 TYR A 310 ARG 0.002 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.441 Fit side-chains REVERT: C 276 GLN cc_start: 0.8394 (mt0) cc_final: 0.8020 (mp10) REVERT: C 379 ARG cc_start: 0.6903 (tpt-90) cc_final: 0.6371 (tpm170) REVERT: D 274 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7554 (ttpt) REVERT: D 315 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8825 (mt) REVERT: E 372 GLU cc_start: 0.7967 (mp0) cc_final: 0.7706 (mp0) REVERT: E 379 ARG cc_start: 0.6688 (tpt-90) cc_final: 0.6364 (pmt-80) outliers start: 12 outliers final: 5 residues processed: 85 average time/residue: 0.8396 time to fit residues: 74.7655 Evaluate side-chains 83 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 44 optimal weight: 0.0270 chunk 27 optimal weight: 0.4980 chunk 19 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.4440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN A 307 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN E 276 GLN E 288 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4115 Z= 0.219 Angle : 0.540 6.954 5495 Z= 0.271 Chirality : 0.050 0.144 615 Planarity : 0.003 0.030 705 Dihedral : 4.649 15.623 550 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.58 % Allowed : 19.78 % Favored : 77.63 % 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: -2.74 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 362 PHE 0.016 0.002 PHE D 346 TYR 0.012 0.002 TYR C 310 ARG 0.002 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.495 Fit side-chains REVERT: C 379 ARG cc_start: 0.6941 (tpt-90) cc_final: 0.6360 (tpm170) REVERT: D 315 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8750 (mp) REVERT: D 345 ASP cc_start: 0.7173 (t0) cc_final: 0.6881 (t70) REVERT: E 372 GLU cc_start: 0.7975 (mp0) cc_final: 0.7698 (mp0) outliers start: 12 outliers final: 7 residues processed: 86 average time/residue: 0.8169 time to fit residues: 73.6837 Evaluate side-chains 84 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN A 307 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 279 ASN C 288 GLN E 276 GLN E 288 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4115 Z= 0.373 Angle : 0.599 7.353 5495 Z= 0.305 Chirality : 0.051 0.190 615 Planarity : 0.004 0.034 705 Dihedral : 5.020 16.628 550 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.80 % Allowed : 20.43 % 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: -2.85 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.21), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.018 0.003 PHE D 346 TYR 0.014 0.002 TYR C 310 ARG 0.002 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.491 Fit side-chains REVERT: A 315 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9043 (mt) REVERT: C 276 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8075 (mp10) REVERT: C 379 ARG cc_start: 0.6936 (tpt-90) cc_final: 0.6396 (tpm170) REVERT: D 315 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8731 (mp) REVERT: D 345 ASP cc_start: 0.7361 (t0) cc_final: 0.7042 (t70) outliers start: 13 outliers final: 7 residues processed: 87 average time/residue: 0.7596 time to fit residues: 69.6392 Evaluate side-chains 90 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 279 ASN E 276 GLN E 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4115 Z= 0.181 Angle : 0.551 6.859 5495 Z= 0.278 Chirality : 0.050 0.140 615 Planarity : 0.003 0.031 705 Dihedral : 4.776 15.800 550 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.15 % Allowed : 20.65 % Favored : 77.20 % 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: -2.82 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.016 0.002 PHE D 346 TYR 0.011 0.002 TYR C 310 ARG 0.005 0.000 ARG B 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.365 Fit side-chains REVERT: A 315 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9067 (mt) REVERT: C 276 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.8071 (mp10) REVERT: C 379 ARG cc_start: 0.6847 (tpt-90) cc_final: 0.6369 (tpm170) REVERT: D 315 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8822 (mt) REVERT: D 345 ASP cc_start: 0.7181 (t0) cc_final: 0.6853 (t70) REVERT: D 372 GLU cc_start: 0.7865 (mp0) cc_final: 0.7558 (mm-30) outliers start: 10 outliers final: 5 residues processed: 83 average time/residue: 0.5989 time to fit residues: 52.2706 Evaluate side-chains 86 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 28 optimal weight: 0.0370 chunk 45 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN A 307 GLN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 288 GLN D 276 GLN E 276 GLN E 288 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.101602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.090453 restraints weight = 6105.427| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.07 r_work: 0.3332 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 4115 Z= 0.523 Angle : 0.675 7.562 5495 Z= 0.348 Chirality : 0.054 0.219 615 Planarity : 0.004 0.037 705 Dihedral : 5.200 17.075 550 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.58 % Allowed : 20.43 % Favored : 76.99 % 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: -2.97 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.21), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 330 PHE 0.018 0.003 PHE D 346 TYR 0.016 0.003 TYR B 310 ARG 0.007 0.001 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1950.22 seconds wall clock time: 36 minutes 36.13 seconds (2196.13 seconds total)