Starting phenix.real_space_refine on Sun Mar 10 17:09:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8l_18254/03_2024/8q8l_18254.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8l_18254/03_2024/8q8l_18254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8l_18254/03_2024/8q8l_18254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8l_18254/03_2024/8q8l_18254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8l_18254/03_2024/8q8l_18254.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8l_18254/03_2024/8q8l_18254.pdb" } resolution = 3.04 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 2139 2.51 5 N 624 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 372": "OE1" <-> "OE2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3405 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: "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: "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: "B" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 2.20, per 1000 atoms: 0.65 Number of scatterers: 3405 At special positions: 0 Unit cell: (112.064, 116.184, 42.024, 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 636 8.00 N 624 7.00 C 2139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 666.9 milliseconds 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 21 sheets defined 0.0% alpha, 44.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.611A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.688A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 320 removed outlier: 6.586A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.505A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.490A pdb=" N GLN A 336 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL C 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU A 338 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.155A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 351 through 352 removed outlier: 6.210A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.436A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.436A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N HIS E 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.482A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR E 373 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 307 through 310 Processing sheet with id=AB3, first strand: chain 'D' and resid 313 through 314 removed outlier: 7.004A pdb=" N VAL B 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.404A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLY D 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS B 322 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU D 325 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N SER B 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.374A pdb=" N ILE B 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 337 through 340 removed outlier: 6.551A pdb=" N GLU B 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 343 through 346 Processing sheet with id=AB8, first strand: chain 'D' and resid 351 through 354 removed outlier: 6.403A pdb=" N GLN B 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE F 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS B 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 357 through 358 removed outlier: 6.751A pdb=" N LEU B 357 " --> pdb=" O ASP D 358 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.515A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.417A pdb=" N ASN B 368 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ILE D 371 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS B 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR D 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU B 372 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS B 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLU F 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE B 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 376 through 377 removed outlier: 6.697A pdb=" N LEU B 376 " --> pdb=" O THR D 377 " (cutoff:3.500A) 56 hydrogen bonds defined for protein. 168 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: 0.84 Time building geometry restraints manager: 1.31 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: 965 1.33 - 1.45: 417 1.45 - 1.57: 2071 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3459 Sorted by residual: bond pdb=" CA GLY E 366 " pdb=" C GLY E 366 " ideal model delta sigma weight residual 1.510 1.563 -0.053 1.39e-02 5.18e+03 1.46e+01 bond pdb=" CA LYS B 331 " pdb=" C LYS B 331 " ideal model delta sigma weight residual 1.532 1.554 -0.022 6.50e-03 2.37e+04 1.17e+01 bond pdb=" CA LYS E 331 " pdb=" C LYS E 331 " ideal model delta sigma weight residual 1.524 1.564 -0.040 1.26e-02 6.30e+03 1.02e+01 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.60e+00 bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.40e+00 ... (remaining 3454 not shown) Histogram of bond angle deviations from ideal: 101.20 - 107.84: 293 107.84 - 114.48: 1837 114.48 - 121.12: 1444 121.12 - 127.76: 1036 127.76 - 134.40: 19 Bond angle restraints: 4629 Sorted by residual: angle pdb=" N CYS E 322 " pdb=" CA CYS E 322 " pdb=" C CYS E 322 " ideal model delta sigma weight residual 108.32 124.79 -16.47 1.64e+00 3.72e-01 1.01e+02 angle pdb=" C GLY E 323 " pdb=" N SER E 324 " pdb=" CA SER E 324 " ideal model delta sigma weight residual 122.44 134.40 -11.96 1.45e+00 4.76e-01 6.80e+01 angle pdb=" C GLY E 366 " pdb=" N GLY E 367 " pdb=" CA GLY E 367 " ideal model delta sigma weight residual 120.64 130.18 -9.54 1.26e+00 6.30e-01 5.73e+01 angle pdb=" N GLY E 323 " pdb=" CA GLY E 323 " pdb=" C GLY E 323 " ideal model delta sigma weight residual 112.22 125.05 -12.83 1.74e+00 3.30e-01 5.44e+01 angle pdb=" C GLY E 326 " pdb=" N ASN E 327 " pdb=" CA ASN E 327 " ideal model delta sigma weight residual 121.24 111.22 10.02 1.44e+00 4.82e-01 4.84e+01 ... (remaining 4624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.44: 1778 11.44 - 22.88: 253 22.88 - 34.31: 53 34.31 - 45.75: 11 45.75 - 57.19: 8 Dihedral angle restraints: 2103 sinusoidal: 876 harmonic: 1227 Sorted by residual: dihedral pdb=" C LYS E 347 " pdb=" N LYS E 347 " pdb=" CA LYS E 347 " pdb=" CB LYS E 347 " ideal model delta harmonic sigma weight residual -122.60 -143.32 20.72 0 2.50e+00 1.60e-01 6.87e+01 dihedral pdb=" N LYS E 347 " pdb=" C LYS E 347 " pdb=" CA LYS E 347 " pdb=" CB LYS E 347 " ideal model delta harmonic sigma weight residual 122.80 142.01 -19.21 0 2.50e+00 1.60e-01 5.91e+01 dihedral pdb=" CA CYS E 322 " pdb=" C CYS E 322 " pdb=" N GLY E 323 " pdb=" CA GLY E 323 " ideal model delta harmonic sigma weight residual 180.00 149.93 30.07 0 5.00e+00 4.00e-02 3.62e+01 ... (remaining 2100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 466 0.173 - 0.346: 52 0.346 - 0.519: 3 0.519 - 0.693: 0 0.693 - 0.866: 1 Chirality restraints: 522 Sorted by residual: chirality pdb=" CA LYS E 347 " pdb=" N LYS E 347 " pdb=" C LYS E 347 " pdb=" CB LYS E 347 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.87e+01 chirality pdb=" CA LYS D 347 " pdb=" N LYS D 347 " pdb=" C LYS D 347 " pdb=" CB LYS D 347 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.34e+00 chirality pdb=" CA LYS B 347 " pdb=" N LYS B 347 " pdb=" C LYS B 347 " pdb=" CB LYS B 347 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.36e+00 ... (remaining 519 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.160 2.00e-02 2.50e+03 8.90e-02 1.58e+02 pdb=" CG TYR A 310 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.078 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.047 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.144 2.00e-02 2.50e+03 8.01e-02 1.28e+02 pdb=" CG TYR C 310 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.070 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.045 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 362 " -0.081 2.00e-02 2.50e+03 6.04e-02 5.46e+01 pdb=" CG HIS E 362 " 0.096 2.00e-02 2.50e+03 pdb=" ND1 HIS E 362 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS E 362 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 HIS E 362 " -0.046 2.00e-02 2.50e+03 pdb=" NE2 HIS E 362 " -0.039 2.00e-02 2.50e+03 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1722 3.01 - 3.48: 2786 3.48 - 3.96: 5333 3.96 - 4.43: 5408 4.43 - 4.90: 10265 Nonbonded interactions: 25514 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.539 2.440 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.544 2.440 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.546 2.440 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.554 2.440 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.563 2.440 ... (remaining 25509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 306 through 378) selection = chain 'B' selection = (chain 'C' and resid 306 through 378) selection = chain 'D' selection = (chain 'E' and resid 306 through 378) 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: 2.460 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: 11.350 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.050 Find NCS groups from input model: 0.250 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 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 0.053 3459 Z= 0.769 Angle : 2.075 16.473 4629 Z= 1.364 Chirality : 0.115 0.866 522 Planarity : 0.012 0.089 588 Dihedral : 11.489 57.185 1323 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.29 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.17 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.040 0.004 HIS E 330 PHE 0.045 0.014 PHE E 378 TYR 0.160 0.039 TYR A 310 ARG 0.006 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.407 Fit side-chains REVERT: C 321 LYS cc_start: 0.7785 (mttt) cc_final: 0.7209 (ttmm) REVERT: C 349 ARG cc_start: 0.7314 (mtm180) cc_final: 0.7041 (mtp-110) REVERT: C 358 ASP cc_start: 0.7265 (m-30) cc_final: 0.6335 (m-30) REVERT: E 311 LYS cc_start: 0.8214 (pttt) cc_final: 0.7736 (ptmm) REVERT: E 317 LYS cc_start: 0.7356 (pttt) cc_final: 0.6673 (ptmt) REVERT: B 375 LYS cc_start: 0.7998 (tttt) cc_final: 0.7628 (tttp) REVERT: D 322 CYS cc_start: 0.8257 (p) cc_final: 0.7470 (m) REVERT: D 347 LYS cc_start: 0.7106 (ptmt) cc_final: 0.6475 (tppt) REVERT: D 372 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8258 (mt-10) REVERT: F 375 LYS cc_start: 0.8564 (tttt) cc_final: 0.8105 (ttmt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2952 time to fit residues: 20.3060 Evaluate side-chains 44 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 362 HIS E 330 HIS E 362 HIS B 327 ASN B 362 HIS D 327 ASN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 ASN ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3459 Z= 0.249 Angle : 0.780 9.461 4629 Z= 0.405 Chirality : 0.055 0.181 522 Planarity : 0.004 0.042 588 Dihedral : 7.756 39.339 456 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.51 % Allowed : 10.51 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -1.91 (0.33), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 362 PHE 0.010 0.002 PHE E 378 TYR 0.019 0.004 TYR A 310 ARG 0.003 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.402 Fit side-chains REVERT: A 317 LYS cc_start: 0.7097 (mttt) cc_final: 0.6867 (mttm) REVERT: C 321 LYS cc_start: 0.7777 (mttt) cc_final: 0.7166 (ttmm) REVERT: C 349 ARG cc_start: 0.7514 (mtm180) cc_final: 0.7187 (mtp-110) REVERT: B 322 CYS cc_start: 0.7979 (p) cc_final: 0.7347 (m) REVERT: B 375 LYS cc_start: 0.7908 (tttt) cc_final: 0.7655 (ttmt) REVERT: D 317 LYS cc_start: 0.7374 (pttt) cc_final: 0.6665 (ptpp) REVERT: D 322 CYS cc_start: 0.8351 (p) cc_final: 0.7614 (m) REVERT: D 347 LYS cc_start: 0.7021 (ptmt) cc_final: 0.6579 (tptt) REVERT: D 375 LYS cc_start: 0.8068 (tttt) cc_final: 0.7540 (ttmt) REVERT: F 375 LYS cc_start: 0.8615 (tttt) cc_final: 0.8076 (ttmt) outliers start: 2 outliers final: 2 residues processed: 49 average time/residue: 0.3349 time to fit residues: 18.3478 Evaluate side-chains 39 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 319 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 0.1980 chunk 19 optimal weight: 9.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3459 Z= 0.361 Angle : 0.787 10.912 4629 Z= 0.406 Chirality : 0.057 0.173 522 Planarity : 0.004 0.041 588 Dihedral : 7.209 29.526 456 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.05 % Allowed : 11.54 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.33), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 329 PHE 0.008 0.002 PHE E 346 TYR 0.026 0.004 TYR C 310 ARG 0.002 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.405 Fit side-chains REVERT: A 317 LYS cc_start: 0.7121 (mttt) cc_final: 0.6903 (mttm) REVERT: A 321 LYS cc_start: 0.7092 (mttt) cc_final: 0.6573 (ttmm) REVERT: C 321 LYS cc_start: 0.7804 (mttt) cc_final: 0.7166 (ttmm) REVERT: C 349 ARG cc_start: 0.7499 (mtm180) cc_final: 0.7174 (mtp-110) REVERT: B 375 LYS cc_start: 0.7912 (tttt) cc_final: 0.7668 (ttmt) REVERT: D 317 LYS cc_start: 0.7324 (pttt) cc_final: 0.6724 (ptpp) REVERT: D 322 CYS cc_start: 0.8282 (p) cc_final: 0.7768 (m) REVERT: D 347 LYS cc_start: 0.7057 (ptmt) cc_final: 0.6646 (tptt) REVERT: D 375 LYS cc_start: 0.8125 (tttt) cc_final: 0.7636 (ttmt) REVERT: F 316 SER cc_start: 0.8066 (m) cc_final: 0.7560 (p) REVERT: F 375 LYS cc_start: 0.8628 (tttt) cc_final: 0.8075 (ttmt) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 0.3102 time to fit residues: 17.4316 Evaluate side-chains 42 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 319 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 0.0370 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3459 Z= 0.293 Angle : 0.716 8.966 4629 Z= 0.364 Chirality : 0.053 0.149 522 Planarity : 0.004 0.040 588 Dihedral : 6.783 32.734 456 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.59 % Allowed : 9.74 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.03 (0.33), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 329 PHE 0.006 0.001 PHE E 346 TYR 0.019 0.004 TYR C 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 36 time to evaluate : 0.373 Fit side-chains REVERT: A 317 LYS cc_start: 0.7150 (mttt) cc_final: 0.6902 (mttm) REVERT: C 321 LYS cc_start: 0.7812 (mttt) cc_final: 0.7249 (ttmm) REVERT: C 349 ARG cc_start: 0.7523 (mtm180) cc_final: 0.7125 (mtp-110) REVERT: E 311 LYS cc_start: 0.8086 (pttt) cc_final: 0.7796 (ptmm) REVERT: E 324 SER cc_start: 0.7530 (t) cc_final: 0.7274 (m) REVERT: E 360 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7496 (mp) REVERT: B 375 LYS cc_start: 0.7861 (tttt) cc_final: 0.7627 (ttmt) REVERT: D 317 LYS cc_start: 0.7320 (pttt) cc_final: 0.6743 (ptpp) REVERT: D 322 CYS cc_start: 0.8196 (p) cc_final: 0.7698 (m) REVERT: D 375 LYS cc_start: 0.8132 (tttt) cc_final: 0.7647 (ttmt) REVERT: F 314 ASP cc_start: 0.8055 (t0) cc_final: 0.7791 (t0) REVERT: F 316 SER cc_start: 0.7981 (m) cc_final: 0.7483 (p) REVERT: F 375 LYS cc_start: 0.8629 (tttt) cc_final: 0.8091 (ttmt) outliers start: 14 outliers final: 9 residues processed: 42 average time/residue: 0.3600 time to fit residues: 16.8131 Evaluate side-chains 45 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.0010 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3459 Z= 0.309 Angle : 0.712 8.951 4629 Z= 0.362 Chirality : 0.053 0.150 522 Planarity : 0.004 0.042 588 Dihedral : 6.601 29.359 456 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.59 % Allowed : 10.26 % Favored : 86.15 % 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: -2.15 (0.33), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 362 PHE 0.008 0.001 PHE E 346 TYR 0.022 0.004 TYR C 310 ARG 0.002 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.410 Fit side-chains REVERT: A 317 LYS cc_start: 0.7139 (mttt) cc_final: 0.6905 (mttp) REVERT: C 321 LYS cc_start: 0.7803 (mttt) cc_final: 0.7295 (ttmm) REVERT: C 349 ARG cc_start: 0.7523 (mtm180) cc_final: 0.7118 (mtp-110) REVERT: E 311 LYS cc_start: 0.8121 (pttt) cc_final: 0.7853 (ptmm) REVERT: E 324 SER cc_start: 0.7985 (t) cc_final: 0.7582 (m) REVERT: E 360 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7452 (mp) REVERT: B 375 LYS cc_start: 0.7928 (tttt) cc_final: 0.7700 (ttmt) REVERT: D 317 LYS cc_start: 0.7392 (pttt) cc_final: 0.6803 (ptpp) REVERT: D 322 CYS cc_start: 0.8219 (p) cc_final: 0.7751 (m) REVERT: D 347 LYS cc_start: 0.6986 (ptmt) cc_final: 0.6336 (tppt) REVERT: D 353 LYS cc_start: 0.7017 (mttt) cc_final: 0.6685 (mttp) REVERT: D 375 LYS cc_start: 0.8173 (tttt) cc_final: 0.7684 (ttmt) REVERT: F 314 ASP cc_start: 0.7994 (t0) cc_final: 0.7715 (t0) REVERT: F 316 SER cc_start: 0.7957 (m) cc_final: 0.7438 (p) REVERT: F 375 LYS cc_start: 0.8633 (tttt) cc_final: 0.8095 (ttmt) outliers start: 14 outliers final: 13 residues processed: 49 average time/residue: 0.3550 time to fit residues: 19.3998 Evaluate side-chains 52 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 38 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3459 Z= 0.382 Angle : 0.742 8.252 4629 Z= 0.381 Chirality : 0.054 0.157 522 Planarity : 0.004 0.041 588 Dihedral : 6.685 31.494 456 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.62 % Allowed : 10.00 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.31 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 362 PHE 0.010 0.002 PHE E 346 TYR 0.024 0.005 TYR E 310 ARG 0.002 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 43 time to evaluate : 0.408 Fit side-chains REVERT: A 317 LYS cc_start: 0.7167 (mttt) cc_final: 0.6911 (mttp) REVERT: A 321 LYS cc_start: 0.7096 (mttt) cc_final: 0.6714 (ttmm) REVERT: C 321 LYS cc_start: 0.7840 (mttt) cc_final: 0.7324 (ttmm) REVERT: C 349 ARG cc_start: 0.7543 (mtm180) cc_final: 0.7118 (mtp-110) REVERT: E 311 LYS cc_start: 0.8142 (pttt) cc_final: 0.7881 (ptmm) REVERT: E 324 SER cc_start: 0.8056 (t) cc_final: 0.7700 (m) REVERT: E 360 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7458 (mp) REVERT: B 317 LYS cc_start: 0.6911 (pttt) cc_final: 0.6439 (ptpp) REVERT: B 353 LYS cc_start: 0.7147 (mttt) cc_final: 0.6883 (mttp) REVERT: B 358 ASP cc_start: 0.7609 (t0) cc_final: 0.6838 (m-30) REVERT: B 375 LYS cc_start: 0.7943 (tttt) cc_final: 0.7723 (ttmt) REVERT: D 317 LYS cc_start: 0.7435 (pttt) cc_final: 0.6757 (ptpp) REVERT: D 322 CYS cc_start: 0.8223 (p) cc_final: 0.7811 (m) REVERT: D 347 LYS cc_start: 0.6979 (ptmt) cc_final: 0.6684 (tptt) REVERT: F 314 ASP cc_start: 0.8050 (t0) cc_final: 0.7685 (t0) REVERT: F 316 SER cc_start: 0.7957 (m) cc_final: 0.7433 (p) REVERT: F 358 ASP cc_start: 0.7920 (t0) cc_final: 0.7400 (m-30) REVERT: F 375 LYS cc_start: 0.8636 (tttt) cc_final: 0.8108 (ttmt) outliers start: 18 outliers final: 13 residues processed: 52 average time/residue: 0.3246 time to fit residues: 18.9172 Evaluate side-chains 56 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3459 Z= 0.224 Angle : 0.645 7.336 4629 Z= 0.329 Chirality : 0.051 0.139 522 Planarity : 0.004 0.043 588 Dihedral : 6.281 30.502 456 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.82 % Allowed : 11.54 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.37 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.007 0.001 PHE B 346 TYR 0.015 0.003 TYR E 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 0.420 Fit side-chains REVERT: A 317 LYS cc_start: 0.7153 (mttt) cc_final: 0.6936 (mttm) REVERT: C 349 ARG cc_start: 0.7511 (mtm180) cc_final: 0.7077 (mtp-110) REVERT: E 311 LYS cc_start: 0.8127 (pttt) cc_final: 0.7895 (ptmm) REVERT: E 317 LYS cc_start: 0.7364 (pttt) cc_final: 0.6787 (ptmt) REVERT: E 324 SER cc_start: 0.8121 (t) cc_final: 0.7728 (m) REVERT: E 360 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7415 (mp) REVERT: B 375 LYS cc_start: 0.7953 (tttt) cc_final: 0.7574 (ttmp) REVERT: D 317 LYS cc_start: 0.7345 (pttt) cc_final: 0.6745 (ptpp) REVERT: D 322 CYS cc_start: 0.8224 (p) cc_final: 0.7839 (m) REVERT: D 353 LYS cc_start: 0.6961 (mttt) cc_final: 0.6657 (mttp) REVERT: D 358 ASP cc_start: 0.7997 (t0) cc_final: 0.7033 (m-30) REVERT: D 375 LYS cc_start: 0.8194 (tttt) cc_final: 0.7705 (ttmt) REVERT: F 314 ASP cc_start: 0.8021 (t0) cc_final: 0.7700 (t0) REVERT: F 316 SER cc_start: 0.7955 (m) cc_final: 0.7444 (p) REVERT: F 358 ASP cc_start: 0.7870 (t0) cc_final: 0.7395 (m-30) REVERT: F 375 LYS cc_start: 0.8638 (tttt) cc_final: 0.8092 (ttmt) outliers start: 11 outliers final: 9 residues processed: 46 average time/residue: 0.3498 time to fit residues: 18.0270 Evaluate side-chains 50 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3459 Z= 0.220 Angle : 0.641 6.921 4629 Z= 0.325 Chirality : 0.051 0.137 522 Planarity : 0.004 0.046 588 Dihedral : 6.088 30.297 456 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.59 % Allowed : 10.51 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.35 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.006 0.001 PHE B 346 TYR 0.015 0.003 TYR E 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 41 time to evaluate : 0.434 Fit side-chains REVERT: C 349 ARG cc_start: 0.7491 (mtm180) cc_final: 0.7078 (mtp-110) REVERT: E 311 LYS cc_start: 0.8162 (pttt) cc_final: 0.7911 (ptmm) REVERT: E 317 LYS cc_start: 0.7392 (pttt) cc_final: 0.6825 (ptmt) REVERT: E 324 SER cc_start: 0.8158 (t) cc_final: 0.7804 (m) REVERT: E 360 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7408 (mp) REVERT: B 375 LYS cc_start: 0.7953 (tttt) cc_final: 0.7576 (ttmp) REVERT: D 317 LYS cc_start: 0.7318 (pttt) cc_final: 0.6721 (ptpp) REVERT: D 321 LYS cc_start: 0.7505 (mttt) cc_final: 0.6981 (mttm) REVERT: D 322 CYS cc_start: 0.8246 (p) cc_final: 0.7856 (m) REVERT: D 353 LYS cc_start: 0.6966 (mttt) cc_final: 0.6655 (mttp) REVERT: D 358 ASP cc_start: 0.7979 (t0) cc_final: 0.7011 (m-30) REVERT: D 375 LYS cc_start: 0.8208 (tttt) cc_final: 0.7712 (ttmt) REVERT: F 314 ASP cc_start: 0.8018 (t0) cc_final: 0.7709 (t0) REVERT: F 316 SER cc_start: 0.7969 (m) cc_final: 0.7453 (p) REVERT: F 358 ASP cc_start: 0.7843 (t0) cc_final: 0.7391 (m-30) REVERT: F 375 LYS cc_start: 0.8634 (tttt) cc_final: 0.8089 (ttmt) outliers start: 14 outliers final: 12 residues processed: 48 average time/residue: 0.3505 time to fit residues: 18.9179 Evaluate side-chains 52 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 0.0570 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3459 Z= 0.307 Angle : 0.688 7.318 4629 Z= 0.351 Chirality : 0.052 0.146 522 Planarity : 0.004 0.048 588 Dihedral : 6.228 30.479 456 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.08 % Allowed : 11.79 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.39 (0.33), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 362 PHE 0.008 0.002 PHE E 346 TYR 0.020 0.004 TYR E 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.414 Fit side-chains REVERT: C 321 LYS cc_start: 0.7811 (mttt) cc_final: 0.7313 (ttmm) REVERT: C 349 ARG cc_start: 0.7516 (mtm180) cc_final: 0.7087 (mtp-110) REVERT: E 311 LYS cc_start: 0.8191 (pttt) cc_final: 0.7857 (ptmm) REVERT: E 317 LYS cc_start: 0.7379 (pttt) cc_final: 0.6795 (ptmt) REVERT: E 324 SER cc_start: 0.8252 (t) cc_final: 0.7908 (m) REVERT: E 360 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7407 (mp) REVERT: B 358 ASP cc_start: 0.7589 (t0) cc_final: 0.6869 (m-30) REVERT: B 375 LYS cc_start: 0.7976 (tttt) cc_final: 0.7599 (ttmp) REVERT: D 317 LYS cc_start: 0.7375 (pttt) cc_final: 0.6763 (ptpp) REVERT: D 321 LYS cc_start: 0.7509 (mttt) cc_final: 0.6879 (mtpt) REVERT: D 322 CYS cc_start: 0.8251 (p) cc_final: 0.7901 (m) REVERT: D 353 LYS cc_start: 0.6961 (mttt) cc_final: 0.6681 (mttp) REVERT: D 358 ASP cc_start: 0.8011 (t0) cc_final: 0.7057 (m-30) REVERT: D 375 LYS cc_start: 0.8201 (tttt) cc_final: 0.7703 (ttmt) REVERT: F 314 ASP cc_start: 0.8041 (t0) cc_final: 0.7656 (t0) REVERT: F 316 SER cc_start: 0.7958 (m) cc_final: 0.7428 (p) REVERT: F 358 ASP cc_start: 0.7858 (t0) cc_final: 0.7388 (m-30) REVERT: F 375 LYS cc_start: 0.8632 (tttt) cc_final: 0.8093 (ttmt) outliers start: 12 outliers final: 11 residues processed: 48 average time/residue: 0.3507 time to fit residues: 18.8531 Evaluate side-chains 54 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN B 307 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3459 Z= 0.349 Angle : 0.725 7.646 4629 Z= 0.372 Chirality : 0.053 0.156 522 Planarity : 0.004 0.051 588 Dihedral : 6.474 31.456 456 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.85 % Allowed : 11.79 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 (0.33), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 362 PHE 0.010 0.002 PHE C 346 TYR 0.022 0.004 TYR E 310 ARG 0.001 0.000 ARG A 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 47 time to evaluate : 0.389 Fit side-chains REVERT: C 321 LYS cc_start: 0.7841 (mttt) cc_final: 0.7339 (ttmm) REVERT: C 349 ARG cc_start: 0.7496 (mtm180) cc_final: 0.7209 (mtp-110) REVERT: E 311 LYS cc_start: 0.8196 (pttt) cc_final: 0.7859 (ptmm) REVERT: E 317 LYS cc_start: 0.7376 (pttt) cc_final: 0.6783 (ptmt) REVERT: E 324 SER cc_start: 0.8260 (t) cc_final: 0.7916 (m) REVERT: E 360 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7464 (mp) REVERT: B 317 LYS cc_start: 0.6896 (pttt) cc_final: 0.6328 (ptpp) REVERT: B 358 ASP cc_start: 0.7597 (t0) cc_final: 0.6897 (m-30) REVERT: B 375 LYS cc_start: 0.7978 (tttt) cc_final: 0.7605 (ttmp) REVERT: D 317 LYS cc_start: 0.7396 (pttt) cc_final: 0.6708 (ptpp) REVERT: D 321 LYS cc_start: 0.7561 (mttt) cc_final: 0.6921 (mtpt) REVERT: D 322 CYS cc_start: 0.8188 (p) cc_final: 0.7924 (m) REVERT: D 353 LYS cc_start: 0.6930 (mttt) cc_final: 0.6645 (mttp) REVERT: D 358 ASP cc_start: 0.8034 (t0) cc_final: 0.7066 (m-30) REVERT: D 375 LYS cc_start: 0.8186 (tttt) cc_final: 0.7697 (ttmt) REVERT: F 314 ASP cc_start: 0.8040 (t0) cc_final: 0.7607 (t0) REVERT: F 316 SER cc_start: 0.7964 (m) cc_final: 0.7405 (p) REVERT: F 317 LYS cc_start: 0.7682 (pttt) cc_final: 0.7181 (ptpp) REVERT: F 340 LYS cc_start: 0.8307 (tttt) cc_final: 0.8039 (tttm) REVERT: F 358 ASP cc_start: 0.7850 (t0) cc_final: 0.7395 (m-30) REVERT: F 375 LYS cc_start: 0.8647 (tttt) cc_final: 0.8106 (ttmt) outliers start: 15 outliers final: 14 residues processed: 55 average time/residue: 0.3636 time to fit residues: 22.1369 Evaluate side-chains 61 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 46 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.249653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.211265 restraints weight = 3989.999| |-----------------------------------------------------------------------------| r_work (start): 0.4533 rms_B_bonded: 1.00 r_work: 0.4861 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.4814 rms_B_bonded: 0.89 restraints_weight: 0.2500 r_work: 0.4624 rms_B_bonded: 3.14 restraints_weight: 0.1250 r_work (final): 0.4624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.137 3459 Z= 0.349 Angle : 1.320 59.199 4629 Z= 0.764 Chirality : 0.054 0.203 522 Planarity : 0.004 0.051 588 Dihedral : 6.492 32.908 456 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.59 % Allowed : 12.05 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 (0.33), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 362 PHE 0.009 0.002 PHE E 346 TYR 0.021 0.004 TYR E 310 ARG 0.001 0.000 ARG A 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1331.91 seconds wall clock time: 24 minutes 37.54 seconds (1477.54 seconds total)