Starting phenix.real_space_refine on Fri Aug 2 15:58:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8l_18254/08_2024/8q8l_18254.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8l_18254/08_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_18254/08_2024/8q8l_18254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8l_18254/08_2024/8q8l_18254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8l_18254/08_2024/8q8l_18254.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8l_18254/08_2024/8q8l_18254.cif" } 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-5409/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: 3.62, per 1000 atoms: 1.06 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: 1.17 Conformation dependent library (CDL) restraints added in 626.6 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: 0.64 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: 0.82 Time building geometry restraints manager: 1.32 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 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.544 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.546 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.554 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.563 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 5.260 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.430 Find NCS groups from input model: 0.150 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.910 ------------------------------------------------------------------------------- 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 : 0.390 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: 0.2927 time to fit residues: 20.1175 Evaluate side-chains 44 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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: 3.9990 chunk 17 optimal weight: 0.0870 chunk 10 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- 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 330 HIS D 362 HIS 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: 0.7090 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3459 Z= 0.218 Angle : 0.806 9.280 4629 Z= 0.421 Chirality : 0.056 0.208 522 Planarity : 0.004 0.043 588 Dihedral : 8.023 41.904 456 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.26 % Allowed : 10.00 % Favored : 89.74 % 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: -1.89 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (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 378 TYR 0.017 0.004 TYR E 310 ARG 0.003 0.000 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 48 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.401 Fit side-chains REVERT: C 321 LYS cc_start: 0.7794 (mttt) cc_final: 0.7164 (ttmm) REVERT: C 349 ARG cc_start: 0.7555 (mtm180) cc_final: 0.7163 (mtp-110) REVERT: E 311 LYS cc_start: 0.8076 (pttt) cc_final: 0.7597 (ptmm) REVERT: E 317 LYS cc_start: 0.7171 (pttt) cc_final: 0.6757 (ptmt) REVERT: E 360 ILE cc_start: 0.8093 (tt) cc_final: 0.7681 (mp) REVERT: B 322 CYS cc_start: 0.7889 (p) cc_final: 0.7227 (m) REVERT: D 317 LYS cc_start: 0.7352 (pttt) cc_final: 0.6596 (ptpp) REVERT: D 322 CYS cc_start: 0.8332 (p) cc_final: 0.7632 (m) REVERT: D 347 LYS cc_start: 0.6985 (ptmt) cc_final: 0.6565 (tptt) REVERT: D 375 LYS cc_start: 0.8063 (tttt) cc_final: 0.7534 (ttmt) REVERT: F 375 LYS cc_start: 0.8607 (tttt) cc_final: 0.8054 (ttmt) outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.3444 time to fit residues: 18.0324 Evaluate side-chains 43 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 38 optimal weight: 10.0000 chunk 41 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN F 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3459 Z= 0.409 Angle : 0.834 11.461 4629 Z= 0.432 Chirality : 0.059 0.199 522 Planarity : 0.005 0.042 588 Dihedral : 7.460 30.457 456 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.79 % Allowed : 12.05 % Favored : 86.15 % 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: -1.89 (0.33), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 329 PHE 0.012 0.002 PHE E 346 TYR 0.029 0.005 TYR C 310 ARG 0.003 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 55 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.406 Fit side-chains REVERT: A 317 LYS cc_start: 0.7142 (mttt) cc_final: 0.6927 (mttp) REVERT: A 321 LYS cc_start: 0.7162 (mttt) cc_final: 0.6681 (ttmm) REVERT: C 321 LYS cc_start: 0.7815 (mttt) cc_final: 0.7182 (ttmm) REVERT: C 349 ARG cc_start: 0.7590 (mtm180) cc_final: 0.7115 (mtp-110) REVERT: B 331 LYS cc_start: 0.8325 (mttt) cc_final: 0.8068 (mttt) REVERT: D 317 LYS cc_start: 0.7362 (pttt) cc_final: 0.6764 (ptpp) REVERT: D 322 CYS cc_start: 0.8287 (p) cc_final: 0.7782 (m) REVERT: D 347 LYS cc_start: 0.7069 (ptmt) cc_final: 0.6652 (tptt) REVERT: D 375 LYS cc_start: 0.8124 (tttt) cc_final: 0.7628 (ttmt) REVERT: F 314 ASP cc_start: 0.8101 (t0) cc_final: 0.7862 (t0) REVERT: F 316 SER cc_start: 0.8131 (m) cc_final: 0.7642 (p) REVERT: F 375 LYS cc_start: 0.8636 (tttt) cc_final: 0.8080 (ttmt) outliers start: 7 outliers final: 5 residues processed: 53 average time/residue: 0.3171 time to fit residues: 18.8331 Evaluate side-chains 43 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR 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: 1.9990 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3440 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= 0.218 Angle : 0.679 8.753 4629 Z= 0.344 Chirality : 0.052 0.137 522 Planarity : 0.004 0.044 588 Dihedral : 6.679 30.806 456 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.76 % Favored : 97.01 % Rotamer: Outliers : 2.56 % Allowed : 11.03 % Favored : 86.41 % 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: -1.94 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (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 E 378 TYR 0.014 0.003 TYR E 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 49 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.391 Fit side-chains REVERT: A 317 LYS cc_start: 0.7145 (mttt) cc_final: 0.6911 (mttm) REVERT: C 349 ARG cc_start: 0.7540 (mtm180) cc_final: 0.7098 (mtp-110) REVERT: E 311 LYS cc_start: 0.8052 (pttt) cc_final: 0.7771 (ptmm) REVERT: E 324 SER cc_start: 0.7455 (t) cc_final: 0.7207 (m) REVERT: E 360 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7534 (mp) REVERT: D 317 LYS cc_start: 0.7247 (pttt) cc_final: 0.6718 (ptpp) REVERT: D 322 CYS cc_start: 0.8219 (p) cc_final: 0.7725 (m) REVERT: D 375 LYS cc_start: 0.8107 (tttt) cc_final: 0.7608 (ttmt) REVERT: F 314 ASP cc_start: 0.8118 (t0) cc_final: 0.7896 (t0) REVERT: F 316 SER cc_start: 0.8041 (m) cc_final: 0.7609 (p) REVERT: F 375 LYS cc_start: 0.8581 (tttt) cc_final: 0.8046 (ttmt) outliers start: 10 outliers final: 7 residues processed: 42 average time/residue: 0.3464 time to fit residues: 16.3725 Evaluate side-chains 44 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 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 319 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 3459 Z= 0.453 Angle : 0.813 9.647 4629 Z= 0.419 Chirality : 0.057 0.180 522 Planarity : 0.005 0.042 588 Dihedral : 7.129 30.547 456 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.82 % Allowed : 11.79 % 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: -2.12 (0.33), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 362 PHE 0.013 0.002 PHE E 346 TYR 0.030 0.006 TYR E 310 ARG 0.003 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 59 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7171 (mttt) cc_final: 0.6923 (mttp) REVERT: A 321 LYS cc_start: 0.7122 (mttt) cc_final: 0.6711 (ttmm) REVERT: C 321 LYS cc_start: 0.7773 (mttt) cc_final: 0.7202 (ttmm) REVERT: C 349 ARG cc_start: 0.7580 (mtm180) cc_final: 0.7099 (mtp-110) REVERT: E 311 LYS cc_start: 0.8145 (pttt) cc_final: 0.7828 (ptmm) REVERT: E 360 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7517 (mp) REVERT: B 321 LYS cc_start: 0.7007 (mttt) cc_final: 0.6566 (mttm) REVERT: B 353 LYS cc_start: 0.7233 (mttt) cc_final: 0.6835 (mttp) REVERT: D 317 LYS cc_start: 0.7393 (pttt) cc_final: 0.6778 (ptpp) REVERT: D 321 LYS cc_start: 0.7586 (mttt) cc_final: 0.6905 (mtpt) REVERT: D 322 CYS cc_start: 0.8191 (p) cc_final: 0.7808 (m) REVERT: D 347 LYS cc_start: 0.7071 (ptmt) cc_final: 0.6601 (tptt) REVERT: D 353 LYS cc_start: 0.7100 (mttt) cc_final: 0.6735 (mttp) REVERT: D 375 LYS cc_start: 0.8105 (tttt) cc_final: 0.7624 (ttmt) REVERT: F 314 ASP cc_start: 0.8095 (t0) cc_final: 0.7702 (t0) REVERT: F 316 SER cc_start: 0.7971 (m) cc_final: 0.7471 (p) REVERT: F 375 LYS cc_start: 0.8623 (tttt) cc_final: 0.8092 (ttmt) outliers start: 11 outliers final: 7 residues processed: 54 average time/residue: 0.3862 time to fit residues: 22.9179 Evaluate side-chains 40 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 325 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 3459 Z= 0.446 Angle : 0.800 8.657 4629 Z= 0.412 Chirality : 0.056 0.187 522 Planarity : 0.005 0.043 588 Dihedral : 7.119 33.600 456 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.85 % Allowed : 13.08 % Favored : 83.08 % 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: -2.40 (0.32), 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 0.006 0.001 HIS E 362 PHE 0.011 0.002 PHE E 346 TYR 0.028 0.005 TYR E 310 ARG 0.002 0.000 ARG A 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 52 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 37 time to evaluate : 0.420 Fit side-chains REVERT: A 317 LYS cc_start: 0.7265 (mttt) cc_final: 0.6996 (mttm) REVERT: A 321 LYS cc_start: 0.7196 (mttt) cc_final: 0.6831 (ttmm) REVERT: C 349 ARG cc_start: 0.7593 (mtm180) cc_final: 0.7086 (mtp-110) REVERT: E 311 LYS cc_start: 0.8149 (pttt) cc_final: 0.7862 (ptmm) REVERT: E 360 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7573 (mp) REVERT: D 317 LYS cc_start: 0.7415 (pttt) cc_final: 0.6760 (ptpp) REVERT: D 322 CYS cc_start: 0.8187 (p) cc_final: 0.7976 (m) REVERT: F 314 ASP cc_start: 0.8014 (t0) cc_final: 0.7607 (t0) REVERT: F 316 SER cc_start: 0.8003 (m) cc_final: 0.7478 (p) REVERT: F 317 LYS cc_start: 0.7789 (pttt) cc_final: 0.7183 (ptpp) REVERT: F 375 LYS cc_start: 0.8628 (tttt) cc_final: 0.8085 (ttmt) outliers start: 15 outliers final: 11 residues processed: 45 average time/residue: 0.3338 time to fit residues: 16.8954 Evaluate side-chains 48 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 36 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 325 LEU 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 316 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 360 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 0.0000 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN D 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3459 Z= 0.231 Angle : 0.669 7.340 4629 Z= 0.340 Chirality : 0.052 0.139 522 Planarity : 0.004 0.042 588 Dihedral : 6.530 30.578 456 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.82 % Allowed : 13.85 % Favored : 83.33 % 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 0.004 0.001 HIS E 362 PHE 0.005 0.001 PHE B 346 TYR 0.015 0.003 TYR A 310 ARG 0.001 0.000 ARG F 349 *********************** 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 45 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 34 time to evaluate : 0.405 Fit side-chains REVERT: A 317 LYS cc_start: 0.7207 (mttt) cc_final: 0.6997 (mttm) REVERT: C 349 ARG cc_start: 0.7549 (mtm180) cc_final: 0.7062 (mtp-110) REVERT: E 311 LYS cc_start: 0.8148 (pttt) cc_final: 0.7889 (ptmm) REVERT: E 317 LYS cc_start: 0.7380 (pttt) cc_final: 0.6750 (ptmt) REVERT: E 360 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7522 (mp) REVERT: D 375 LYS cc_start: 0.8190 (tttt) cc_final: 0.7697 (ttmt) REVERT: F 314 ASP cc_start: 0.7913 (t0) cc_final: 0.7584 (t0) REVERT: F 316 SER cc_start: 0.8033 (m) cc_final: 0.7568 (p) REVERT: F 375 LYS cc_start: 0.8635 (tttt) cc_final: 0.8090 (ttmt) outliers start: 11 outliers final: 9 residues processed: 40 average time/residue: 0.3436 time to fit residues: 15.5519 Evaluate side-chains 38 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 28 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR 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 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 316 SER 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: 9.9990 chunk 31 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 0.0000 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3459 Z= 0.193 Angle : 0.627 6.469 4629 Z= 0.318 Chirality : 0.051 0.129 522 Planarity : 0.004 0.040 588 Dihedral : 6.062 31.926 456 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.31 % Allowed : 13.85 % Favored : 83.85 % 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: -2.38 (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 0.005 0.001 PHE B 346 TYR 0.013 0.003 TYR E 310 ARG 0.001 0.000 ARG F 349 *********************** 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 43 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.448 Fit side-chains REVERT: A 317 LYS cc_start: 0.7167 (mttt) cc_final: 0.6953 (mttm) REVERT: C 349 ARG cc_start: 0.7494 (mtm180) cc_final: 0.7022 (mtp-110) REVERT: E 311 LYS cc_start: 0.8097 (pttt) cc_final: 0.7873 (ptmm) REVERT: E 317 LYS cc_start: 0.7379 (pttt) cc_final: 0.6769 (ptmt) REVERT: E 324 SER cc_start: 0.8077 (t) cc_final: 0.7685 (m) REVERT: E 360 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7491 (mp) REVERT: F 314 ASP cc_start: 0.7873 (t0) cc_final: 0.7610 (t0) REVERT: F 316 SER cc_start: 0.7900 (m) cc_final: 0.7470 (p) REVERT: F 375 LYS cc_start: 0.8637 (tttt) cc_final: 0.8093 (ttmt) outliers start: 9 outliers final: 8 residues processed: 38 average time/residue: 0.3009 time to fit residues: 13.2738 Evaluate side-chains 37 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 28 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 325 LEU 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 316 SER 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: 0.5980 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 0.3980 chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3459 Z= 0.132 Angle : 0.580 5.784 4629 Z= 0.292 Chirality : 0.050 0.124 522 Planarity : 0.004 0.047 588 Dihedral : 5.498 26.667 456 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.28 % Allowed : 15.38 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS E 330 PHE 0.005 0.001 PHE E 378 TYR 0.011 0.002 TYR B 310 ARG 0.002 0.000 ARG F 349 *********************** 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 41 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.388 Fit side-chains REVERT: C 349 ARG cc_start: 0.7464 (mtm180) cc_final: 0.7024 (mtp-110) REVERT: E 311 LYS cc_start: 0.8078 (pttt) cc_final: 0.7855 (ptmm) REVERT: E 317 LYS cc_start: 0.7374 (pttt) cc_final: 0.6789 (ptmt) REVERT: E 324 SER cc_start: 0.8047 (t) cc_final: 0.7766 (m) REVERT: F 316 SER cc_start: 0.7769 (m) cc_final: 0.7400 (p) REVERT: F 317 LYS cc_start: 0.7833 (pttt) cc_final: 0.7335 (ptpp) REVERT: F 375 LYS cc_start: 0.8595 (tttt) cc_final: 0.8043 (ttmt) outliers start: 5 outliers final: 5 residues processed: 38 average time/residue: 0.2991 time to fit residues: 13.1814 Evaluate side-chains 32 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 27 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain D residue 316 SER 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: 8.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3459 Z= 0.269 Angle : 0.656 6.601 4629 Z= 0.335 Chirality : 0.052 0.138 522 Planarity : 0.004 0.047 588 Dihedral : 5.899 30.023 456 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.79 % Allowed : 15.38 % Favored : 82.82 % 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: -2.33 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 362 PHE 0.008 0.002 PHE E 346 TYR 0.018 0.004 TYR C 310 ARG 0.001 0.000 ARG F 349 ********************** 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 36 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 29 time to evaluate : 0.391 Fit side-chains REVERT: C 349 ARG cc_start: 0.7508 (mtm180) cc_final: 0.7075 (mtp-110) REVERT: E 311 LYS cc_start: 0.8166 (pttt) cc_final: 0.7915 (ptmm) REVERT: E 317 LYS cc_start: 0.7356 (pttt) cc_final: 0.6737 (ptmt) REVERT: E 324 SER cc_start: 0.8051 (t) cc_final: 0.7753 (m) REVERT: F 316 SER cc_start: 0.7940 (m) cc_final: 0.7507 (p) REVERT: F 317 LYS cc_start: 0.7823 (pttt) cc_final: 0.7272 (ptpp) REVERT: F 375 LYS cc_start: 0.8658 (tttt) cc_final: 0.8116 (ttmt) outliers start: 7 outliers final: 6 residues processed: 32 average time/residue: 0.3223 time to fit residues: 11.8112 Evaluate side-chains 33 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain D residue 316 SER 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: 0.0770 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 overall best weight: 3.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.251226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.214150 restraints weight = 3943.949| |-----------------------------------------------------------------------------| r_work (start): 0.4561 rms_B_bonded: 0.97 r_work: 0.4889 rms_B_bonded: 0.47 restraints_weight: 0.5000 r_work: 0.4846 rms_B_bonded: 0.87 restraints_weight: 0.2500 r_work: 0.4657 rms_B_bonded: 3.08 restraints_weight: 0.1250 r_work (final): 0.4657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4380 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= 0.309 Angle : 0.687 7.193 4629 Z= 0.352 Chirality : 0.053 0.150 522 Planarity : 0.004 0.049 588 Dihedral : 6.188 29.898 456 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.56 % Allowed : 15.13 % Favored : 82.31 % 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: -2.40 (0.32), 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 C 346 TYR 0.020 0.004 TYR E 310 ARG 0.001 0.000 ARG C 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1348.11 seconds wall clock time: 25 minutes 1.73 seconds (1501.73 seconds total)