Starting phenix.real_space_refine on Fri Aug 22 13:45:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9c_18276/08_2025/8q9c_18276.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9c_18276/08_2025/8q9c_18276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8q9c_18276/08_2025/8q9c_18276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9c_18276/08_2025/8q9c_18276.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q9c_18276/08_2025/8q9c_18276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9c_18276/08_2025/8q9c_18276.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3444 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 1.04, per 1000 atoms: 0.30 Number of scatterers: 3444 At special positions: 0 Unit cell: (108.768, 120.304, 51.088, 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 642 8.00 N 636 7.00 C 2160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 134.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 42.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.591A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.830A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 325 removed outlier: 6.303A pdb=" N VAL C 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LYS D 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER C 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N GLY D 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N CYS C 322 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU D 325 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER C 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 337 through 342 removed outlier: 6.506A pdb=" N GLU B 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N SER D 341 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS B 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLU D 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER C 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.478A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 362 removed outlier: 6.911A pdb=" N GLN D 351 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER B 352 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS D 353 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE B 354 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY D 355 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER B 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N GLN C 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 10.431A pdb=" N ILE D 354 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N LYS C 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 10.301A pdb=" N SER D 356 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLY C 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ASP D 358 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU C 357 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE D 360 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN C 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N HIS D 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 369 through 371 removed outlier: 6.343A pdb=" N LYS C 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 374 through 375 removed outlier: 6.442A pdb=" N HIS C 374 " --> pdb=" O LYS D 375 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.547A pdb=" N GLN A 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N TYR F 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.815A pdb=" N VAL A 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 318 through 320 removed outlier: 6.323A pdb=" N VAL E 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.670A pdb=" N SER E 324 " --> pdb=" O LEU F 325 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 337 through 342 removed outlier: 6.436A pdb=" N GLU A 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N SER F 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS A 340 " --> pdb=" O SER F 341 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.480A pdb=" N ASP A 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 350 through 362 removed outlier: 6.797A pdb=" N GLN F 351 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER A 352 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS F 353 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE A 354 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY F 355 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER A 356 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N GLN E 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N ILE F 354 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N LYS E 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 10.228A pdb=" N SER F 356 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLY E 355 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ASP F 358 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU E 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE F 360 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN E 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N HIS F 362 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR E 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.404A pdb=" N LYS E 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 374 through 375 removed outlier: 6.427A pdb=" N HIS E 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) 46 hydrogen bonds defined for protein. 138 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: 0.45 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1045 1.34 - 1.46: 386 1.46 - 1.57: 2061 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3498 Sorted by residual: bond pdb=" CA LYS A 331 " pdb=" C LYS A 331 " ideal model delta sigma weight residual 1.532 1.549 -0.017 6.50e-03 2.37e+04 7.14e+00 bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.97e+00 bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.91e+00 bond pdb=" CZ ARG E 379 " pdb=" NH2 ARG E 379 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.56e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.17e+00 ... (remaining 3493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 2970 1.65 - 3.31: 1261 3.31 - 4.96: 354 4.96 - 6.62: 87 6.62 - 8.27: 8 Bond angle restraints: 4680 Sorted by residual: angle pdb=" C LYS A 331 " pdb=" CA LYS A 331 " pdb=" CB LYS A 331 " ideal model delta sigma weight residual 110.71 115.43 -4.72 9.40e-01 1.13e+00 2.52e+01 angle pdb=" C ASP B 348 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " ideal model delta sigma weight residual 121.97 130.24 -8.27 1.73e+00 3.34e-01 2.29e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 117.30 -4.70 1.00e+00 1.00e+00 2.21e+01 angle pdb=" CD ARG B 349 " pdb=" NE ARG B 349 " pdb=" CZ ARG B 349 " ideal model delta sigma weight residual 124.40 130.88 -6.48 1.40e+00 5.10e-01 2.14e+01 angle pdb=" CA ASP D 358 " pdb=" CB ASP D 358 " pdb=" CG ASP D 358 " ideal model delta sigma weight residual 112.60 117.04 -4.44 1.00e+00 1.00e+00 1.97e+01 ... (remaining 4675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.89: 1775 7.89 - 15.79: 247 15.79 - 23.68: 65 23.68 - 31.58: 30 31.58 - 39.47: 19 Dihedral angle restraints: 2136 sinusoidal: 894 harmonic: 1242 Sorted by residual: dihedral pdb=" C LYS B 347 " pdb=" N LYS B 347 " pdb=" CA LYS B 347 " pdb=" CB LYS B 347 " ideal model delta harmonic sigma weight residual -122.60 -133.81 11.21 0 2.50e+00 1.60e-01 2.01e+01 dihedral pdb=" CA ASN A 359 " pdb=" C ASN A 359 " pdb=" N ILE A 360 " pdb=" CA ILE A 360 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLY A 333 " pdb=" C GLY A 333 " pdb=" N GLY A 334 " pdb=" CA GLY A 334 " ideal model delta harmonic sigma weight residual 180.00 161.03 18.97 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 2133 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.077: 317 0.077 - 0.154: 171 0.154 - 0.231: 34 0.231 - 0.307: 5 0.307 - 0.384: 1 Chirality restraints: 528 Sorted by residual: 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 2.13 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA LYS A 347 " pdb=" N LYS A 347 " pdb=" C LYS A 347 " pdb=" CB LYS A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ASP E 348 " pdb=" N ASP E 348 " pdb=" C ASP E 348 " pdb=" CB ASP E 348 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 525 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " 0.141 2.00e-02 2.50e+03 7.56e-02 1.14e+02 pdb=" CG TYR B 310 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " -0.072 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " 0.136 2.00e-02 2.50e+03 7.27e-02 1.06e+02 pdb=" CG TYR D 310 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " -0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " -0.066 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.104 2.00e-02 2.50e+03 5.49e-02 6.02e+01 pdb=" CG TYR F 310 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.079 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 1667 3.00 - 3.47: 2854 3.47 - 3.95: 5200 3.95 - 4.42: 5227 4.42 - 4.90: 10821 Nonbonded interactions: 25769 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.524 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.525 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.549 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.556 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.583 3.040 ... (remaining 25764 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 3.980 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: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.120 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 0.034 3498 Z= 0.678 Angle : 1.964 8.274 4680 Z= 1.272 Chirality : 0.091 0.384 528 Planarity : 0.013 0.112 594 Dihedral : 9.222 39.470 1344 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.98 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 349 TYR 0.141 0.041 TYR B 310 PHE 0.052 0.014 PHE A 346 HIS 0.013 0.004 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.01090 ( 3498) covalent geometry : angle 1.96386 ( 4680) hydrogen bonds : bond 0.06978 ( 46) hydrogen bonds : angle 6.03134 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.162 Fit side-chains REVERT: B 311 LYS cc_start: 0.7501 (mttt) cc_final: 0.7125 (mmtm) REVERT: C 327 ASN cc_start: 0.7032 (m-40) cc_final: 0.6418 (m110) REVERT: D 369 LYS cc_start: 0.7708 (tttt) cc_final: 0.7444 (tttp) REVERT: D 375 LYS cc_start: 0.7107 (tttt) cc_final: 0.6848 (tttm) REVERT: A 347 LYS cc_start: 0.8756 (mttt) cc_final: 0.8466 (mttp) REVERT: E 351 GLN cc_start: 0.8023 (tt0) cc_final: 0.7243 (mt0) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1652 time to fit residues: 12.9534 Evaluate side-chains 38 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN C 327 ASN D 327 ASN A 327 ASN A 368 ASN E 327 ASN F 327 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.104786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.094821 restraints weight = 5354.751| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.26 r_work: 0.3551 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3498 Z= 0.143 Angle : 0.698 7.083 4680 Z= 0.339 Chirality : 0.052 0.129 528 Planarity : 0.004 0.033 594 Dihedral : 5.224 16.023 462 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.01 % Allowed : 5.81 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 379 TYR 0.016 0.004 TYR D 310 PHE 0.012 0.002 PHE A 378 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 3498) covalent geometry : angle 0.69768 ( 4680) hydrogen bonds : bond 0.02016 ( 46) hydrogen bonds : angle 4.24180 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.155 Fit side-chains REVERT: B 311 LYS cc_start: 0.8036 (mttt) cc_final: 0.7619 (mmtt) REVERT: B 342 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7367 (mp0) REVERT: C 327 ASN cc_start: 0.7682 (m110) cc_final: 0.7271 (m110) REVERT: D 327 ASN cc_start: 0.8080 (m110) cc_final: 0.7863 (m-40) REVERT: E 351 GLN cc_start: 0.8299 (tt0) cc_final: 0.7783 (mt0) outliers start: 4 outliers final: 2 residues processed: 46 average time/residue: 0.1435 time to fit residues: 7.4635 Evaluate side-chains 37 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain A residue 327 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.099695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.090370 restraints weight = 5447.790| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.09 r_work: 0.3504 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3498 Z= 0.243 Angle : 0.676 7.094 4680 Z= 0.333 Chirality : 0.051 0.166 528 Planarity : 0.004 0.029 594 Dihedral : 5.367 15.001 462 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.77 % Allowed : 8.08 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 379 TYR 0.019 0.005 TYR D 310 PHE 0.008 0.002 PHE E 346 HIS 0.005 0.002 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 3498) covalent geometry : angle 0.67643 ( 4680) hydrogen bonds : bond 0.01878 ( 46) hydrogen bonds : angle 3.96885 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.147 Fit side-chains REVERT: B 311 LYS cc_start: 0.8227 (mttt) cc_final: 0.7699 (mmtt) REVERT: B 342 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7467 (mp0) REVERT: E 351 GLN cc_start: 0.8326 (tt0) cc_final: 0.7860 (mt0) outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 0.1405 time to fit residues: 6.5539 Evaluate side-chains 34 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain E residue 320 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.079491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.069733 restraints weight = 6808.073| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.63 r_work: 0.3379 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 3498 Z= 0.375 Angle : 0.731 5.502 4680 Z= 0.371 Chirality : 0.053 0.140 528 Planarity : 0.005 0.057 594 Dihedral : 5.841 15.712 462 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.53 % Allowed : 9.34 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 379 TYR 0.024 0.006 TYR E 310 PHE 0.012 0.003 PHE F 346 HIS 0.008 0.003 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00828 ( 3498) covalent geometry : angle 0.73119 ( 4680) hydrogen bonds : bond 0.02080 ( 46) hydrogen bonds : angle 4.03532 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.156 Fit side-chains REVERT: B 311 LYS cc_start: 0.8436 (mttt) cc_final: 0.7991 (mmtm) REVERT: B 342 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7520 (mp0) REVERT: B 348 ASP cc_start: 0.7565 (t70) cc_final: 0.7364 (t70) REVERT: C 321 LYS cc_start: 0.8537 (mttt) cc_final: 0.8077 (mttp) REVERT: C 375 LYS cc_start: 0.8560 (tttt) cc_final: 0.8199 (tttm) REVERT: E 351 GLN cc_start: 0.8386 (tt0) cc_final: 0.7900 (mt0) REVERT: F 311 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8216 (ptpt) outliers start: 10 outliers final: 7 residues processed: 50 average time/residue: 0.1484 time to fit residues: 8.3358 Evaluate side-chains 44 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.081792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.071609 restraints weight = 6624.858| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.77 r_work: 0.3414 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3498 Z= 0.206 Angle : 0.626 6.808 4680 Z= 0.306 Chirality : 0.050 0.136 528 Planarity : 0.003 0.030 594 Dihedral : 5.353 15.344 462 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.02 % Allowed : 11.36 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 379 TYR 0.013 0.003 TYR D 310 PHE 0.006 0.001 PHE E 346 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 3498) covalent geometry : angle 0.62627 ( 4680) hydrogen bonds : bond 0.01538 ( 46) hydrogen bonds : angle 3.89857 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.146 Fit side-chains REVERT: B 311 LYS cc_start: 0.8374 (mttt) cc_final: 0.7906 (mmtm) REVERT: B 342 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7464 (mp0) REVERT: A 311 LYS cc_start: 0.4679 (mmtm) cc_final: 0.3974 (tppt) REVERT: E 351 GLN cc_start: 0.8255 (tt0) cc_final: 0.7657 (mt0) outliers start: 8 outliers final: 7 residues processed: 38 average time/residue: 0.1485 time to fit residues: 6.4433 Evaluate side-chains 38 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.079524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.069734 restraints weight = 6734.305| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.72 r_work: 0.3378 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 3498 Z= 0.327 Angle : 0.693 5.912 4680 Z= 0.349 Chirality : 0.052 0.134 528 Planarity : 0.005 0.054 594 Dihedral : 5.684 15.631 462 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.53 % Allowed : 11.11 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.022 0.005 TYR F 310 PHE 0.010 0.002 PHE E 378 HIS 0.005 0.002 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00722 ( 3498) covalent geometry : angle 0.69262 ( 4680) hydrogen bonds : bond 0.01776 ( 46) hydrogen bonds : angle 4.04504 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.154 Fit side-chains REVERT: B 311 LYS cc_start: 0.8543 (mttt) cc_final: 0.8006 (mmtm) REVERT: B 342 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7522 (mp0) REVERT: B 348 ASP cc_start: 0.7581 (t70) cc_final: 0.7267 (t70) REVERT: A 311 LYS cc_start: 0.4868 (mmtm) cc_final: 0.4029 (tppt) REVERT: E 351 GLN cc_start: 0.8377 (tt0) cc_final: 0.7856 (mt0) outliers start: 10 outliers final: 9 residues processed: 39 average time/residue: 0.1299 time to fit residues: 5.8382 Evaluate side-chains 39 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.081216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.071268 restraints weight = 6735.859| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.76 r_work: 0.3409 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3498 Z= 0.246 Angle : 0.643 6.479 4680 Z= 0.318 Chirality : 0.050 0.132 528 Planarity : 0.004 0.041 594 Dihedral : 5.428 15.233 462 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.78 % Allowed : 11.11 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 379 TYR 0.017 0.004 TYR D 310 PHE 0.007 0.002 PHE E 346 HIS 0.004 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 3498) covalent geometry : angle 0.64262 ( 4680) hydrogen bonds : bond 0.01583 ( 46) hydrogen bonds : angle 4.03207 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: B 311 LYS cc_start: 0.8567 (mttt) cc_final: 0.7993 (mmtm) REVERT: B 342 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7521 (mp0) REVERT: B 348 ASP cc_start: 0.7561 (t70) cc_final: 0.7224 (t70) REVERT: E 351 GLN cc_start: 0.8378 (tt0) cc_final: 0.7821 (mt0) outliers start: 11 outliers final: 9 residues processed: 38 average time/residue: 0.1295 time to fit residues: 5.6800 Evaluate side-chains 39 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.080321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 18)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.070454 restraints weight = 6783.851| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.75 r_work: 0.3393 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 3498 Z= 0.275 Angle : 0.657 5.957 4680 Z= 0.328 Chirality : 0.051 0.135 528 Planarity : 0.004 0.049 594 Dihedral : 5.506 15.239 462 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.78 % Allowed : 11.87 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.019 0.005 TYR E 310 PHE 0.008 0.002 PHE E 346 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00609 ( 3498) covalent geometry : angle 0.65746 ( 4680) hydrogen bonds : bond 0.01591 ( 46) hydrogen bonds : angle 4.10941 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.145 Fit side-chains REVERT: B 311 LYS cc_start: 0.8568 (mttt) cc_final: 0.7987 (mmtm) REVERT: B 342 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7517 (mp0) REVERT: A 311 LYS cc_start: 0.4745 (mmtm) cc_final: 0.3619 (tppt) REVERT: A 379 ARG cc_start: 0.3770 (OUTLIER) cc_final: 0.1340 (ttp80) REVERT: E 351 GLN cc_start: 0.8434 (tt0) cc_final: 0.7816 (mt0) outliers start: 11 outliers final: 8 residues processed: 41 average time/residue: 0.1260 time to fit residues: 5.9561 Evaluate side-chains 40 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.079570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.069713 restraints weight = 6812.970| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.74 r_work: 0.3380 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 3498 Z= 0.313 Angle : 0.699 8.091 4680 Z= 0.350 Chirality : 0.052 0.134 528 Planarity : 0.005 0.056 594 Dihedral : 5.665 15.510 462 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.27 % Allowed : 12.37 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 379 TYR 0.022 0.005 TYR E 310 PHE 0.008 0.002 PHE E 346 HIS 0.004 0.002 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00694 ( 3498) covalent geometry : angle 0.69901 ( 4680) hydrogen bonds : bond 0.01734 ( 46) hydrogen bonds : angle 4.20984 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.152 Fit side-chains REVERT: B 311 LYS cc_start: 0.8577 (mttt) cc_final: 0.8007 (mmtm) REVERT: B 342 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7514 (mp0) REVERT: A 311 LYS cc_start: 0.5001 (mmtm) cc_final: 0.3837 (tppt) REVERT: A 379 ARG cc_start: 0.3773 (OUTLIER) cc_final: 0.1359 (ttp80) outliers start: 9 outliers final: 7 residues processed: 38 average time/residue: 0.1316 time to fit residues: 5.7631 Evaluate side-chains 40 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.080885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.070947 restraints weight = 6749.596| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.76 r_work: 0.3406 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3498 Z= 0.234 Angle : 0.652 7.677 4680 Z= 0.320 Chirality : 0.050 0.129 528 Planarity : 0.004 0.042 594 Dihedral : 5.431 15.248 462 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.53 % Allowed : 12.37 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.016 0.004 TYR E 310 PHE 0.007 0.002 PHE E 346 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 3498) covalent geometry : angle 0.65181 ( 4680) hydrogen bonds : bond 0.01536 ( 46) hydrogen bonds : angle 4.16503 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.159 Fit side-chains REVERT: B 311 LYS cc_start: 0.8561 (mttt) cc_final: 0.7990 (mmtm) REVERT: B 342 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7468 (mp0) REVERT: A 311 LYS cc_start: 0.4837 (mmtm) cc_final: 0.3700 (tppt) REVERT: A 379 ARG cc_start: 0.3797 (OUTLIER) cc_final: 0.1432 (ttp80) outliers start: 10 outliers final: 9 residues processed: 39 average time/residue: 0.1290 time to fit residues: 5.8152 Evaluate side-chains 40 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 0.0040 chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 overall best weight: 4.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.080180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.070288 restraints weight = 6815.416| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.76 r_work: 0.3393 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 3498 Z= 0.264 Angle : 0.679 8.649 4680 Z= 0.334 Chirality : 0.051 0.128 528 Planarity : 0.004 0.049 594 Dihedral : 5.480 15.040 462 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.53 % Allowed : 12.63 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 379 TYR 0.019 0.005 TYR E 310 PHE 0.007 0.002 PHE E 346 HIS 0.004 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 3498) covalent geometry : angle 0.67914 ( 4680) hydrogen bonds : bond 0.01582 ( 46) hydrogen bonds : angle 4.22906 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1227.95 seconds wall clock time: 21 minutes 51.58 seconds (1311.58 seconds total)