Starting phenix.real_space_refine on Wed Jun 3 10:40:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r89_53808/06_2026/9r89_53808.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r89_53808/06_2026/9r89_53808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r89_53808/06_2026/9r89_53808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r89_53808/06_2026/9r89_53808.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r89_53808/06_2026/9r89_53808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r89_53808/06_2026/9r89_53808.map" } resolution = 3.2 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= 0.002 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 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 36 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3444 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 0.70, per 1000 atoms: 0.20 Number of scatterers: 3444 At special positions: 0 Unit cell: (134.312, 107.12, 35.432, 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: 0.20 Conformation dependent library (CDL) restraints added in 143.0 milliseconds 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 10 sheets defined 0.0% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 321 through 322 removed outlier: 6.382A pdb=" N LYS A 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.420A pdb=" N ILE A 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 337 through 346 removed outlier: 9.028A pdb=" N VAL A 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 10.248A pdb=" N LYS D 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N VAL A 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N GLU D 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N SER A 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N LEU D 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS A 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N PHE D 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP A 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLU A 338 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL F 339 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS A 340 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N SER F 341 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU A 342 " --> pdb=" O SER F 341 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS F 343 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 350 through 360 removed outlier: 6.532A pdb=" N GLN A 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ILE D 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS A 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N SER D 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLY A 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASP D 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N LEU A 357 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE D 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ASN A 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN F 359 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE A 360 " --> pdb=" O ASN F 359 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 370 through 375 removed outlier: 6.222A pdb=" N ILE A 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N HIS D 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR A 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 321 through 322 removed outlier: 6.382A pdb=" N LYS B 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LYS C 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 328 through 330 Processing sheet with id=AA8, first strand: chain 'B' and resid 337 through 346 removed outlier: 9.028A pdb=" N VAL B 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 10.249A pdb=" N LYS C 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N VAL B 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N GLU C 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N SER B 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 9.206A pdb=" N LEU C 344 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS B 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N PHE C 346 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP B 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 10.249A pdb=" N LYS E 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N VAL C 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 10.305A pdb=" N GLU E 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N SER C 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 9.206A pdb=" N LEU E 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS C 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N PHE E 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 350 through 360 removed outlier: 6.532A pdb=" N GLN B 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ILE C 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS B 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N SER C 356 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLY B 355 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP C 358 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N LEU B 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE C 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ASN B 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN C 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ILE E 354 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS C 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N SER E 356 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLY C 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP E 358 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N LEU C 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE E 360 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 370 through 375 removed outlier: 6.222A pdb=" N ILE B 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N HIS C 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR B 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE C 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N HIS E 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR C 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 23 hydrogen bonds defined for protein. 69 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: 0.39 Time building geometry restraints manager: 0.31 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: 788 1.34 - 1.45: 877 1.45 - 1.57: 1827 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3498 Sorted by residual: bond pdb=" CG HIS D 330 " pdb=" CD2 HIS D 330 " ideal model delta sigma weight residual 1.354 1.311 0.043 1.10e-02 8.26e+03 1.51e+01 bond pdb=" CG HIS C 330 " pdb=" CD2 HIS C 330 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.48e+01 bond pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.48e+01 bond pdb=" CG HIS F 330 " pdb=" CD2 HIS F 330 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.48e+01 bond pdb=" CG HIS B 330 " pdb=" CD2 HIS B 330 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.44e+01 ... (remaining 3493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 3762 2.04 - 4.09: 695 4.09 - 6.13: 181 6.13 - 8.17: 36 8.17 - 10.21: 6 Bond angle restraints: 4680 Sorted by residual: angle pdb=" C ASN B 327 " pdb=" CA ASN B 327 " pdb=" CB ASN B 327 " ideal model delta sigma weight residual 111.89 119.21 -7.32 1.42e+00 4.96e-01 2.66e+01 angle pdb=" C ASN F 327 " pdb=" CA ASN F 327 " pdb=" CB ASN F 327 " ideal model delta sigma weight residual 111.89 119.20 -7.31 1.42e+00 4.96e-01 2.65e+01 angle pdb=" C ASN A 327 " pdb=" CA ASN A 327 " pdb=" CB ASN A 327 " ideal model delta sigma weight residual 111.89 119.20 -7.31 1.42e+00 4.96e-01 2.65e+01 angle pdb=" C ASN D 327 " pdb=" CA ASN D 327 " pdb=" CB ASN D 327 " ideal model delta sigma weight residual 111.89 119.20 -7.31 1.42e+00 4.96e-01 2.65e+01 angle pdb=" C ASN E 327 " pdb=" CA ASN E 327 " pdb=" CB ASN E 327 " ideal model delta sigma weight residual 111.89 119.20 -7.31 1.42e+00 4.96e-01 2.65e+01 ... (remaining 4675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 2007 16.11 - 32.21: 105 32.21 - 48.32: 18 48.32 - 64.42: 0 64.42 - 80.53: 6 Dihedral angle restraints: 2136 sinusoidal: 894 harmonic: 1242 Sorted by residual: dihedral pdb=" CA THR F 319 " pdb=" C THR F 319 " pdb=" N SER F 320 " pdb=" CA SER F 320 " ideal model delta harmonic sigma weight residual 180.00 156.59 23.41 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA THR A 319 " pdb=" C THR A 319 " pdb=" N SER A 320 " pdb=" CA SER A 320 " ideal model delta harmonic sigma weight residual 180.00 156.59 23.41 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA THR D 319 " pdb=" C THR D 319 " pdb=" N SER D 320 " pdb=" CA SER D 320 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 2133 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.073: 315 0.073 - 0.144: 165 0.144 - 0.216: 36 0.216 - 0.288: 6 0.288 - 0.360: 6 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA PRO F 312 " pdb=" N PRO F 312 " pdb=" C PRO F 312 " pdb=" CB PRO F 312 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CA PRO D 312 " pdb=" N PRO D 312 " pdb=" C PRO D 312 " pdb=" CB PRO D 312 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CA PRO A 312 " pdb=" N PRO A 312 " pdb=" C PRO A 312 " pdb=" CB PRO A 312 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 525 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 378 " -0.028 2.00e-02 2.50e+03 1.81e-02 5.76e+00 pdb=" CG PHE F 378 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE F 378 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE F 378 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE F 378 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 378 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE F 378 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 378 " 0.028 2.00e-02 2.50e+03 1.81e-02 5.76e+00 pdb=" CG PHE C 378 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE C 378 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 378 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 378 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 378 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 378 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 378 " 0.028 2.00e-02 2.50e+03 1.81e-02 5.73e+00 pdb=" CG PHE B 378 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 378 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 378 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 378 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 378 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 378 " 0.019 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 731 2.82 - 3.34: 3118 3.34 - 3.86: 5540 3.86 - 4.38: 5936 4.38 - 4.90: 11574 Nonbonded interactions: 26899 Sorted by model distance: nonbonded pdb=" OG1 THR A 361 " pdb=" ND1 HIS F 330 " model vdw 2.294 3.120 nonbonded pdb=" ND1 HIS A 330 " pdb=" OG1 THR D 361 " model vdw 2.294 3.120 nonbonded pdb=" ND1 HIS B 330 " pdb=" OG1 THR C 361 " model vdw 2.294 3.120 nonbonded pdb=" ND1 HIS C 330 " pdb=" OG1 THR E 361 " model vdw 2.294 3.120 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.367 3.040 ... (remaining 26894 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.980 Find NCS groups from input model: 0.010 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 0.057 3498 Z= 0.646 Angle : 1.880 10.214 4680 Z= 1.195 Chirality : 0.093 0.360 528 Planarity : 0.012 0.069 594 Dihedral : 11.369 80.528 1344 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.03 % Allowed : 6.06 % Favored : 90.91 % Cbeta Deviations : 1.52 % 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 are not related in a simple way. whole: -4.47 (0.24), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.19), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.003 ARG E 379 TYR 0.015 0.009 TYR E 310 PHE 0.033 0.010 PHE F 378 HIS 0.006 0.003 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.01060 / 0.65 ( 3498) covalent geometry : angle 1.88003 / 1.20 ( 4680) hydrogen bonds : bond 0.16292 / 9.10 ( 23) hydrogen bonds : angle 7.31914 / 4.81 ( 69) *********************** 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 139 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.112 Fit side-chains REVERT: A 345 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8123 (t0) REVERT: A 369 LYS cc_start: 0.8109 (mttt) cc_final: 0.7772 (tttt) REVERT: A 375 LYS cc_start: 0.8260 (tttt) cc_final: 0.7321 (mmtm) REVERT: B 349 ARG cc_start: 0.8722 (mtt180) cc_final: 0.7600 (mmp-170) REVERT: B 369 LYS cc_start: 0.8267 (mttt) cc_final: 0.7872 (tttt) REVERT: C 345 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8158 (t0) REVERT: C 369 LYS cc_start: 0.8184 (mttt) cc_final: 0.7860 (tttt) REVERT: D 369 LYS cc_start: 0.8214 (mttt) cc_final: 0.7942 (tttt) REVERT: E 348 ASP cc_start: 0.8218 (t0) cc_final: 0.7652 (p0) REVERT: E 369 LYS cc_start: 0.8243 (mttt) cc_final: 0.7956 (tttt) REVERT: F 369 LYS cc_start: 0.8204 (mttt) cc_final: 0.7842 (tttt) REVERT: F 375 LYS cc_start: 0.8197 (tttt) cc_final: 0.7236 (mmtm) outliers start: 12 outliers final: 0 residues processed: 127 average time/residue: 0.0803 time to fit residues: 12.0018 Evaluate side-chains 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain C residue 345 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.194271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.165974 restraints weight = 4342.116| |-----------------------------------------------------------------------------| r_work (start): 0.4520 rms_B_bonded: 2.67 r_work: 0.4410 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3498 Z= 0.136 Angle : 0.593 4.775 4680 Z= 0.309 Chirality : 0.048 0.126 528 Planarity : 0.007 0.060 594 Dihedral : 5.006 19.268 466 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.27 % Allowed : 15.40 % Favored : 82.32 % 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 are not related in a simple way. whole: -3.82 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.023 0.005 TYR A 310 PHE 0.008 0.001 PHE A 346 HIS 0.006 0.002 HIS F 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 3498) covalent geometry : angle 0.59337 / 0.31 ( 4680) hydrogen bonds : bond 0.02159 / 1.27 ( 23) hydrogen bonds : angle 5.25837 / 3.59 ( 69) *********************** 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 107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 369 LYS cc_start: 0.7693 (mttt) cc_final: 0.7239 (tttt) REVERT: A 375 LYS cc_start: 0.8054 (tttt) cc_final: 0.7075 (mmtm) REVERT: B 345 ASP cc_start: 0.8333 (t0) cc_final: 0.8117 (t0) REVERT: B 347 LYS cc_start: 0.8264 (mttt) cc_final: 0.7938 (mttm) REVERT: B 349 ARG cc_start: 0.8475 (mtt180) cc_final: 0.7311 (mmp-170) REVERT: B 369 LYS cc_start: 0.7504 (mttt) cc_final: 0.7225 (tttt) REVERT: B 375 LYS cc_start: 0.8042 (tttt) cc_final: 0.7045 (mmtm) REVERT: C 369 LYS cc_start: 0.7613 (mttt) cc_final: 0.7282 (tttt) REVERT: D 340 LYS cc_start: 0.8335 (mtpm) cc_final: 0.7480 (mttt) REVERT: D 375 LYS cc_start: 0.7820 (tttt) cc_final: 0.7097 (mmtm) REVERT: E 347 LYS cc_start: 0.8229 (mttp) cc_final: 0.7955 (mmtm) REVERT: E 369 LYS cc_start: 0.7520 (mttt) cc_final: 0.7282 (tttt) REVERT: E 375 LYS cc_start: 0.7809 (tttt) cc_final: 0.7027 (mmtm) REVERT: F 347 LYS cc_start: 0.8310 (mttt) cc_final: 0.8018 (mmtm) REVERT: F 369 LYS cc_start: 0.7551 (mttt) cc_final: 0.7229 (tttt) outliers start: 9 outliers final: 6 residues processed: 107 average time/residue: 0.0870 time to fit residues: 10.9315 Evaluate side-chains 90 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 34 optimal weight: 0.4980 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN D 368 ASN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN F 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.184262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.155631 restraints weight = 4392.342| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 2.56 r_work: 0.4276 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.4176 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3498 Z= 0.198 Angle : 0.642 5.256 4680 Z= 0.338 Chirality : 0.051 0.134 528 Planarity : 0.007 0.057 594 Dihedral : 5.065 18.419 462 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.78 % Allowed : 17.42 % Favored : 79.80 % 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 are not related in a simple way. whole: -3.75 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.029 0.007 TYR A 310 PHE 0.015 0.003 PHE A 346 HIS 0.008 0.003 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 ( 3498) covalent geometry : angle 0.64225 / 0.34 ( 4680) hydrogen bonds : bond 0.02486 / 1.39 ( 23) hydrogen bonds : angle 4.80798 / 3.29 ( 69) *********************** 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 100 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 348 ASP cc_start: 0.8016 (t0) cc_final: 0.7816 (t0) REVERT: A 375 LYS cc_start: 0.8241 (tttt) cc_final: 0.8024 (tttp) REVERT: A 376 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5978 (mp) REVERT: B 310 TYR cc_start: 0.6513 (t80) cc_final: 0.6283 (t80) REVERT: B 347 LYS cc_start: 0.8459 (mttt) cc_final: 0.8230 (mmtm) REVERT: B 349 ARG cc_start: 0.8633 (mtt180) cc_final: 0.7369 (mmp-170) REVERT: C 348 ASP cc_start: 0.7910 (t0) cc_final: 0.7682 (t0) REVERT: C 369 LYS cc_start: 0.7903 (mttt) cc_final: 0.7354 (tttt) REVERT: C 375 LYS cc_start: 0.7900 (tttp) cc_final: 0.6778 (mtmm) REVERT: E 369 LYS cc_start: 0.7792 (mttt) cc_final: 0.7366 (tttt) REVERT: F 375 LYS cc_start: 0.8111 (tttt) cc_final: 0.7011 (mmtm) outliers start: 11 outliers final: 8 residues processed: 99 average time/residue: 0.0956 time to fit residues: 11.0394 Evaluate side-chains 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 4.9990 chunk 40 optimal weight: 0.0670 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN C 368 ASN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN F 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.182620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.155180 restraints weight = 4397.516| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 2.61 r_work: 0.4276 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.4180 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3498 Z= 0.120 Angle : 0.561 6.880 4680 Z= 0.288 Chirality : 0.048 0.117 528 Planarity : 0.007 0.065 594 Dihedral : 4.642 16.047 462 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.53 % Allowed : 17.42 % Favored : 80.05 % 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 are not related in a simple way. whole: -3.65 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 379 TYR 0.018 0.004 TYR A 310 PHE 0.009 0.002 PHE A 346 HIS 0.005 0.002 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 3498) covalent geometry : angle 0.56073 / 0.29 ( 4680) hydrogen bonds : bond 0.01829 / 1.06 ( 23) hydrogen bonds : angle 4.36310 / 3.12 ( 69) *********************** 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 92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.148 Fit side-chains REVERT: A 347 LYS cc_start: 0.8389 (mttt) cc_final: 0.8074 (mttm) REVERT: A 348 ASP cc_start: 0.8027 (t0) cc_final: 0.7815 (t0) REVERT: B 347 LYS cc_start: 0.8384 (mttt) cc_final: 0.8139 (mmtm) REVERT: B 349 ARG cc_start: 0.8499 (mtt180) cc_final: 0.7180 (mmp-170) REVERT: C 345 ASP cc_start: 0.8504 (t0) cc_final: 0.8304 (t0) REVERT: C 369 LYS cc_start: 0.7914 (mttt) cc_final: 0.7268 (tttt) REVERT: C 375 LYS cc_start: 0.7771 (tttp) cc_final: 0.6680 (mtmm) REVERT: D 369 LYS cc_start: 0.8082 (tttt) cc_final: 0.7868 (tttp) REVERT: E 347 LYS cc_start: 0.8491 (mmtt) cc_final: 0.8138 (mmtm) REVERT: E 369 LYS cc_start: 0.7773 (mttt) cc_final: 0.7266 (tttt) REVERT: F 375 LYS cc_start: 0.8010 (tttt) cc_final: 0.6908 (mmtm) outliers start: 10 outliers final: 8 residues processed: 92 average time/residue: 0.0897 time to fit residues: 9.6061 Evaluate side-chains 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E 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: 8.9990 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** 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 = 0.4638 r_free = 0.4638 target = 0.178542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.150996 restraints weight = 4413.282| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 2.65 r_work: 0.4229 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4130 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3498 Z= 0.147 Angle : 0.594 6.200 4680 Z= 0.303 Chirality : 0.048 0.121 528 Planarity : 0.006 0.060 594 Dihedral : 4.746 15.841 462 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.02 % Allowed : 17.42 % Favored : 80.56 % 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 are not related in a simple way. whole: -3.54 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 379 TYR 0.017 0.004 TYR D 310 PHE 0.017 0.002 PHE A 378 HIS 0.005 0.002 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 3498) covalent geometry : angle 0.59405 / 0.30 ( 4680) hydrogen bonds : bond 0.01998 / 1.16 ( 23) hydrogen bonds : angle 4.43518 / 3.15 ( 69) *********************** 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 89 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 348 ASP cc_start: 0.8112 (t0) cc_final: 0.7872 (t0) REVERT: C 369 LYS cc_start: 0.7854 (mttt) cc_final: 0.7209 (tttt) REVERT: C 375 LYS cc_start: 0.7781 (tttp) cc_final: 0.6730 (mtmm) REVERT: D 347 LYS cc_start: 0.8612 (mmtt) cc_final: 0.8288 (mmtm) REVERT: D 369 LYS cc_start: 0.8089 (tttt) cc_final: 0.7865 (tttp) REVERT: E 347 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8112 (mmtm) REVERT: E 369 LYS cc_start: 0.7832 (mttt) cc_final: 0.7274 (tttt) REVERT: F 375 LYS cc_start: 0.8042 (tttt) cc_final: 0.6886 (mmtm) outliers start: 8 outliers final: 7 residues processed: 89 average time/residue: 0.0788 time to fit residues: 8.3354 Evaluate side-chains 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E 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: 7.9990 chunk 14 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 9 optimal weight: 0.0970 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.174218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.147216 restraints weight = 4415.657| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.60 r_work: 0.4169 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4075 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3498 Z= 0.228 Angle : 0.683 6.222 4680 Z= 0.355 Chirality : 0.051 0.128 528 Planarity : 0.007 0.060 594 Dihedral : 5.641 19.455 462 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.78 % Allowed : 18.18 % Favored : 79.04 % 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 are not related in a simple way. whole: -3.67 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 379 TYR 0.018 0.005 TYR C 310 PHE 0.030 0.003 PHE A 378 HIS 0.007 0.003 HIS C 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.23 ( 3498) covalent geometry : angle 0.68335 / 0.35 ( 4680) hydrogen bonds : bond 0.02395 / 1.35 ( 23) hydrogen bonds : angle 4.95769 / 3.39 ( 69) *********************** 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 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.178 Fit side-chains REVERT: A 348 ASP cc_start: 0.8119 (t0) cc_final: 0.7909 (t0) REVERT: A 376 LEU cc_start: 0.6246 (OUTLIER) cc_final: 0.5737 (mm) REVERT: C 375 LYS cc_start: 0.7841 (tttp) cc_final: 0.6700 (mtmm) REVERT: D 347 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8369 (mmtm) REVERT: D 369 LYS cc_start: 0.8145 (tttt) cc_final: 0.7943 (tttp) REVERT: E 347 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8243 (mmtm) REVERT: F 347 LYS cc_start: 0.8552 (mmtm) cc_final: 0.8082 (mptt) REVERT: F 375 LYS cc_start: 0.7986 (tttt) cc_final: 0.6694 (mmtm) outliers start: 11 outliers final: 9 residues processed: 86 average time/residue: 0.0526 time to fit residues: 5.7977 Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E 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: 4.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 7 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.182007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.155379 restraints weight = 4439.792| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.55 r_work: 0.4258 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.4161 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3498 Z= 0.159 Angle : 0.603 8.644 4680 Z= 0.309 Chirality : 0.050 0.127 528 Planarity : 0.007 0.065 594 Dihedral : 5.213 17.393 462 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.04 % Allowed : 19.44 % Favored : 76.52 % 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 are not related in a simple way. whole: -3.67 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 379 TYR 0.014 0.003 TYR C 310 PHE 0.031 0.003 PHE A 378 HIS 0.005 0.002 HIS C 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 3498) covalent geometry : angle 0.60315 / 0.31 ( 4680) hydrogen bonds : bond 0.02117 / 1.21 ( 23) hydrogen bonds : angle 4.69356 / 3.27 ( 69) *********************** 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 92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.126 Fit side-chains REVERT: C 375 LYS cc_start: 0.7767 (tttp) cc_final: 0.6795 (mtmm) REVERT: D 347 LYS cc_start: 0.8679 (mmtt) cc_final: 0.8375 (mmtm) REVERT: E 347 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8298 (mmtm) REVERT: F 347 LYS cc_start: 0.8590 (mmtm) cc_final: 0.8088 (mptt) REVERT: F 375 LYS cc_start: 0.8046 (tttt) cc_final: 0.6812 (mmtm) outliers start: 16 outliers final: 14 residues processed: 86 average time/residue: 0.0588 time to fit residues: 6.3707 Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 306 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.181054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.154855 restraints weight = 4365.033| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 2.46 r_work: 0.4276 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4181 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3498 Z= 0.150 Angle : 0.616 6.901 4680 Z= 0.313 Chirality : 0.050 0.127 528 Planarity : 0.007 0.065 594 Dihedral : 5.056 15.882 462 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.79 % Allowed : 19.44 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.014 0.004 TYR D 310 PHE 0.021 0.002 PHE A 378 HIS 0.005 0.002 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 3498) covalent geometry : angle 0.61557 / 0.31 ( 4680) hydrogen bonds : bond 0.02171 / 1.25 ( 23) hydrogen bonds : angle 4.73289 / 3.30 ( 69) *********************** 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 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.143 Fit side-chains REVERT: C 375 LYS cc_start: 0.7791 (tttp) cc_final: 0.6786 (mtmm) REVERT: D 347 LYS cc_start: 0.8685 (mmtt) cc_final: 0.8399 (mmtm) REVERT: E 347 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8299 (mmtm) REVERT: F 375 LYS cc_start: 0.8068 (tttt) cc_final: 0.6845 (mmtm) outliers start: 15 outliers final: 15 residues processed: 81 average time/residue: 0.0576 time to fit residues: 5.9197 Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 306 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** 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 = 0.4585 r_free = 0.4585 target = 0.175755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.150174 restraints weight = 4429.218| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.45 r_work: 0.4216 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4116 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.6282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3498 Z= 0.221 Angle : 0.678 4.787 4680 Z= 0.356 Chirality : 0.051 0.136 528 Planarity : 0.007 0.064 594 Dihedral : 5.560 17.953 462 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.04 % Allowed : 18.94 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 349 TYR 0.020 0.004 TYR A 310 PHE 0.017 0.002 PHE A 378 HIS 0.007 0.002 HIS C 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 ( 3498) covalent geometry : angle 0.67790 / 0.36 ( 4680) hydrogen bonds : bond 0.02464 / 1.44 ( 23) hydrogen bonds : angle 4.90985 / 3.37 ( 69) *********************** 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 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.139 Fit side-chains REVERT: D 347 LYS cc_start: 0.8672 (mmtt) cc_final: 0.8375 (mmtm) REVERT: E 347 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8334 (mmtm) REVERT: F 375 LYS cc_start: 0.8061 (tttt) cc_final: 0.6845 (mmtm) outliers start: 16 outliers final: 16 residues processed: 71 average time/residue: 0.0523 time to fit residues: 4.9160 Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS E 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.181913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.156179 restraints weight = 4360.928| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 2.47 r_work: 0.4289 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4192 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.6366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3498 Z= 0.126 Angle : 0.583 4.752 4680 Z= 0.306 Chirality : 0.050 0.127 528 Planarity : 0.007 0.066 594 Dihedral : 5.025 15.816 462 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.79 % Allowed : 19.19 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.014 0.003 TYR A 310 PHE 0.017 0.002 PHE A 378 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 3498) covalent geometry : angle 0.58322 / 0.31 ( 4680) hydrogen bonds : bond 0.02030 / 1.19 ( 23) hydrogen bonds : angle 4.69792 / 3.30 ( 69) ********************** 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 82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.088 Fit side-chains REVERT: C 347 LYS cc_start: 0.8556 (mmtm) cc_final: 0.8296 (mptt) REVERT: C 375 LYS cc_start: 0.7717 (tttp) cc_final: 0.6623 (mtmm) REVERT: D 347 LYS cc_start: 0.8642 (mmtt) cc_final: 0.8344 (mmtm) REVERT: E 347 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8337 (mmtm) REVERT: F 347 LYS cc_start: 0.8634 (mmtm) cc_final: 0.8232 (mptt) REVERT: F 349 ARG cc_start: 0.8582 (mtt180) cc_final: 0.7244 (mmp-170) REVERT: F 375 LYS cc_start: 0.8072 (tttt) cc_final: 0.6859 (mmtm) outliers start: 15 outliers final: 15 residues processed: 77 average time/residue: 0.0368 time to fit residues: 3.6317 Evaluate side-chains 80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 30 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.187430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.160953 restraints weight = 4349.771| |-----------------------------------------------------------------------------| r_work (start): 0.4431 rms_B_bonded: 2.56 r_work: 0.4327 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.4229 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3498 Z= 0.103 Angle : 0.562 4.856 4680 Z= 0.295 Chirality : 0.049 0.134 528 Planarity : 0.007 0.066 594 Dihedral : 4.589 13.701 462 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.79 % Allowed : 19.70 % Favored : 76.52 % 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 are not related in a simple way. whole: -3.54 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 379 TYR 0.012 0.002 TYR A 310 PHE 0.025 0.002 PHE D 378 HIS 0.003 0.001 HIS C 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 3498) covalent geometry : angle 0.56175 / 0.30 ( 4680) hydrogen bonds : bond 0.01879 / 1.12 ( 23) hydrogen bonds : angle 4.49592 / 3.21 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1195.10 seconds wall clock time: 21 minutes 41.81 seconds (1301.81 seconds total)