Starting phenix.real_space_refine on Wed Sep 17 07:37:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r2f_53527/09_2025/9r2f_53527.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r2f_53527/09_2025/9r2f_53527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r2f_53527/09_2025/9r2f_53527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r2f_53527/09_2025/9r2f_53527.map" model { file = "/net/cci-nas-00/data/ceres_data/9r2f_53527/09_2025/9r2f_53527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r2f_53527/09_2025/9r2f_53527.cif" } resolution = 2.8 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 C 2076 2.51 5 N 600 2.21 5 O 618 1.98 5 H 3426 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6720 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1120 Classifications: {'peptide': 72} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "B" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1120 Classifications: {'peptide': 72} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "C" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1120 Classifications: {'peptide': 72} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "D" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1120 Classifications: {'peptide': 72} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "E" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1120 Classifications: {'peptide': 72} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "F" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1120 Classifications: {'peptide': 72} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Time building chain proxies: 1.50, per 1000 atoms: 0.22 Number of scatterers: 6720 At special positions: 0 Unit cell: (129.368, 117.832, 32.136, 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) O 618 8.00 N 600 7.00 C 2076 6.00 H 3426 1.00 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: 0.34 Conformation dependent library (CDL) restraints added in 195.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 308 through 310 removed outlier: 6.531A pdb=" N ILE A 308 " --> pdb=" O VAL B 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 317 through 319 removed outlier: 6.707A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.463A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 336 through 341 Processing sheet with id=AA5, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.835A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 351 through 362 removed outlier: 8.991A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 10.051A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N SER B 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY A 355 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ASP B 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 357 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ILE B 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN A 359 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N HIS B 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER A 352 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS C 353 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 354 " --> pdb=" O LYS C 353 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 370 through 374 removed outlier: 6.522A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 308 through 310 removed outlier: 6.450A pdb=" N ILE D 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 317 through 319 removed outlier: 6.747A pdb=" N LYS D 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 328 through 330 removed outlier: 6.426A pdb=" N HIS D 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 336 through 341 removed outlier: 6.681A pdb=" N GLN D 336 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N VAL F 339 " --> pdb=" O GLN D 336 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU D 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N SER F 341 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS D 340 " --> pdb=" O SER F 341 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.835A pdb=" N ASP D 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 351 through 362 removed outlier: 8.934A pdb=" N GLN D 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 9.960A pdb=" N ILE E 354 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS D 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N SER E 356 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY D 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ASP E 358 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU D 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ILE E 360 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN D 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N HIS E 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR D 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N SER D 352 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS F 353 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE D 354 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 370 through 374 removed outlier: 6.556A pdb=" N ILE D 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N HIS F 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR D 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) 53 hydrogen bonds defined for protein. 159 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.07: 804 1.07 - 1.19: 2622 1.19 - 1.31: 584 1.31 - 1.43: 742 1.43 - 1.55: 2022 Bond restraints: 6774 Sorted by residual: bond pdb=" N THR B 373 " pdb=" H THR B 373 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N HIS C 329 " pdb=" H HIS C 329 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE1 HIS C 329 " pdb=" HE1 HIS C 329 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD1 PHE A 346 " pdb=" HD1 PHE A 346 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" ND2 ASN B 327 " pdb="HD21 ASN B 327 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 6769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 8704 1.89 - 3.79: 2423 3.79 - 5.68: 868 5.68 - 7.57: 324 7.57 - 9.47: 41 Bond angle restraints: 12360 Sorted by residual: angle pdb=" N LYS E 347 " pdb=" CA LYS E 347 " pdb=" C LYS E 347 " ideal model delta sigma weight residual 113.12 121.63 -8.51 1.25e+00 6.40e-01 4.63e+01 angle pdb=" N LYS B 347 " pdb=" CA LYS B 347 " pdb=" C LYS B 347 " ideal model delta sigma weight residual 113.12 121.50 -8.38 1.25e+00 6.40e-01 4.49e+01 angle pdb=" N LYS C 347 " pdb=" CA LYS C 347 " pdb=" C LYS C 347 " ideal model delta sigma weight residual 113.12 121.29 -8.17 1.25e+00 6.40e-01 4.28e+01 angle pdb=" N THR F 319 " pdb=" CA THR F 319 " pdb=" C THR F 319 " ideal model delta sigma weight residual 109.24 118.71 -9.47 1.51e+00 4.39e-01 3.93e+01 angle pdb=" N THR D 319 " pdb=" CA THR D 319 " pdb=" C THR D 319 " ideal model delta sigma weight residual 109.24 118.69 -9.45 1.51e+00 4.39e-01 3.91e+01 ... (remaining 12355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.79: 2730 13.79 - 27.57: 171 27.57 - 41.36: 83 41.36 - 55.15: 53 55.15 - 68.93: 77 Dihedral angle restraints: 3114 sinusoidal: 1770 harmonic: 1344 Sorted by residual: dihedral pdb=" CA LEU A 357 " pdb=" C LEU A 357 " pdb=" N ASP A 358 " pdb=" CA ASP A 358 " ideal model delta harmonic sigma weight residual -180.00 -151.52 -28.48 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA SER A 324 " pdb=" C SER A 324 " pdb=" N LEU A 325 " pdb=" CA LEU A 325 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" C LEU D 344 " pdb=" N LEU D 344 " pdb=" CA LEU D 344 " pdb=" CB LEU D 344 " ideal model delta harmonic sigma weight residual -122.60 -134.76 12.16 0 2.50e+00 1.60e-01 2.37e+01 ... (remaining 3111 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.087: 268 0.087 - 0.173: 163 0.173 - 0.260: 54 0.260 - 0.346: 10 0.346 - 0.432: 9 Chirality restraints: 504 Sorted by residual: chirality pdb=" CA LEU D 344 " pdb=" N LEU D 344 " pdb=" C LEU D 344 " pdb=" CB LEU D 344 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" CA GLU A 342 " pdb=" N GLU A 342 " pdb=" C GLU A 342 " pdb=" CB GLU A 342 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA LEU F 344 " pdb=" N LEU F 344 " pdb=" C LEU F 344 " pdb=" CB LEU F 344 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.98e+00 ... (remaining 501 not shown) Planarity restraints: 978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.185 2.00e-02 2.50e+03 7.67e-02 1.76e+02 pdb=" CG TYR C 310 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.051 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.143 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " -0.038 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " -0.177 2.00e-02 2.50e+03 7.30e-02 1.60e+02 pdb=" CG TYR E 310 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " 0.064 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.031 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " -0.131 2.00e-02 2.50e+03 pdb=" HD1 TYR E 310 " 0.011 2.00e-02 2.50e+03 pdb=" HD2 TYR E 310 " 0.038 2.00e-02 2.50e+03 pdb=" HE1 TYR E 310 " 0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR E 310 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.161 2.00e-02 2.50e+03 6.84e-02 1.40e+02 pdb=" CG TYR A 310 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.127 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " 0.030 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " 0.007 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " -0.008 2.00e-02 2.50e+03 ... (remaining 975 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.18: 426 2.18 - 2.76: 10515 2.76 - 3.34: 16977 3.34 - 3.92: 21178 3.92 - 4.50: 29276 Nonbonded interactions: 78372 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.596 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.631 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.648 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.649 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.678 2.450 ... (remaining 78367 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: 3.590 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: 0.020 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.240 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:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 0.035 3348 Z= 0.735 Angle : 2.271 9.465 4482 Z= 1.493 Chirality : 0.127 0.432 504 Planarity : 0.012 0.092 570 Dihedral : 11.015 68.932 1278 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 0.27 % Allowed : 4.30 % Favored : 95.43 % Cbeta Deviations : 1.06 % 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: -3.55 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG C 349 TYR 0.169 0.061 TYR C 310 PHE 0.035 0.012 PHE D 346 HIS 0.013 0.005 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.01146 ( 3348) covalent geometry : angle 2.27101 ( 4482) hydrogen bonds : bond 0.12958 ( 53) hydrogen bonds : angle 7.34249 ( 159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 102 average time/residue: 1.3356 time to fit residues: 139.2986 Evaluate side-chains 77 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN A 374 HIS B 351 GLN C 336 GLN C 351 GLN D 351 GLN E 351 GLN E 374 HIS F 336 GLN F 351 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.174091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.152277 restraints weight = 12321.383| |-----------------------------------------------------------------------------| r_work (start): 0.4683 rms_B_bonded: 2.87 r_work: 0.4572 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3348 Z= 0.173 Angle : 0.766 6.148 4482 Z= 0.410 Chirality : 0.051 0.149 504 Planarity : 0.004 0.026 570 Dihedral : 7.616 21.898 439 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 0.81 % Allowed : 18.55 % Favored : 80.65 % 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: -3.12 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 349 TYR 0.016 0.003 TYR C 310 PHE 0.009 0.001 PHE E 346 HIS 0.005 0.002 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 3348) covalent geometry : angle 0.76603 ( 4482) hydrogen bonds : bond 0.02736 ( 53) hydrogen bonds : angle 5.58896 ( 159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8097 (mttt) cc_final: 0.7842 (mtmt) REVERT: B 348 ASP cc_start: 0.8187 (t0) cc_final: 0.7922 (t0) REVERT: D 369 LYS cc_start: 0.8831 (mttp) cc_final: 0.8208 (tttt) outliers start: 3 outliers final: 0 residues processed: 71 average time/residue: 1.6359 time to fit residues: 118.3392 Evaluate side-chains 52 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS F 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.173544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.151840 restraints weight = 12206.586| |-----------------------------------------------------------------------------| r_work (start): 0.4696 rms_B_bonded: 2.86 r_work: 0.4607 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3348 Z= 0.157 Angle : 0.707 4.940 4482 Z= 0.381 Chirality : 0.052 0.158 504 Planarity : 0.005 0.032 570 Dihedral : 7.251 20.436 438 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 1.08 % Allowed : 18.55 % Favored : 80.38 % 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: -2.95 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG E 349 TYR 0.020 0.004 TYR C 310 PHE 0.006 0.002 PHE A 346 HIS 0.004 0.002 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 3348) covalent geometry : angle 0.70652 ( 4482) hydrogen bonds : bond 0.02592 ( 53) hydrogen bonds : angle 5.14539 ( 159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.202 Fit side-chains REVERT: A 314 ASP cc_start: 0.8305 (t0) cc_final: 0.8100 (t0) REVERT: A 347 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7369 (mppt) REVERT: C 369 LYS cc_start: 0.8766 (tttt) cc_final: 0.8458 (tptm) REVERT: F 340 LYS cc_start: 0.8534 (mttt) cc_final: 0.8205 (mtpm) outliers start: 4 outliers final: 1 residues processed: 68 average time/residue: 1.7838 time to fit residues: 123.4837 Evaluate side-chains 62 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS 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 35 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.172481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.150693 restraints weight = 12285.765| |-----------------------------------------------------------------------------| r_work (start): 0.4682 rms_B_bonded: 2.87 r_work: 0.4589 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3348 Z= 0.150 Angle : 0.676 4.934 4482 Z= 0.359 Chirality : 0.051 0.148 504 Planarity : 0.004 0.032 570 Dihedral : 7.059 19.354 438 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 1.34 % Allowed : 18.82 % Favored : 79.84 % 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: -2.86 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 349 TYR 0.022 0.004 TYR C 310 PHE 0.007 0.001 PHE A 346 HIS 0.004 0.002 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 3348) covalent geometry : angle 0.67595 ( 4482) hydrogen bonds : bond 0.02110 ( 53) hydrogen bonds : angle 4.85714 ( 159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.201 Fit side-chains REVERT: A 347 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7394 (mppt) REVERT: B 317 LYS cc_start: 0.8029 (ttmt) cc_final: 0.7703 (mtpm) REVERT: C 369 LYS cc_start: 0.8759 (tttt) cc_final: 0.8365 (tptm) REVERT: F 340 LYS cc_start: 0.8550 (mttt) cc_final: 0.8214 (mtpm) outliers start: 5 outliers final: 1 residues processed: 68 average time/residue: 1.8078 time to fit residues: 125.2106 Evaluate side-chains 59 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain E residue 320 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4912 r_free = 0.4912 target = 0.175903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.154077 restraints weight = 12274.827| |-----------------------------------------------------------------------------| r_work (start): 0.4720 rms_B_bonded: 2.90 r_work: 0.4621 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3348 Z= 0.109 Angle : 0.649 4.463 4482 Z= 0.339 Chirality : 0.050 0.143 504 Planarity : 0.005 0.036 570 Dihedral : 6.667 18.440 438 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 1.88 % Allowed : 18.82 % Favored : 79.30 % 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: -2.89 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 349 TYR 0.019 0.003 TYR C 310 PHE 0.004 0.001 PHE A 346 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 3348) covalent geometry : angle 0.64931 ( 4482) hydrogen bonds : bond 0.01664 ( 53) hydrogen bonds : angle 4.64184 ( 159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.206 Fit side-chains REVERT: B 317 LYS cc_start: 0.8017 (ttmt) cc_final: 0.7662 (mtpm) REVERT: C 340 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8298 (mttp) REVERT: C 369 LYS cc_start: 0.8759 (tttt) cc_final: 0.8368 (tptm) REVERT: D 369 LYS cc_start: 0.8856 (mttp) cc_final: 0.8231 (tttt) REVERT: E 348 ASP cc_start: 0.8049 (t0) cc_final: 0.7840 (t0) REVERT: F 340 LYS cc_start: 0.8530 (mttt) cc_final: 0.8214 (mtpm) outliers start: 7 outliers final: 2 residues processed: 70 average time/residue: 1.7155 time to fit residues: 122.3771 Evaluate side-chains 62 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain E residue 320 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.166539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.145016 restraints weight = 12580.711| |-----------------------------------------------------------------------------| r_work (start): 0.4621 rms_B_bonded: 2.78 r_work: 0.4532 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4421 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3348 Z= 0.218 Angle : 0.738 4.691 4482 Z= 0.392 Chirality : 0.052 0.146 504 Planarity : 0.005 0.032 570 Dihedral : 7.052 19.094 438 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 1.34 % Allowed : 21.77 % Favored : 76.88 % 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: -2.97 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.021 0.005 TYR F 310 PHE 0.007 0.002 PHE F 378 HIS 0.005 0.002 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 3348) covalent geometry : angle 0.73781 ( 4482) hydrogen bonds : bond 0.02018 ( 53) hydrogen bonds : angle 4.74743 ( 159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.198 Fit side-chains REVERT: A 321 LYS cc_start: 0.7946 (mtpp) cc_final: 0.7498 (mttt) REVERT: A 347 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7417 (mppt) REVERT: C 369 LYS cc_start: 0.8843 (tttt) cc_final: 0.8452 (tptm) REVERT: E 348 ASP cc_start: 0.8055 (t0) cc_final: 0.7844 (t0) REVERT: F 340 LYS cc_start: 0.8583 (mttt) cc_final: 0.8219 (mtpm) outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 1.7482 time to fit residues: 98.0883 Evaluate side-chains 54 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain E residue 320 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 0.0020 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.165856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.144504 restraints weight = 12437.701| |-----------------------------------------------------------------------------| r_work (start): 0.4617 rms_B_bonded: 2.78 r_work: 0.4529 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4413 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3348 Z= 0.217 Angle : 0.748 4.938 4482 Z= 0.395 Chirality : 0.052 0.146 504 Planarity : 0.005 0.034 570 Dihedral : 7.093 19.483 438 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 1.88 % Allowed : 21.51 % Favored : 76.61 % 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: -3.08 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.022 0.005 TYR C 310 PHE 0.007 0.002 PHE C 378 HIS 0.004 0.002 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 3348) covalent geometry : angle 0.74799 ( 4482) hydrogen bonds : bond 0.02131 ( 53) hydrogen bonds : angle 4.80838 ( 159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.200 Fit side-chains REVERT: A 321 LYS cc_start: 0.8038 (mtpp) cc_final: 0.7618 (mttt) REVERT: A 347 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7539 (mppt) REVERT: C 369 LYS cc_start: 0.8847 (tttt) cc_final: 0.8472 (tptm) REVERT: E 348 ASP cc_start: 0.8051 (t0) cc_final: 0.7831 (t0) REVERT: F 340 LYS cc_start: 0.8619 (mttt) cc_final: 0.8402 (mttp) outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 1.6761 time to fit residues: 95.7867 Evaluate side-chains 54 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain E residue 320 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4834 r_free = 0.4834 target = 0.169167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.147793 restraints weight = 12363.154| |-----------------------------------------------------------------------------| r_work (start): 0.4651 rms_B_bonded: 2.80 r_work: 0.4560 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.4444 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3348 Z= 0.143 Angle : 0.713 5.282 4482 Z= 0.369 Chirality : 0.050 0.142 504 Planarity : 0.005 0.038 570 Dihedral : 6.783 18.092 438 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.61 % Allowed : 23.39 % Favored : 75.00 % 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: -3.05 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 349 TYR 0.020 0.004 TYR C 310 PHE 0.004 0.001 PHE C 378 HIS 0.003 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 3348) covalent geometry : angle 0.71347 ( 4482) hydrogen bonds : bond 0.01729 ( 53) hydrogen bonds : angle 4.59845 ( 159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.196 Fit side-chains REVERT: A 321 LYS cc_start: 0.8072 (mtpp) cc_final: 0.7670 (mttt) REVERT: A 347 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7541 (mppt) REVERT: C 369 LYS cc_start: 0.8829 (tttt) cc_final: 0.8468 (tptm) REVERT: F 340 LYS cc_start: 0.8606 (mttt) cc_final: 0.8256 (mtpm) outliers start: 6 outliers final: 4 residues processed: 59 average time/residue: 1.6555 time to fit residues: 99.7849 Evaluate side-chains 56 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain E residue 320 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4883 r_free = 0.4883 target = 0.172988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.151494 restraints weight = 12389.345| |-----------------------------------------------------------------------------| r_work (start): 0.4700 rms_B_bonded: 2.87 r_work: 0.4611 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.4611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3348 Z= 0.113 Angle : 0.691 5.371 4482 Z= 0.354 Chirality : 0.050 0.139 504 Planarity : 0.005 0.035 570 Dihedral : 6.426 17.763 438 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.08 % Allowed : 24.73 % Favored : 74.19 % 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: -2.92 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 349 TYR 0.017 0.003 TYR C 310 PHE 0.003 0.000 PHE A 346 HIS 0.002 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3348) covalent geometry : angle 0.69073 ( 4482) hydrogen bonds : bond 0.01377 ( 53) hydrogen bonds : angle 4.33496 ( 159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.203 Fit side-chains REVERT: A 321 LYS cc_start: 0.7942 (mtpp) cc_final: 0.7551 (mttt) REVERT: A 347 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7387 (mppt) REVERT: B 317 LYS cc_start: 0.8007 (ttmt) cc_final: 0.7597 (mtpm) REVERT: C 369 LYS cc_start: 0.8735 (tttt) cc_final: 0.8272 (tptm) REVERT: F 340 LYS cc_start: 0.8529 (mttt) cc_final: 0.8269 (ttmm) REVERT: F 349 ARG cc_start: 0.7917 (ttm110) cc_final: 0.7438 (mtp180) outliers start: 4 outliers final: 3 residues processed: 61 average time/residue: 1.5251 time to fit residues: 95.1032 Evaluate side-chains 60 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain E residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.166920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.145516 restraints weight = 12526.054| |-----------------------------------------------------------------------------| r_work (start): 0.4636 rms_B_bonded: 2.80 r_work: 0.4548 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4432 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3348 Z= 0.192 Angle : 0.748 5.664 4482 Z= 0.393 Chirality : 0.051 0.143 504 Planarity : 0.005 0.034 570 Dihedral : 6.702 18.426 438 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 2.42 % Allowed : 23.92 % Favored : 73.66 % 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: -3.07 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.018 0.004 TYR F 310 PHE 0.006 0.001 PHE F 378 HIS 0.004 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 3348) covalent geometry : angle 0.74823 ( 4482) hydrogen bonds : bond 0.01773 ( 53) hydrogen bonds : angle 4.52181 ( 159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.232 Fit side-chains REVERT: A 321 LYS cc_start: 0.8097 (mtpp) cc_final: 0.7663 (mttt) REVERT: A 347 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7579 (mppt) REVERT: C 369 LYS cc_start: 0.8841 (tttt) cc_final: 0.8460 (tptm) REVERT: F 340 LYS cc_start: 0.8613 (mttt) cc_final: 0.8252 (mtpm) REVERT: F 349 ARG cc_start: 0.8046 (ttm110) cc_final: 0.7523 (mtp180) outliers start: 9 outliers final: 6 residues processed: 54 average time/residue: 1.6266 time to fit residues: 89.7688 Evaluate side-chains 57 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain E residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 0.0270 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.2042 ------------------------------------------------------------------------------- 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 = 0.4871 r_free = 0.4871 target = 0.171794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.150369 restraints weight = 12351.642| |-----------------------------------------------------------------------------| r_work (start): 0.4688 rms_B_bonded: 2.84 r_work: 0.4599 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.4485 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.5927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3348 Z= 0.122 Angle : 0.707 5.681 4482 Z= 0.362 Chirality : 0.050 0.137 504 Planarity : 0.005 0.036 570 Dihedral : 6.414 17.688 438 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.34 % Allowed : 25.00 % Favored : 73.66 % 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: -2.93 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.017 0.003 TYR C 310 PHE 0.002 0.001 PHE F 378 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3348) covalent geometry : angle 0.70688 ( 4482) hydrogen bonds : bond 0.01448 ( 53) hydrogen bonds : angle 4.32538 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3327.20 seconds wall clock time: 57 minutes 10.09 seconds (3430.09 seconds total)