Starting phenix.real_space_refine on Tue Mar 3 16:28:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r4t_14316/03_2026/7r4t_14316.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r4t_14316/03_2026/7r4t_14316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r4t_14316/03_2026/7r4t_14316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r4t_14316/03_2026/7r4t_14316.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r4t_14316/03_2026/7r4t_14316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r4t_14316/03_2026/7r4t_14316.map" } resolution = 2.75 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2172 2.51 5 N 642 2.21 5 O 648 1.98 5 H 3606 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7074 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "D" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 1.26, per 1000 atoms: 0.18 Number of scatterers: 7074 At special positions: 0 Unit cell: (132.664, 112.888, 40.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 648 8.00 N 642 7.00 C 2172 6.00 H 3606 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: 0.42 Conformation dependent library (CDL) restraints added in 256.5 milliseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 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 18 sheets defined 0.0% alpha, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.595A pdb=" N GLN F 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N TYR D 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL F 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.708A pdb=" N VAL F 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 324 removed outlier: 6.178A pdb=" N LYS F 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N SER D 320 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR F 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N CYS D 322 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LYS F 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N SER D 324 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY F 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.368A pdb=" N ILE F 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 341 removed outlier: 6.467A pdb=" N GLN F 336 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL D 339 " --> pdb=" O GLN F 336 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU F 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N SER D 341 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS F 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.593A pdb=" N ASP F 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 350 through 354 removed outlier: 6.364A pdb=" N GLN F 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE D 354 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS F 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 357 through 362 removed outlier: 6.532A pdb=" N LEU F 357 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE B 360 " --> pdb=" O LEU F 357 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN F 359 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N HIS B 362 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR F 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP F 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR D 361 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE F 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 378 removed outlier: 6.509A pdb=" N LYS F 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLU D 372 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE F 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N HIS D 374 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N THR F 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU D 376 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS F 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N PHE D 378 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR F 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.723A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 324 removed outlier: 6.169A pdb=" N LYS A 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N SER E 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR A 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N CYS E 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS A 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N SER E 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY A 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.404A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 336 through 338 removed outlier: 6.501A pdb=" N GLN A 336 " --> pdb=" O VAL E 337 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.605A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.377A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.503A pdb=" N LEU A 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE C 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 368 through 378 removed outlier: 6.440A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N PHE E 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR A 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 222 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: 1.41 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3600 1.12 - 1.29: 576 1.29 - 1.47: 1176 1.47 - 1.64: 1770 1.64 - 1.82: 6 Bond restraints: 7128 Sorted by residual: bond pdb=" N GLU F 338 " pdb=" H GLU F 338 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY F 335 " pdb=" H GLY F 335 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N SER F 341 " pdb=" H SER F 341 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE2 HIS D 374 " pdb=" HE2 HIS D 374 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD2 PHE B 346 " pdb=" HD2 PHE B 346 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 7123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 11940 3.65 - 7.31: 1001 7.31 - 10.96: 38 10.96 - 14.62: 2 14.62 - 18.27: 3 Bond angle restraints: 12984 Sorted by residual: angle pdb=" C VAL C 339 " pdb=" N LYS C 340 " pdb=" H LYS C 340 " ideal model delta sigma weight residual 123.83 105.55 18.27 3.00e+00 1.11e-01 3.71e+01 angle pdb=" C VAL A 339 " pdb=" N LYS A 340 " pdb=" H LYS A 340 " ideal model delta sigma weight residual 123.83 106.86 16.96 3.00e+00 1.11e-01 3.20e+01 angle pdb=" C VAL E 339 " pdb=" N LYS E 340 " pdb=" H LYS E 340 " ideal model delta sigma weight residual 123.83 108.19 15.63 3.00e+00 1.11e-01 2.71e+01 angle pdb=" CB HIS F 362 " pdb=" CG HIS F 362 " pdb=" CD2 HIS F 362 " ideal model delta sigma weight residual 131.20 125.02 6.18 1.30e+00 5.92e-01 2.26e+01 angle pdb=" CB HIS A 329 " pdb=" CG HIS A 329 " pdb=" CD2 HIS A 329 " ideal model delta sigma weight residual 131.20 125.11 6.09 1.30e+00 5.92e-01 2.20e+01 ... (remaining 12979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.45: 2806 13.45 - 26.89: 253 26.89 - 40.34: 103 40.34 - 53.78: 46 53.78 - 67.23: 74 Dihedral angle restraints: 3282 sinusoidal: 1878 harmonic: 1404 Sorted by residual: dihedral pdb=" CA VAL E 350 " pdb=" C VAL E 350 " pdb=" N GLN E 351 " pdb=" CA GLN E 351 " ideal model delta harmonic sigma weight residual 180.00 153.90 26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA VAL D 350 " pdb=" C VAL D 350 " pdb=" N GLN D 351 " pdb=" CA GLN D 351 " ideal model delta harmonic sigma weight residual 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA VAL F 350 " pdb=" C VAL F 350 " pdb=" N GLN F 351 " pdb=" CA GLN F 351 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 3279 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.070: 310 0.070 - 0.138: 174 0.138 - 0.207: 31 0.207 - 0.276: 10 0.276 - 0.345: 3 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS F 340 " pdb=" N LYS F 340 " pdb=" C LYS F 340 " pdb=" CB LYS F 340 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA LYS A 340 " pdb=" N LYS A 340 " pdb=" C LYS A 340 " pdb=" CB LYS A 340 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA LYS B 340 " pdb=" N LYS B 340 " pdb=" C LYS B 340 " pdb=" CB LYS B 340 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 525 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 339 " 0.059 2.00e-02 2.50e+03 1.13e-01 1.29e+02 pdb=" N LYS A 340 " -0.196 2.00e-02 2.50e+03 pdb=" CA LYS A 340 " 0.059 2.00e-02 2.50e+03 pdb=" H LYS A 340 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 339 " 0.059 2.00e-02 2.50e+03 1.12e-01 1.26e+02 pdb=" N LYS C 340 " -0.194 2.00e-02 2.50e+03 pdb=" CA LYS C 340 " 0.060 2.00e-02 2.50e+03 pdb=" H LYS C 340 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 339 " 0.053 2.00e-02 2.50e+03 1.02e-01 1.03e+02 pdb=" N LYS E 340 " -0.176 2.00e-02 2.50e+03 pdb=" CA LYS E 340 " 0.053 2.00e-02 2.50e+03 pdb=" H LYS E 340 " 0.069 2.00e-02 2.50e+03 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 592 2.17 - 2.78: 11959 2.78 - 3.38: 18274 3.38 - 3.99: 25297 3.99 - 4.60: 34258 Nonbonded interactions: 90380 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.560 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.567 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.570 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.573 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.594 2.450 ... (remaining 90375 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: 3.760 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: 0.040 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.170 Find NCS groups from input model: 0.070 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:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 3522 Z= 0.658 Angle : 1.775 6.178 4710 Z= 1.174 Chirality : 0.085 0.345 528 Planarity : 0.009 0.050 600 Dihedral : 11.858 51.239 1350 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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: -2.02 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 349 TYR 0.032 0.008 TYR D 310 PHE 0.047 0.018 PHE F 378 HIS 0.008 0.002 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.01059 ( 3522) covalent geometry : angle 1.77467 ( 4710) hydrogen bonds : bond 0.07107 ( 74) hydrogen bonds : angle 8.06672 ( 222) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 347 LYS cc_start: 0.8346 (ttpt) cc_final: 0.7938 (mptt) REVERT: A 347 LYS cc_start: 0.8450 (ttpt) cc_final: 0.7990 (mptt) REVERT: B 347 LYS cc_start: 0.8339 (ttpt) cc_final: 0.7945 (mmtm) REVERT: B 349 ARG cc_start: 0.8218 (mtt180) cc_final: 0.6477 (mmp-170) REVERT: C 347 LYS cc_start: 0.8400 (ttpt) cc_final: 0.7967 (mmtm) REVERT: C 349 ARG cc_start: 0.8156 (mtt180) cc_final: 0.6364 (mmp-170) REVERT: D 347 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8240 (mptt) REVERT: D 348 ASP cc_start: 0.8537 (t70) cc_final: 0.8029 (t0) REVERT: D 349 ARG cc_start: 0.7334 (mtt180) cc_final: 0.5890 (pmt-80) REVERT: E 347 LYS cc_start: 0.8447 (ttpt) cc_final: 0.8122 (mptt) REVERT: E 348 ASP cc_start: 0.8595 (t70) cc_final: 0.8209 (t0) REVERT: E 349 ARG cc_start: 0.7266 (mtt180) cc_final: 0.5876 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 1.5356 time to fit residues: 212.9711 Evaluate side-chains 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.132681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.122533 restraints weight = 13572.621| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.59 r_work: 0.3791 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3522 Z= 0.135 Angle : 0.566 4.691 4710 Z= 0.293 Chirality : 0.053 0.149 528 Planarity : 0.003 0.021 600 Dihedral : 5.978 19.893 468 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.53 % Allowed : 14.90 % Favored : 82.58 % 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: -1.48 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 349 TYR 0.008 0.001 TYR D 310 PHE 0.011 0.002 PHE D 378 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 3522) covalent geometry : angle 0.56591 ( 4710) hydrogen bonds : bond 0.02824 ( 74) hydrogen bonds : angle 5.78092 ( 222) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.272 Fit side-chains REVERT: A 338 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: A 347 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8319 (mptt) REVERT: A 349 ARG cc_start: 0.7751 (mtm180) cc_final: 0.7550 (mtt180) REVERT: B 349 ARG cc_start: 0.8213 (mtt180) cc_final: 0.6597 (mmp80) REVERT: C 338 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: C 349 ARG cc_start: 0.8222 (mtt180) cc_final: 0.6614 (mmp-170) REVERT: D 338 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: D 348 ASP cc_start: 0.8387 (t70) cc_final: 0.8169 (t0) REVERT: D 349 ARG cc_start: 0.7485 (mtt180) cc_final: 0.6452 (pmt-80) REVERT: E 338 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: E 340 LYS cc_start: 0.8592 (ptpp) cc_final: 0.8341 (ptpt) REVERT: E 348 ASP cc_start: 0.8417 (t70) cc_final: 0.8162 (t0) REVERT: E 349 ARG cc_start: 0.7360 (mtt180) cc_final: 0.6389 (pmt-80) outliers start: 10 outliers final: 0 residues processed: 92 average time/residue: 1.5469 time to fit residues: 145.3661 Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 39 optimal weight: 0.0980 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.127601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.118020 restraints weight = 14344.166| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.61 r_work: 0.3757 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3522 Z= 0.107 Angle : 0.488 3.791 4710 Z= 0.245 Chirality : 0.051 0.134 528 Planarity : 0.002 0.016 600 Dihedral : 4.939 17.111 468 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.78 % Allowed : 16.92 % Favored : 80.30 % 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 are not related in a simple way. whole: -1.43 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 349 TYR 0.007 0.001 TYR A 310 PHE 0.007 0.001 PHE B 378 HIS 0.001 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 3522) covalent geometry : angle 0.48849 ( 4710) hydrogen bonds : bond 0.01909 ( 74) hydrogen bonds : angle 4.94853 ( 222) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.209 Fit side-chains REVERT: A 338 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: B 338 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: B 349 ARG cc_start: 0.8326 (mtt180) cc_final: 0.6725 (mmp80) REVERT: C 338 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: C 349 ARG cc_start: 0.8260 (mtt180) cc_final: 0.6625 (mmp-170) REVERT: D 338 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: D 348 ASP cc_start: 0.8444 (t70) cc_final: 0.8223 (t0) REVERT: D 349 ARG cc_start: 0.7755 (mtt180) cc_final: 0.6556 (pmt-80) REVERT: E 338 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: E 348 ASP cc_start: 0.8433 (t70) cc_final: 0.8210 (t0) REVERT: E 349 ARG cc_start: 0.7569 (mtt180) cc_final: 0.6425 (pmt-80) outliers start: 11 outliers final: 1 residues processed: 69 average time/residue: 1.3347 time to fit residues: 94.3880 Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 0.1980 chunk 28 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.125017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.114585 restraints weight = 12673.478| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.59 r_work: 0.3731 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3522 Z= 0.172 Angle : 0.501 3.585 4710 Z= 0.251 Chirality : 0.051 0.139 528 Planarity : 0.002 0.013 600 Dihedral : 4.786 16.198 468 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.78 % Allowed : 16.92 % Favored : 80.30 % 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 are not related in a simple way. whole: -1.38 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 349 TYR 0.006 0.001 TYR D 310 PHE 0.010 0.001 PHE B 378 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 3522) covalent geometry : angle 0.50090 ( 4710) hydrogen bonds : bond 0.02164 ( 74) hydrogen bonds : angle 4.70129 ( 222) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.265 Fit side-chains REVERT: A 338 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: B 349 ARG cc_start: 0.8373 (mtt180) cc_final: 0.6691 (mmp80) REVERT: C 338 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: C 349 ARG cc_start: 0.8239 (mtt180) cc_final: 0.6640 (mmp-170) REVERT: D 348 ASP cc_start: 0.8452 (t70) cc_final: 0.8237 (t0) REVERT: D 349 ARG cc_start: 0.7844 (mtt180) cc_final: 0.6409 (pmt-80) REVERT: E 311 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8708 (ptmt) REVERT: E 348 ASP cc_start: 0.8460 (t70) cc_final: 0.8213 (t0) REVERT: E 349 ARG cc_start: 0.7812 (mtt180) cc_final: 0.6368 (pmt-80) outliers start: 11 outliers final: 2 residues processed: 70 average time/residue: 1.3035 time to fit residues: 93.6019 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 311 LYS 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 36 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.128986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.118884 restraints weight = 13117.182| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.61 r_work: 0.3792 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3522 Z= 0.085 Angle : 0.462 3.468 4710 Z= 0.229 Chirality : 0.051 0.126 528 Planarity : 0.002 0.012 600 Dihedral : 4.322 15.240 468 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.77 % Allowed : 18.43 % 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: -1.37 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.005 0.001 TYR A 310 PHE 0.004 0.001 PHE D 378 HIS 0.002 0.000 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 3522) covalent geometry : angle 0.46221 ( 4710) hydrogen bonds : bond 0.01521 ( 74) hydrogen bonds : angle 4.26368 ( 222) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.145 Fit side-chains REVERT: F 351 GLN cc_start: 0.8666 (tt0) cc_final: 0.8433 (tt0) REVERT: B 349 ARG cc_start: 0.8353 (mtt180) cc_final: 0.6696 (mmp-170) REVERT: C 338 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: C 349 ARG cc_start: 0.8241 (mtt180) cc_final: 0.6605 (mmp-170) REVERT: D 348 ASP cc_start: 0.8451 (t70) cc_final: 0.8131 (t0) REVERT: D 349 ARG cc_start: 0.7875 (mtt180) cc_final: 0.6417 (pmt-80) REVERT: E 311 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8638 (ptmt) REVERT: E 348 ASP cc_start: 0.8462 (t70) cc_final: 0.8239 (t0) REVERT: E 349 ARG cc_start: 0.7829 (mtt180) cc_final: 0.6464 (pmt-80) outliers start: 7 outliers final: 2 residues processed: 62 average time/residue: 1.2505 time to fit residues: 79.6090 Evaluate side-chains 61 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain E residue 311 LYS 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 38 optimal weight: 0.0980 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.128729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.118602 restraints weight = 12920.053| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.61 r_work: 0.3791 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3522 Z= 0.097 Angle : 0.451 3.446 4710 Z= 0.222 Chirality : 0.050 0.128 528 Planarity : 0.002 0.013 600 Dihedral : 4.158 14.057 468 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.52 % Allowed : 18.18 % Favored : 80.30 % 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 are not related in a simple way. whole: -1.36 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.005 0.001 TYR A 310 PHE 0.004 0.001 PHE C 378 HIS 0.001 0.000 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 3522) covalent geometry : angle 0.45141 ( 4710) hydrogen bonds : bond 0.01537 ( 74) hydrogen bonds : angle 4.05751 ( 222) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.211 Fit side-chains REVERT: F 351 GLN cc_start: 0.8662 (tt0) cc_final: 0.8423 (tt0) REVERT: A 338 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: B 349 ARG cc_start: 0.8370 (mtt180) cc_final: 0.6745 (mmp-170) REVERT: C 338 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: C 349 ARG cc_start: 0.8233 (mtt180) cc_final: 0.6610 (mmp-170) REVERT: D 348 ASP cc_start: 0.8443 (t70) cc_final: 0.8110 (t0) REVERT: D 349 ARG cc_start: 0.7954 (mtt180) cc_final: 0.6452 (pmt-80) REVERT: E 311 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8630 (ptmt) REVERT: E 348 ASP cc_start: 0.8452 (t70) cc_final: 0.8231 (t0) REVERT: E 349 ARG cc_start: 0.7882 (mtt180) cc_final: 0.6413 (pmt-80) outliers start: 6 outliers final: 2 residues processed: 60 average time/residue: 1.2426 time to fit residues: 76.5577 Evaluate side-chains 61 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain E residue 311 LYS 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 30 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.125901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.115760 restraints weight = 12479.796| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.56 r_work: 0.3756 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3522 Z= 0.123 Angle : 0.466 3.449 4710 Z= 0.231 Chirality : 0.050 0.131 528 Planarity : 0.002 0.013 600 Dihedral : 4.149 13.545 468 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.26 % Allowed : 18.43 % Favored : 80.30 % 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 are not related in a simple way. whole: -1.38 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.005 0.001 TYR A 310 PHE 0.005 0.001 PHE D 378 HIS 0.002 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3522) covalent geometry : angle 0.46564 ( 4710) hydrogen bonds : bond 0.01725 ( 74) hydrogen bonds : angle 4.06134 ( 222) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.230 Fit side-chains REVERT: F 345 ASP cc_start: 0.8479 (m-30) cc_final: 0.8267 (m-30) REVERT: F 349 ARG cc_start: 0.8085 (mtt180) cc_final: 0.7801 (mtt180) REVERT: F 351 GLN cc_start: 0.8626 (tt0) cc_final: 0.8415 (tt0) REVERT: A 338 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: B 349 ARG cc_start: 0.8403 (mtt180) cc_final: 0.6789 (mmp-170) REVERT: C 349 ARG cc_start: 0.8251 (mtt180) cc_final: 0.6681 (mmp-170) REVERT: D 348 ASP cc_start: 0.8446 (t70) cc_final: 0.8117 (t0) REVERT: D 349 ARG cc_start: 0.8078 (mtt180) cc_final: 0.6499 (pmt-80) REVERT: E 348 ASP cc_start: 0.8432 (t70) cc_final: 0.8191 (t0) REVERT: E 349 ARG cc_start: 0.8018 (mtt180) cc_final: 0.6480 (pmt-80) outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 1.3453 time to fit residues: 86.7927 Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.122855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.112720 restraints weight = 12772.320| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.58 r_work: 0.3704 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3522 Z= 0.196 Angle : 0.507 3.570 4710 Z= 0.254 Chirality : 0.050 0.138 528 Planarity : 0.002 0.014 600 Dihedral : 4.404 14.051 468 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.26 % Allowed : 18.18 % 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: -1.47 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.005 0.001 TYR A 310 PHE 0.006 0.001 PHE D 378 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 3522) covalent geometry : angle 0.50721 ( 4710) hydrogen bonds : bond 0.02210 ( 74) hydrogen bonds : angle 4.27273 ( 222) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.146 Fit side-chains REVERT: F 345 ASP cc_start: 0.8496 (m-30) cc_final: 0.8277 (m-30) REVERT: F 351 GLN cc_start: 0.8667 (tt0) cc_final: 0.8455 (tt0) REVERT: A 338 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: B 338 GLU cc_start: 0.7492 (mp0) cc_final: 0.7152 (mt-10) REVERT: B 349 ARG cc_start: 0.8440 (mtt180) cc_final: 0.6876 (mmp-170) REVERT: C 349 ARG cc_start: 0.8250 (mtt180) cc_final: 0.6715 (mmp80) REVERT: D 348 ASP cc_start: 0.8461 (t70) cc_final: 0.8117 (t0) REVERT: D 349 ARG cc_start: 0.8180 (mtt180) cc_final: 0.6460 (pmt-80) REVERT: E 349 ARG cc_start: 0.8114 (mtt180) cc_final: 0.6423 (pmt-80) outliers start: 5 outliers final: 3 residues processed: 61 average time/residue: 1.3435 time to fit residues: 83.9818 Evaluate side-chains 60 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.123629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.113606 restraints weight = 12597.675| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.57 r_work: 0.3720 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3522 Z= 0.151 Angle : 0.485 3.578 4710 Z= 0.241 Chirality : 0.050 0.134 528 Planarity : 0.002 0.014 600 Dihedral : 4.307 13.643 468 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.26 % Allowed : 17.93 % Favored : 80.81 % 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: -1.54 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.005 0.001 TYR A 310 PHE 0.006 0.001 PHE B 378 HIS 0.002 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3522) covalent geometry : angle 0.48511 ( 4710) hydrogen bonds : bond 0.01943 ( 74) hydrogen bonds : angle 4.17791 ( 222) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.126 Fit side-chains REVERT: F 345 ASP cc_start: 0.8509 (m-30) cc_final: 0.8283 (m-30) REVERT: F 351 GLN cc_start: 0.8673 (tt0) cc_final: 0.8469 (tt0) REVERT: A 338 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: B 338 GLU cc_start: 0.7456 (mp0) cc_final: 0.7109 (mt-10) REVERT: B 349 ARG cc_start: 0.8419 (mtt180) cc_final: 0.6836 (mmp80) REVERT: C 349 ARG cc_start: 0.8262 (mtt180) cc_final: 0.6761 (mmp-170) REVERT: D 348 ASP cc_start: 0.8468 (t70) cc_final: 0.8138 (t0) REVERT: D 349 ARG cc_start: 0.8192 (mtt180) cc_final: 0.6488 (pmt-80) REVERT: E 349 ARG cc_start: 0.8167 (mtt180) cc_final: 0.6381 (pmt-80) outliers start: 5 outliers final: 4 residues processed: 63 average time/residue: 1.3284 time to fit residues: 85.7793 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.124757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.115540 restraints weight = 13470.448| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.53 r_work: 0.3757 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3522 Z= 0.094 Angle : 0.458 3.460 4710 Z= 0.225 Chirality : 0.050 0.125 528 Planarity : 0.002 0.013 600 Dihedral : 4.077 12.951 468 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.01 % Allowed : 17.93 % Favored : 81.06 % 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: -1.48 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.005 0.001 TYR A 310 PHE 0.005 0.001 PHE B 378 HIS 0.001 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 3522) covalent geometry : angle 0.45797 ( 4710) hydrogen bonds : bond 0.01611 ( 74) hydrogen bonds : angle 3.94807 ( 222) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.244 Fit side-chains REVERT: B 338 GLU cc_start: 0.7431 (mp0) cc_final: 0.7111 (mt-10) REVERT: B 349 ARG cc_start: 0.8392 (mtt180) cc_final: 0.6874 (mmp80) REVERT: C 349 ARG cc_start: 0.8239 (mtt180) cc_final: 0.6771 (mmp-170) REVERT: D 348 ASP cc_start: 0.8434 (t70) cc_final: 0.8201 (t0) REVERT: D 349 ARG cc_start: 0.8225 (mtt180) cc_final: 0.6534 (pmt-80) REVERT: E 349 ARG cc_start: 0.8196 (mtt180) cc_final: 0.6420 (pmt-80) REVERT: E 351 GLN cc_start: 0.8659 (tt0) cc_final: 0.8438 (tt0) outliers start: 4 outliers final: 4 residues processed: 61 average time/residue: 1.3596 time to fit residues: 85.0703 Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN A 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.124786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.114702 restraints weight = 12670.974| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.57 r_work: 0.3738 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 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 : 0.003 0.018 3522 Z= 0.123 Angle : 0.463 3.429 4710 Z= 0.229 Chirality : 0.050 0.132 528 Planarity : 0.002 0.012 600 Dihedral : 4.114 13.024 468 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.01 % Allowed : 17.68 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.51 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.005 0.001 TYR A 310 PHE 0.006 0.001 PHE B 378 HIS 0.002 0.000 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3522) covalent geometry : angle 0.46347 ( 4710) hydrogen bonds : bond 0.01780 ( 74) hydrogen bonds : angle 3.99956 ( 222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3146.73 seconds wall clock time: 53 minutes 54.20 seconds (3234.20 seconds total)