Starting phenix.real_space_refine on Fri Aug 22 19:04:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8v_18262/08_2025/8q8v_18262.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8v_18262/08_2025/8q8v_18262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q8v_18262/08_2025/8q8v_18262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8v_18262/08_2025/8q8v_18262.map" model { file = "/net/cci-nas-00/data/ceres_data/8q8v_18262/08_2025/8q8v_18262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8v_18262/08_2025/8q8v_18262.cif" } resolution = 3.8 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 H 3588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7032 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 1.28, per 1000 atoms: 0.18 Number of scatterers: 7032 At special positions: 0 Unit cell: (146.672, 119.48, 50.264, 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 642 8.00 N 636 7.00 C 2160 6.00 H 3588 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: 0.56 Conformation dependent library (CDL) restraints added in 231.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 39.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.410A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.983A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.199A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N SER C 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLY A 323 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.258A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.531A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.961A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 353 removed outlier: 6.278A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.340A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 373 removed outlier: 6.436A pdb=" N LYS A 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR E 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU A 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.409A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.983A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.199A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.257A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 337 through 339 removed outlier: 6.532A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.961A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 353 removed outlier: 6.278A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LYS F 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER B 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.340A pdb=" N ASP B 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N THR D 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE B 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 369 through 373 removed outlier: 6.437A pdb=" N LYS B 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR F 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU B 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) 60 hydrogen bonds defined for protein. 180 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: 1.40 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 3582 1.12 - 1.29: 573 1.29 - 1.47: 1092 1.47 - 1.64: 1833 1.64 - 1.82: 6 Bond restraints: 7086 Sorted by residual: bond pdb=" CE2 PHE B 346 " pdb=" HE2 PHE B 346 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" NH1 ARG B 349 " pdb="HH11 ARG B 349 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" CE1 HIS B 330 " pdb=" HE1 HIS B 330 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N GLU B 338 " pdb=" H GLU B 338 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.74e+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 5.72e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 10615 2.47 - 4.94: 1775 4.94 - 7.41: 479 7.41 - 9.88: 31 9.88 - 12.35: 12 Bond angle restraints: 12912 Sorted by residual: angle pdb=" CA LYS A 331 " pdb=" C LYS A 331 " pdb=" N PRO A 332 " ideal model delta sigma weight residual 118.16 123.34 -5.18 7.00e-01 2.04e+00 5.47e+01 angle pdb=" C ASP E 348 " pdb=" N ARG E 349 " pdb=" CA ARG E 349 " ideal model delta sigma weight residual 121.31 129.69 -8.38 1.49e+00 4.50e-01 3.16e+01 angle pdb=" C ASP F 348 " pdb=" N ARG F 349 " pdb=" CA ARG F 349 " ideal model delta sigma weight residual 121.31 129.65 -8.34 1.49e+00 4.50e-01 3.13e+01 angle pdb=" C LYS E 343 " pdb=" N LEU E 344 " pdb=" CA LEU E 344 " ideal model delta sigma weight residual 120.71 128.24 -7.53 1.42e+00 4.96e-01 2.81e+01 angle pdb=" C LYS F 343 " pdb=" N LEU F 344 " pdb=" CA LEU F 344 " ideal model delta sigma weight residual 120.71 128.22 -7.51 1.42e+00 4.96e-01 2.80e+01 ... (remaining 12907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 2836 15.61 - 31.21: 200 31.21 - 46.82: 98 46.82 - 62.43: 82 62.43 - 78.03: 48 Dihedral angle restraints: 3264 sinusoidal: 1866 harmonic: 1398 Sorted by residual: dihedral pdb=" CA ASN D 359 " pdb=" C ASN D 359 " pdb=" N ILE D 360 " pdb=" CA ILE D 360 " ideal model delta harmonic sigma weight residual -180.00 -152.74 -27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA ASN C 359 " pdb=" C ASN C 359 " pdb=" N ILE C 360 " pdb=" CA ILE C 360 " ideal model delta harmonic sigma weight residual -180.00 -152.77 -27.23 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA SER C 341 " pdb=" C SER C 341 " pdb=" N GLU C 342 " pdb=" CA GLU C 342 " ideal model delta harmonic sigma weight residual -180.00 -154.37 -25.63 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 309 0.070 - 0.139: 170 0.139 - 0.209: 41 0.209 - 0.279: 6 0.279 - 0.348: 2 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS E 343 " pdb=" N LYS E 343 " pdb=" C LYS E 343 " pdb=" CB LYS E 343 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA LYS F 343 " pdb=" N LYS F 343 " pdb=" C LYS F 343 " pdb=" CB LYS F 343 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA LYS F 331 " pdb=" N LYS F 331 " pdb=" C LYS F 331 " pdb=" CB LYS F 331 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 525 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " -0.161 2.00e-02 2.50e+03 7.45e-02 1.66e+02 pdb=" CG TYR E 310 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " 0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.063 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " -0.161 2.00e-02 2.50e+03 pdb=" HD1 TYR E 310 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR E 310 " 0.052 2.00e-02 2.50e+03 pdb=" HE1 TYR E 310 " 0.039 2.00e-02 2.50e+03 pdb=" HE2 TYR E 310 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " -0.160 2.00e-02 2.50e+03 7.43e-02 1.66e+02 pdb=" CG TYR F 310 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " 0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " 0.063 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " 0.031 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " -0.160 2.00e-02 2.50e+03 pdb=" HD1 TYR F 310 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR F 310 " 0.051 2.00e-02 2.50e+03 pdb=" HE1 TYR F 310 " 0.039 2.00e-02 2.50e+03 pdb=" HE2 TYR F 310 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 346 " -0.144 2.00e-02 2.50e+03 5.79e-02 1.01e+02 pdb=" CG PHE B 346 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 346 " 0.066 2.00e-02 2.50e+03 pdb=" CD2 PHE B 346 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE B 346 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 PHE B 346 " 0.028 2.00e-02 2.50e+03 pdb=" CZ PHE B 346 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE B 346 " 0.039 2.00e-02 2.50e+03 pdb=" HD2 PHE B 346 " 0.024 2.00e-02 2.50e+03 pdb=" HE1 PHE B 346 " -0.028 2.00e-02 2.50e+03 pdb=" HE2 PHE B 346 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B 346 " -0.085 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 435 2.16 - 2.77: 11926 2.77 - 3.38: 19125 3.38 - 3.99: 23717 3.99 - 4.60: 34447 Nonbonded interactions: 89650 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.551 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.551 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.561 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.561 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.619 2.450 ... (remaining 89645 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.290 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: 0.030 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.910 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 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 : 0.012 0.040 3498 Z= 0.785 Angle : 1.996 8.922 4680 Z= 1.302 Chirality : 0.087 0.348 528 Planarity : 0.013 0.087 594 Dihedral : 12.459 78.032 1344 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.51 % 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: -2.75 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 349 TYR 0.149 0.029 TYR E 310 PHE 0.089 0.028 PHE E 346 HIS 0.007 0.003 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.01199 ( 3498) covalent geometry : angle 1.99611 ( 4680) hydrogen bonds : bond 0.10689 ( 60) hydrogen bonds : angle 6.76632 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 314 ASP cc_start: 0.7689 (t0) cc_final: 0.7430 (t0) REVERT: C 338 GLU cc_start: 0.7117 (tt0) cc_final: 0.6672 (tm-30) REVERT: E 375 LYS cc_start: 0.7172 (tttt) cc_final: 0.6917 (tttm) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2388 time to fit residues: 26.9521 Evaluate side-chains 62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN D 327 ASN F 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.138829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.115511 restraints weight = 15328.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.118771 restraints weight = 5200.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.120831 restraints weight = 2672.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.121939 restraints weight = 1791.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.122635 restraints weight = 1456.239| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 3498 Z= 0.295 Angle : 0.804 6.373 4680 Z= 0.430 Chirality : 0.050 0.142 528 Planarity : 0.006 0.040 594 Dihedral : 8.045 23.786 462 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.01 % Allowed : 6.31 % Favored : 92.68 % 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: -2.68 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 379 TYR 0.016 0.003 TYR F 310 PHE 0.012 0.002 PHE A 378 HIS 0.006 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00622 ( 3498) covalent geometry : angle 0.80416 ( 4680) hydrogen bonds : bond 0.02746 ( 60) hydrogen bonds : angle 5.98659 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8920 (m-40) cc_final: 0.8640 (m110) REVERT: A 375 LYS cc_start: 0.8213 (tttt) cc_final: 0.8004 (tttm) REVERT: C 327 ASN cc_start: 0.8187 (m-40) cc_final: 0.7958 (m110) REVERT: C 338 GLU cc_start: 0.7389 (tt0) cc_final: 0.6930 (tm-30) REVERT: E 349 ARG cc_start: 0.6953 (mtm180) cc_final: 0.5817 (mmm160) REVERT: B 375 LYS cc_start: 0.8223 (tttt) cc_final: 0.7877 (tttm) REVERT: D 327 ASN cc_start: 0.8315 (m110) cc_final: 0.7923 (m110) REVERT: F 375 LYS cc_start: 0.8499 (tttt) cc_final: 0.8146 (tttm) outliers start: 4 outliers final: 2 residues processed: 78 average time/residue: 0.2199 time to fit residues: 19.3620 Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain F residue 306 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 368 ASN C 327 ASN C 368 ASN E 327 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.133527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.109887 restraints weight = 15051.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.113302 restraints weight = 5120.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.115458 restraints weight = 2637.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.116776 restraints weight = 1752.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.117308 restraints weight = 1374.864| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3498 Z= 0.180 Angle : 0.663 4.955 4680 Z= 0.352 Chirality : 0.052 0.135 528 Planarity : 0.005 0.036 594 Dihedral : 7.060 22.059 462 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.51 % Allowed : 9.34 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 379 TYR 0.014 0.003 TYR F 310 PHE 0.011 0.003 PHE E 346 HIS 0.004 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 3498) covalent geometry : angle 0.66330 ( 4680) hydrogen bonds : bond 0.02233 ( 60) hydrogen bonds : angle 5.42858 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8979 (m110) cc_final: 0.8743 (m110) REVERT: A 375 LYS cc_start: 0.8107 (tttt) cc_final: 0.7842 (tttp) REVERT: C 327 ASN cc_start: 0.8009 (m110) cc_final: 0.7791 (m110) REVERT: E 349 ARG cc_start: 0.6804 (mtm180) cc_final: 0.5807 (mmm160) REVERT: F 340 LYS cc_start: 0.5809 (tptm) cc_final: 0.5153 (mtpt) REVERT: F 375 LYS cc_start: 0.8506 (tttt) cc_final: 0.8173 (tttm) outliers start: 2 outliers final: 1 residues processed: 68 average time/residue: 0.2022 time to fit residues: 15.4372 Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 306 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 39 optimal weight: 0.0770 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 overall best weight: 3.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.130420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.107532 restraints weight = 15797.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.110768 restraints weight = 5387.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.112814 restraints weight = 2782.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.113951 restraints weight = 1843.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.114745 restraints weight = 1474.575| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3498 Z= 0.191 Angle : 0.618 5.425 4680 Z= 0.325 Chirality : 0.051 0.133 528 Planarity : 0.005 0.035 594 Dihedral : 6.394 21.092 462 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.51 % Allowed : 9.09 % Favored : 90.40 % 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: -2.88 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.014 0.002 TYR F 310 PHE 0.007 0.002 PHE E 346 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 3498) covalent geometry : angle 0.61762 ( 4680) hydrogen bonds : bond 0.01913 ( 60) hydrogen bonds : angle 5.21453 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8838 (m110) cc_final: 0.8596 (m110) REVERT: A 375 LYS cc_start: 0.8223 (tttt) cc_final: 0.7960 (tttp) REVERT: C 327 ASN cc_start: 0.8126 (m110) cc_final: 0.7849 (m110) REVERT: E 338 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7194 (tm-30) REVERT: E 349 ARG cc_start: 0.6981 (mtm180) cc_final: 0.5844 (mmm160) REVERT: B 343 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6766 (ttmm) REVERT: F 314 ASP cc_start: 0.6405 (t0) cc_final: 0.5957 (t0) REVERT: F 340 LYS cc_start: 0.5938 (tptm) cc_final: 0.5383 (mtpt) REVERT: F 375 LYS cc_start: 0.8551 (tttt) cc_final: 0.8270 (tttm) outliers start: 2 outliers final: 1 residues processed: 72 average time/residue: 0.1947 time to fit residues: 15.9949 Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain F residue 306 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.133518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.110566 restraints weight = 15408.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.113933 restraints weight = 5158.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.115906 restraints weight = 2627.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.117251 restraints weight = 1768.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.117951 restraints weight = 1384.650| |-----------------------------------------------------------------------------| r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.6154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3498 Z= 0.111 Angle : 0.559 4.497 4680 Z= 0.290 Chirality : 0.052 0.132 528 Planarity : 0.004 0.036 594 Dihedral : 5.763 19.603 462 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.76 % Allowed : 10.86 % Favored : 88.38 % 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: -2.71 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 379 TYR 0.008 0.002 TYR C 310 PHE 0.008 0.002 PHE E 346 HIS 0.003 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3498) covalent geometry : angle 0.55870 ( 4680) hydrogen bonds : bond 0.01647 ( 60) hydrogen bonds : angle 4.79588 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8745 (m110) cc_final: 0.8507 (m110) REVERT: A 375 LYS cc_start: 0.8119 (tttt) cc_final: 0.7882 (tttp) REVERT: C 317 LYS cc_start: 0.8482 (mptt) cc_final: 0.8194 (mttp) REVERT: C 327 ASN cc_start: 0.8075 (m110) cc_final: 0.7847 (m-40) REVERT: C 379 ARG cc_start: 0.7435 (mtp85) cc_final: 0.7147 (mtp85) REVERT: E 349 ARG cc_start: 0.6966 (mtm180) cc_final: 0.5795 (mmm160) REVERT: B 375 LYS cc_start: 0.8133 (tttt) cc_final: 0.7848 (tttm) REVERT: F 340 LYS cc_start: 0.5803 (tptm) cc_final: 0.5333 (mtpt) REVERT: F 375 LYS cc_start: 0.8488 (tttt) cc_final: 0.8192 (tttm) outliers start: 3 outliers final: 1 residues processed: 70 average time/residue: 0.2130 time to fit residues: 16.7608 Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 306 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 32 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.132849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.109942 restraints weight = 15507.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.113241 restraints weight = 5237.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.115323 restraints weight = 2701.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.116560 restraints weight = 1779.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.117292 restraints weight = 1405.922| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.6429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3498 Z= 0.117 Angle : 0.539 4.585 4680 Z= 0.279 Chirality : 0.051 0.129 528 Planarity : 0.004 0.038 594 Dihedral : 5.429 18.662 462 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.51 % Allowed : 12.37 % Favored : 87.12 % 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: -2.69 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 379 TYR 0.009 0.001 TYR C 310 PHE 0.017 0.002 PHE C 378 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 3498) covalent geometry : angle 0.53879 ( 4680) hydrogen bonds : bond 0.01500 ( 60) hydrogen bonds : angle 4.47068 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8729 (m110) cc_final: 0.8482 (m110) REVERT: A 375 LYS cc_start: 0.8205 (tttt) cc_final: 0.7966 (tttp) REVERT: C 317 LYS cc_start: 0.8479 (mptt) cc_final: 0.8213 (mttp) REVERT: C 327 ASN cc_start: 0.8006 (m110) cc_final: 0.7773 (m-40) REVERT: E 340 LYS cc_start: 0.7341 (tptm) cc_final: 0.6139 (mttt) REVERT: E 349 ARG cc_start: 0.7053 (mtm180) cc_final: 0.5874 (mmm160) REVERT: B 375 LYS cc_start: 0.8183 (tttt) cc_final: 0.7862 (tttp) REVERT: F 340 LYS cc_start: 0.5805 (tptm) cc_final: 0.5466 (mtpt) REVERT: F 375 LYS cc_start: 0.8457 (tttt) cc_final: 0.8178 (tttm) outliers start: 2 outliers final: 2 residues processed: 68 average time/residue: 0.2229 time to fit residues: 17.0739 Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.123017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.101124 restraints weight = 16789.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.104061 restraints weight = 5869.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.105963 restraints weight = 3072.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.107183 restraints weight = 2060.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.107778 restraints weight = 1624.376| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.6920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 3498 Z= 0.305 Angle : 0.701 5.696 4680 Z= 0.375 Chirality : 0.053 0.136 528 Planarity : 0.005 0.034 594 Dihedral : 6.285 20.560 462 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 0.51 % Allowed : 12.37 % Favored : 87.12 % 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: -3.60 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 349 TYR 0.024 0.004 TYR F 310 PHE 0.018 0.003 PHE C 378 HIS 0.008 0.003 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00632 ( 3498) covalent geometry : angle 0.70093 ( 4680) hydrogen bonds : bond 0.02262 ( 60) hydrogen bonds : angle 5.29024 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LYS cc_start: 0.8413 (tttt) cc_final: 0.8039 (tttp) REVERT: C 317 LYS cc_start: 0.8573 (mptt) cc_final: 0.8302 (mttp) REVERT: C 327 ASN cc_start: 0.8071 (m110) cc_final: 0.7847 (m110) REVERT: E 349 ARG cc_start: 0.7428 (mtm180) cc_final: 0.6183 (mmp80) REVERT: B 336 GLN cc_start: 0.7962 (tt0) cc_final: 0.7650 (mp10) REVERT: D 336 GLN cc_start: 0.7815 (tt0) cc_final: 0.7408 (mp10) REVERT: F 340 LYS cc_start: 0.6301 (tptm) cc_final: 0.5896 (mtpt) REVERT: F 368 ASN cc_start: 0.8457 (m-40) cc_final: 0.8069 (m-40) REVERT: F 375 LYS cc_start: 0.8556 (tttt) cc_final: 0.8299 (tttm) outliers start: 2 outliers final: 2 residues processed: 74 average time/residue: 0.2134 time to fit residues: 17.9224 Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.4300 r_free = 0.4300 target = 0.127969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.105494 restraints weight = 15938.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.108687 restraints weight = 5406.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.110740 restraints weight = 2784.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.111879 restraints weight = 1848.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.112670 restraints weight = 1478.784| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.7044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3498 Z= 0.125 Angle : 0.584 4.876 4680 Z= 0.302 Chirality : 0.052 0.132 528 Planarity : 0.004 0.041 594 Dihedral : 5.569 19.163 462 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.51 % Allowed : 14.14 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.28 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.005 0.001 TYR B 310 PHE 0.015 0.002 PHE C 378 HIS 0.004 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3498) covalent geometry : angle 0.58360 ( 4680) hydrogen bonds : bond 0.01511 ( 60) hydrogen bonds : angle 4.66692 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LYS cc_start: 0.8260 (tttt) cc_final: 0.7918 (tttp) REVERT: C 317 LYS cc_start: 0.8530 (mptt) cc_final: 0.8269 (mttp) REVERT: E 349 ARG cc_start: 0.7300 (mtm180) cc_final: 0.6065 (mmp80) REVERT: F 340 LYS cc_start: 0.6190 (tptm) cc_final: 0.5861 (mtpt) REVERT: F 368 ASN cc_start: 0.8467 (m-40) cc_final: 0.8000 (m-40) REVERT: F 375 LYS cc_start: 0.8397 (tttt) cc_final: 0.8093 (tttm) outliers start: 2 outliers final: 2 residues processed: 70 average time/residue: 0.2130 time to fit residues: 16.9783 Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 0.0470 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.131784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.110521 restraints weight = 15492.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.113830 restraints weight = 5146.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.115879 restraints weight = 2629.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.117102 restraints weight = 1747.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.117502 restraints weight = 1390.194| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.7212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3498 Z= 0.140 Angle : 0.577 4.904 4680 Z= 0.297 Chirality : 0.052 0.133 528 Planarity : 0.004 0.038 594 Dihedral : 5.383 18.865 462 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.76 % Allowed : 14.14 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.25 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 379 TYR 0.009 0.002 TYR F 310 PHE 0.016 0.002 PHE C 378 HIS 0.003 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3498) covalent geometry : angle 0.57748 ( 4680) hydrogen bonds : bond 0.01524 ( 60) hydrogen bonds : angle 4.50655 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LYS cc_start: 0.8377 (tttt) cc_final: 0.8052 (tttp) REVERT: C 317 LYS cc_start: 0.8599 (mptt) cc_final: 0.8303 (mttp) REVERT: E 340 LYS cc_start: 0.7552 (tptm) cc_final: 0.6479 (mttt) REVERT: E 349 ARG cc_start: 0.7239 (mtm180) cc_final: 0.6146 (mmp80) REVERT: F 340 LYS cc_start: 0.6253 (tptm) cc_final: 0.6017 (mtpt) REVERT: F 368 ASN cc_start: 0.8421 (m-40) cc_final: 0.7943 (m-40) REVERT: F 375 LYS cc_start: 0.8391 (tttt) cc_final: 0.8113 (tttm) outliers start: 3 outliers final: 3 residues processed: 69 average time/residue: 0.2044 time to fit residues: 16.0685 Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.131816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.110344 restraints weight = 15459.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.113732 restraints weight = 4970.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.115837 restraints weight = 2507.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.117126 restraints weight = 1653.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.117722 restraints weight = 1299.892| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.7392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3498 Z= 0.142 Angle : 0.564 4.747 4680 Z= 0.290 Chirality : 0.052 0.129 528 Planarity : 0.004 0.041 594 Dihedral : 5.239 18.231 462 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.76 % Allowed : 13.64 % Favored : 85.61 % 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: -3.28 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 379 TYR 0.008 0.002 TYR F 310 PHE 0.012 0.002 PHE C 378 HIS 0.003 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3498) covalent geometry : angle 0.56360 ( 4680) hydrogen bonds : bond 0.01448 ( 60) hydrogen bonds : angle 4.46599 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LYS cc_start: 0.8299 (tttt) cc_final: 0.7955 (tttp) REVERT: C 317 LYS cc_start: 0.8625 (mptt) cc_final: 0.8366 (mttp) REVERT: E 340 LYS cc_start: 0.7552 (tptm) cc_final: 0.6504 (mttt) REVERT: E 349 ARG cc_start: 0.7244 (mtm180) cc_final: 0.6074 (mmp80) REVERT: F 340 LYS cc_start: 0.6430 (tptm) cc_final: 0.6170 (mtpt) REVERT: F 368 ASN cc_start: 0.8417 (m-40) cc_final: 0.7964 (m-40) REVERT: F 375 LYS cc_start: 0.8329 (tttt) cc_final: 0.8058 (tttm) outliers start: 3 outliers final: 3 residues processed: 69 average time/residue: 0.1953 time to fit residues: 15.2783 Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.130399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.109363 restraints weight = 15494.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.112632 restraints weight = 5183.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.114618 restraints weight = 2639.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.115912 restraints weight = 1763.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.116466 restraints weight = 1382.833| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.7579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3498 Z= 0.165 Angle : 0.590 5.297 4680 Z= 0.303 Chirality : 0.052 0.142 528 Planarity : 0.004 0.037 594 Dihedral : 5.250 18.525 462 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 0.76 % Allowed : 13.64 % Favored : 85.61 % 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: -3.45 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 379 TYR 0.012 0.002 TYR B 310 PHE 0.014 0.002 PHE C 378 HIS 0.003 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3498) covalent geometry : angle 0.58953 ( 4680) hydrogen bonds : bond 0.01581 ( 60) hydrogen bonds : angle 4.53035 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1449.23 seconds wall clock time: 25 minutes 21.75 seconds (1521.75 seconds total)