Starting phenix.real_space_refine on Wed Mar 12 02:25:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8v_18262/03_2025/8q8v_18262.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8v_18262/03_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_18262/03_2025/8q8v_18262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8v_18262/03_2025/8q8v_18262.map" model { file = "/net/cci-nas-00/data/ceres_data/8q8v_18262/03_2025/8q8v_18262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8v_18262/03_2025/8q8v_18262.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.65, per 1000 atoms: 0.80 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: 1.98 Conformation dependent library (CDL) restraints added in 639.5 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 39.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 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: 2.21 Time building geometry restraints manager: 2.30 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: 0.01 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 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: 4.250 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: 0.120 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.090 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.670 ------------------------------------------------------------------------------- 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= 0.810 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.007 0.003 HIS A 362 PHE 0.089 0.028 PHE E 346 TYR 0.149 0.029 TYR E 310 ARG 0.005 0.001 ARG A 349 *********************** 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 : 0.596 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: symmetry clash REVERT: C 314 ASP cc_start: 0.7689 (t0) cc_final: 0.7426 (t0) REVERT: C 338 GLU cc_start: 0.7117 (tt0) cc_final: 0.6669 (tm-30) REVERT: E 375 LYS cc_start: 0.7172 (tttt) cc_final: 0.6914 (tttm) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.5596 time to fit residues: 63.3544 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN D 327 ASN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.134663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.111617 restraints weight = 15186.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.114803 restraints weight = 5295.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.116752 restraints weight = 2755.511| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 3498 Z= 0.514 Angle : 0.858 6.603 4680 Z= 0.469 Chirality : 0.052 0.145 528 Planarity : 0.006 0.037 594 Dihedral : 8.311 24.966 462 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.76 % Allowed : 6.31 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 374 PHE 0.014 0.003 PHE A 378 TYR 0.022 0.004 TYR F 310 ARG 0.006 0.001 ARG C 379 *********************** 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 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8991 (m-40) cc_final: 0.8716 (m110) REVERT: A 375 LYS cc_start: 0.8358 (tttt) cc_final: 0.8141 (tttm) REVERT: C 327 ASN cc_start: 0.8287 (m-40) cc_final: 0.8083 (m110) REVERT: C 338 GLU cc_start: 0.7506 (tt0) cc_final: 0.6921 (tm-30) REVERT: E 349 ARG cc_start: 0.6919 (mtm180) cc_final: 0.5811 (mmm160) REVERT: B 375 LYS cc_start: 0.8359 (tttt) cc_final: 0.8043 (tttm) REVERT: F 375 LYS cc_start: 0.8541 (tttt) cc_final: 0.8204 (tttm) outliers start: 3 outliers final: 1 residues processed: 76 average time/residue: 0.5875 time to fit residues: 50.1689 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 : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 20 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.4426 r_free = 0.4426 target = 0.137767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.114158 restraints weight = 14750.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.117680 restraints weight = 5094.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.119714 restraints weight = 2631.605| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3498 Z= 0.196 Angle : 0.623 4.576 4680 Z= 0.327 Chirality : 0.053 0.134 528 Planarity : 0.004 0.033 594 Dihedral : 6.902 21.362 462 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.51 % Allowed : 7.58 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.020 0.003 PHE C 378 TYR 0.012 0.002 TYR C 310 ARG 0.005 0.000 ARG C 379 *********************** 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 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8834 (m-40) cc_final: 0.8567 (m110) REVERT: A 375 LYS cc_start: 0.8095 (tttt) cc_final: 0.7865 (tttp) REVERT: C 327 ASN cc_start: 0.8143 (m-40) cc_final: 0.7882 (m110) REVERT: E 349 ARG cc_start: 0.6705 (mtm180) cc_final: 0.5707 (mmm160) REVERT: B 375 LYS cc_start: 0.8180 (tttt) cc_final: 0.7857 (tttm) REVERT: F 375 LYS cc_start: 0.8484 (tttt) cc_final: 0.8145 (tttm) outliers start: 2 outliers final: 1 residues processed: 64 average time/residue: 0.5921 time to fit residues: 42.9054 Evaluate side-chains 59 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 20 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN C 327 ASN E 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.132971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.110168 restraints weight = 15416.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.113477 restraints weight = 5380.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.115532 restraints weight = 2814.673| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3498 Z= 0.274 Angle : 0.607 5.071 4680 Z= 0.319 Chirality : 0.051 0.131 528 Planarity : 0.005 0.036 594 Dihedral : 6.512 20.881 462 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.76 % Allowed : 7.83 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 374 PHE 0.013 0.002 PHE C 378 TYR 0.013 0.003 TYR F 310 ARG 0.002 0.000 ARG F 349 *********************** 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 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 ASN cc_start: 0.9032 (m110) cc_final: 0.8780 (m110) REVERT: A 375 LYS cc_start: 0.8218 (tttt) cc_final: 0.7967 (tttp) REVERT: C 327 ASN cc_start: 0.8013 (m110) cc_final: 0.7792 (m110) REVERT: E 349 ARG cc_start: 0.6862 (mtm180) cc_final: 0.5800 (mmm160) REVERT: F 375 LYS cc_start: 0.8560 (tttt) cc_final: 0.8259 (tttm) outliers start: 3 outliers final: 2 residues processed: 69 average time/residue: 0.5646 time to fit residues: 44.1130 Evaluate side-chains 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 324 SER 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 33 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.129090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.106591 restraints weight = 15858.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.109724 restraints weight = 5479.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.111690 restraints weight = 2839.787| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.6249 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= 0.277 Angle : 0.606 5.002 4680 Z= 0.319 Chirality : 0.051 0.130 528 Planarity : 0.005 0.036 594 Dihedral : 6.214 20.485 462 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.51 % Allowed : 12.12 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 374 PHE 0.021 0.002 PHE C 378 TYR 0.014 0.003 TYR F 310 ARG 0.002 0.000 ARG C 379 *********************** 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: 2 poor density : 69 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8948 (m110) cc_final: 0.8720 (m110) REVERT: A 375 LYS cc_start: 0.8220 (tttt) cc_final: 0.7978 (tttp) REVERT: C 317 LYS cc_start: 0.8503 (mptt) cc_final: 0.8162 (mttp) REVERT: C 327 ASN cc_start: 0.8166 (m110) cc_final: 0.7917 (m110) REVERT: E 349 ARG cc_start: 0.7018 (mtm180) cc_final: 0.5907 (mmm160) REVERT: B 375 LYS cc_start: 0.8386 (tttt) cc_final: 0.8074 (tttp) REVERT: F 314 ASP cc_start: 0.6641 (t0) cc_final: 0.6329 (t0) REVERT: F 375 LYS cc_start: 0.8521 (tttt) cc_final: 0.8259 (tttm) outliers start: 2 outliers final: 1 residues processed: 70 average time/residue: 0.5871 time to fit residues: 46.4734 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 : 0.546 ------------------------------------------------------------------------------- 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 7 optimal weight: 0.4980 chunk 25 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 = 0.4362 r_free = 0.4362 target = 0.131884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.109137 restraints weight = 15587.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.112419 restraints weight = 5243.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.114481 restraints weight = 2679.303| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.6450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3498 Z= 0.181 Angle : 0.561 4.547 4680 Z= 0.289 Chirality : 0.052 0.129 528 Planarity : 0.004 0.037 594 Dihedral : 5.670 19.435 462 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.51 % Allowed : 12.63 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.008 0.002 PHE E 346 TYR 0.012 0.002 TYR C 310 ARG 0.002 0.000 ARG C 379 *********************** 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 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8805 (m110) cc_final: 0.8367 (m110) REVERT: A 375 LYS cc_start: 0.8166 (tttt) cc_final: 0.7925 (tttp) REVERT: C 317 LYS cc_start: 0.8484 (mptt) cc_final: 0.8203 (mttp) REVERT: E 349 ARG cc_start: 0.7018 (mtm180) cc_final: 0.5837 (mmm160) REVERT: F 314 ASP cc_start: 0.6361 (t0) cc_final: 0.6069 (t0) REVERT: F 375 LYS cc_start: 0.8453 (tttt) cc_final: 0.8164 (tttm) outliers start: 2 outliers final: 2 residues processed: 69 average time/residue: 0.6037 time to fit residues: 47.0450 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 : 0.618 ------------------------------------------------------------------------------- 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 32 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 ASN E 329 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.127948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.106338 restraints weight = 15602.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.109531 restraints weight = 5231.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.111423 restraints weight = 2676.938| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.6825 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= 0.266 Angle : 0.583 5.010 4680 Z= 0.305 Chirality : 0.052 0.131 528 Planarity : 0.005 0.035 594 Dihedral : 5.724 19.551 462 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.51 % Allowed : 13.13 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 374 PHE 0.007 0.002 PHE C 378 TYR 0.013 0.002 TYR F 310 ARG 0.003 0.001 ARG C 379 *********************** 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 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8736 (m110) cc_final: 0.8484 (m110) REVERT: A 375 LYS cc_start: 0.8315 (tttt) cc_final: 0.7974 (tttp) REVERT: C 317 LYS cc_start: 0.8597 (mptt) cc_final: 0.8305 (mttp) REVERT: E 349 ARG cc_start: 0.7269 (mtm180) cc_final: 0.6043 (mmp80) REVERT: F 368 ASN cc_start: 0.8462 (m-40) cc_final: 0.7981 (m-40) REVERT: F 375 LYS cc_start: 0.8472 (tttt) cc_final: 0.8190 (tttm) outliers start: 2 outliers final: 2 residues processed: 69 average time/residue: 0.5702 time to fit residues: 44.5715 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 : 0.604 ------------------------------------------------------------------------------- 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 39 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.4270 r_free = 0.4270 target = 0.125268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.104279 restraints weight = 16344.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.107247 restraints weight = 5649.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.109125 restraints weight = 2954.955| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.7386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 3498 Z= 0.425 Angle : 0.699 5.450 4680 Z= 0.374 Chirality : 0.053 0.136 528 Planarity : 0.005 0.034 594 Dihedral : 6.271 20.625 462 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % Rotamer: Outliers : 0.51 % Allowed : 14.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 329 PHE 0.026 0.003 PHE B 346 TYR 0.022 0.004 TYR F 310 ARG 0.003 0.001 ARG E 349 *********************** 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 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 375 LYS cc_start: 0.8512 (tttt) cc_final: 0.8180 (tttp) REVERT: C 317 LYS cc_start: 0.8664 (mptt) cc_final: 0.8336 (mttp) REVERT: E 340 LYS cc_start: 0.7745 (tptm) cc_final: 0.6677 (mttt) REVERT: E 349 ARG cc_start: 0.7523 (mtm180) cc_final: 0.6135 (mmp80) REVERT: B 336 GLN cc_start: 0.8049 (tt0) cc_final: 0.7810 (mp10) REVERT: B 375 LYS cc_start: 0.8490 (tttt) cc_final: 0.8223 (tttp) REVERT: F 314 ASP cc_start: 0.6823 (t0) cc_final: 0.6493 (t0) REVERT: F 368 ASN cc_start: 0.8478 (m-40) cc_final: 0.8051 (m-40) REVERT: F 375 LYS cc_start: 0.8466 (tttt) cc_final: 0.8241 (tttm) outliers start: 2 outliers final: 2 residues processed: 69 average time/residue: 0.5352 time to fit residues: 42.4164 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 10 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 ASN E 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.130645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.108951 restraints weight = 16145.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.112106 restraints weight = 5344.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.114101 restraints weight = 2747.381| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.7445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3498 Z= 0.214 Angle : 0.586 4.931 4680 Z= 0.303 Chirality : 0.052 0.136 528 Planarity : 0.004 0.037 594 Dihedral : 5.646 19.299 462 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 362 PHE 0.018 0.002 PHE B 346 TYR 0.007 0.001 TYR B 310 ARG 0.002 0.000 ARG F 379 *********************** 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 : 0.596 Fit side-chains revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7742 (ptp-110) cc_final: 0.7464 (ptp-170) REVERT: A 375 LYS cc_start: 0.8308 (tttt) cc_final: 0.7967 (tttp) REVERT: C 317 LYS cc_start: 0.8601 (mptt) cc_final: 0.8342 (mttp) REVERT: E 349 ARG cc_start: 0.7313 (mtm180) cc_final: 0.5961 (mmp80) REVERT: B 336 GLN cc_start: 0.7597 (tt0) cc_final: 0.7342 (mp10) REVERT: B 375 LYS cc_start: 0.8322 (tttt) cc_final: 0.8032 (tttp) REVERT: F 314 ASP cc_start: 0.6852 (t0) cc_final: 0.6610 (t0) REVERT: F 368 ASN cc_start: 0.8448 (m-40) cc_final: 0.8021 (m-40) REVERT: F 370 LYS cc_start: 0.8569 (tttt) cc_final: 0.8053 (tttm) REVERT: F 375 LYS cc_start: 0.8321 (tttt) cc_final: 0.8014 (tttm) outliers start: 3 outliers final: 3 residues processed: 69 average time/residue: 0.5121 time to fit residues: 40.3995 Evaluate side-chains 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 5 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.128272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.107194 restraints weight = 16211.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.110360 restraints weight = 5308.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.112318 restraints weight = 2702.909| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.7684 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= 0.284 Angle : 0.610 5.017 4680 Z= 0.319 Chirality : 0.052 0.136 528 Planarity : 0.004 0.035 594 Dihedral : 5.665 19.296 462 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 1.01 % Allowed : 14.39 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 374 PHE 0.024 0.003 PHE D 346 TYR 0.014 0.003 TYR F 310 ARG 0.002 0.000 ARG E 349 ********************** 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 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7843 (ptp-110) cc_final: 0.7530 (ptp-170) REVERT: A 375 LYS cc_start: 0.8419 (tttt) cc_final: 0.8084 (tttp) REVERT: C 317 LYS cc_start: 0.8628 (mptt) cc_final: 0.8364 (mttp) REVERT: E 349 ARG cc_start: 0.7423 (mtm180) cc_final: 0.6104 (mmm160) REVERT: B 336 GLN cc_start: 0.7792 (tt0) cc_final: 0.7478 (mp10) REVERT: B 375 LYS cc_start: 0.8370 (tttt) cc_final: 0.8089 (tttp) REVERT: F 368 ASN cc_start: 0.8423 (m-40) cc_final: 0.8033 (m-40) REVERT: F 375 LYS cc_start: 0.8391 (tttt) cc_final: 0.8145 (tttm) outliers start: 4 outliers final: 4 residues processed: 66 average time/residue: 0.5419 time to fit residues: 40.8177 Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain E residue 329 HIS 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 30 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 2.3984 ------------------------------------------------------------------------------- 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 = 0.4285 r_free = 0.4285 target = 0.126281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.104084 restraints weight = 16136.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.107239 restraints weight = 5529.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.109274 restraints weight = 2857.566| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.7757 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= 0.215 Angle : 0.576 4.814 4680 Z= 0.296 Chirality : 0.052 0.137 528 Planarity : 0.004 0.041 594 Dihedral : 5.389 18.703 462 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.01 % Allowed : 14.14 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 362 PHE 0.019 0.002 PHE D 346 TYR 0.009 0.002 TYR B 310 ARG 0.001 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3157.73 seconds wall clock time: 54 minutes 43.37 seconds (3283.37 seconds total)