Starting phenix.real_space_refine on Tue Feb 11 23:55:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9g_18280/02_2025/8q9g_18280.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9g_18280/02_2025/8q9g_18280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q9g_18280/02_2025/8q9g_18280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9g_18280/02_2025/8q9g_18280.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9g_18280/02_2025/8q9g_18280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9g_18280/02_2025/8q9g_18280.cif" } resolution = 2.65 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2106 2.51 5 N 606 2.21 5 O 624 1.98 5 H 3480 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6822 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "B" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 4.68, per 1000 atoms: 0.69 Number of scatterers: 6822 At special positions: 0 Unit cell: (150.489, 92.329, 42.166, 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 624 8.00 N 606 7.00 C 2106 6.00 H 3480 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: 1.64 Conformation dependent library (CDL) restraints added in 655.1 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 50.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.518A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.556A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.339A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330 removed outlier: 5.949A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN A 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.755A pdb=" N GLU A 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N SER E 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS A 340 " --> pdb=" O SER E 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.611A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 357 removed outlier: 6.508A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N SER E 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY A 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.417A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 377 Processing sheet with id=AB1, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.801A pdb=" N ILE B 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.658A pdb=" N VAL B 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 322 removed outlier: 6.250A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 325 through 330 removed outlier: 5.981A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY F 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN B 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 337 through 342 Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.676A pdb=" N ASP B 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.546A pdb=" N GLN B 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE F 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS B 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N SER F 356 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY B 355 " --> pdb=" O SER F 356 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.350A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 369 through 377 removed outlier: 6.233A pdb=" N LYS B 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N THR D 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU B 372 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LYS D 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N HIS B 374 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N THR D 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 376 " --> pdb=" O THR D 377 " (cutoff:3.500A) 83 hydrogen bonds defined for protein. 249 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: 2.35 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 3474 1.11 - 1.29: 558 1.29 - 1.46: 916 1.46 - 1.63: 1922 1.63 - 1.81: 6 Bond restraints: 6876 Sorted by residual: bond pdb=" N SER F 324 " pdb=" H SER F 324 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CD1 TYR B 310 " pdb=" HD1 TYR B 310 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N TYR A 310 " pdb=" H TYR A 310 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" NE2 GLN E 336 " pdb="HE21 GLN E 336 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" NE2 HIS B 362 " pdb=" HE2 HIS B 362 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 ... (remaining 6871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 10268 2.38 - 4.75: 1697 4.75 - 7.12: 536 7.12 - 9.50: 39 9.50 - 11.87: 6 Bond angle restraints: 12546 Sorted by residual: angle pdb=" N SER B 316 " pdb=" CA SER B 316 " pdb=" C SER B 316 " ideal model delta sigma weight residual 110.53 117.64 -7.11 1.32e+00 5.74e-01 2.90e+01 angle pdb=" N GLY B 326 " pdb=" CA GLY B 326 " pdb=" C GLY B 326 " ideal model delta sigma weight residual 110.69 117.25 -6.56 1.33e+00 5.65e-01 2.43e+01 angle pdb=" N GLU F 372 " pdb=" CA GLU F 372 " pdb=" CB GLU F 372 " ideal model delta sigma weight residual 111.13 102.34 8.79 1.79e+00 3.12e-01 2.41e+01 angle pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " pdb=" CD2 HIS E 374 " ideal model delta sigma weight residual 131.20 124.85 6.35 1.30e+00 5.92e-01 2.38e+01 angle pdb=" CB HIS D 329 " pdb=" CG HIS D 329 " pdb=" CD2 HIS D 329 " ideal model delta sigma weight residual 131.20 124.85 6.35 1.30e+00 5.92e-01 2.38e+01 ... (remaining 12541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.63: 2843 14.63 - 29.25: 115 29.25 - 43.87: 81 43.87 - 58.50: 80 58.50 - 73.12: 49 Dihedral angle restraints: 3168 sinusoidal: 1806 harmonic: 1362 Sorted by residual: dihedral pdb=" C LYS C 343 " pdb=" N LYS C 343 " pdb=" CA LYS C 343 " pdb=" CB LYS C 343 " ideal model delta harmonic sigma weight residual -122.60 -132.81 10.21 0 2.50e+00 1.60e-01 1.67e+01 dihedral pdb=" CA ILE A 360 " pdb=" C ILE A 360 " pdb=" N THR A 361 " pdb=" CA THR A 361 " ideal model delta harmonic sigma weight residual 180.00 161.38 18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA LYS A 369 " pdb=" C LYS A 369 " pdb=" N LYS A 370 " pdb=" CA LYS A 370 " ideal model delta harmonic sigma weight residual 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 3165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 303 0.066 - 0.132: 152 0.132 - 0.198: 46 0.198 - 0.264: 13 0.264 - 0.329: 2 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA LYS C 343 " pdb=" N LYS C 343 " pdb=" C LYS C 343 " pdb=" CB LYS C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA ASP D 358 " pdb=" N ASP D 358 " pdb=" C ASP D 358 " pdb=" CB ASP D 358 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA LYS B 317 " pdb=" N LYS B 317 " pdb=" C LYS B 317 " pdb=" CB LYS B 317 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 513 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 362 " -0.075 2.00e-02 2.50e+03 4.52e-02 4.59e+01 pdb=" CG HIS B 362 " 0.054 2.00e-02 2.50e+03 pdb=" ND1 HIS B 362 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 HIS B 362 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 HIS B 362 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS B 362 " 0.039 2.00e-02 2.50e+03 pdb=" HD2 HIS B 362 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 HIS B 362 " -0.035 2.00e-02 2.50e+03 pdb=" HE2 HIS B 362 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " -0.088 2.00e-02 2.50e+03 3.90e-02 4.56e+01 pdb=" CG TYR D 310 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " -0.083 2.00e-02 2.50e+03 pdb=" HD1 TYR D 310 " 0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR D 310 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 TYR D 310 " 0.009 2.00e-02 2.50e+03 pdb=" HE2 TYR D 310 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.079 2.00e-02 2.50e+03 3.54e-02 3.76e+01 pdb=" CG TYR C 310 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.076 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " -0.014 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 616 2.20 - 2.80: 12494 2.80 - 3.40: 17578 3.40 - 4.00: 24431 4.00 - 4.60: 33683 Nonbonded interactions: 88802 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.603 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.610 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.627 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.644 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.653 2.450 ... (remaining 88797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 0.110 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.680 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.038 3396 Z= 0.756 Angle : 1.947 8.792 4548 Z= 1.280 Chirality : 0.085 0.329 516 Planarity : 0.009 0.055 576 Dihedral : 10.250 57.110 1296 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % 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: -1.98 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.005 HIS A 330 PHE 0.043 0.014 PHE C 346 TYR 0.082 0.024 TYR D 310 ARG 0.006 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7097 (mtpt) cc_final: 0.6748 (mttm) REVERT: A 351 GLN cc_start: 0.7879 (mt0) cc_final: 0.7615 (mt0) REVERT: A 358 ASP cc_start: 0.8773 (m-30) cc_final: 0.8567 (m-30) REVERT: C 311 LYS cc_start: 0.5407 (ttpt) cc_final: 0.5090 (mmtm) REVERT: C 321 LYS cc_start: 0.7275 (mtpt) cc_final: 0.6624 (mttt) REVERT: C 345 ASP cc_start: 0.7808 (t0) cc_final: 0.7314 (t70) REVERT: C 349 ARG cc_start: 0.7392 (mtt180) cc_final: 0.5388 (mmp-170) REVERT: C 369 LYS cc_start: 0.6597 (mttt) cc_final: 0.6299 (mttp) REVERT: C 372 GLU cc_start: 0.7657 (tt0) cc_final: 0.7193 (tp30) REVERT: E 321 LYS cc_start: 0.7934 (mtpt) cc_final: 0.7620 (mttp) REVERT: E 345 ASP cc_start: 0.8028 (t0) cc_final: 0.7684 (t0) REVERT: E 347 LYS cc_start: 0.7772 (mttt) cc_final: 0.6817 (pttm) REVERT: B 314 ASP cc_start: 0.5622 (t0) cc_final: 0.5104 (t0) REVERT: B 320 SER cc_start: 0.7792 (t) cc_final: 0.6924 (p) REVERT: B 321 LYS cc_start: 0.7391 (mtpt) cc_final: 0.6989 (mttt) REVERT: B 345 ASP cc_start: 0.6889 (t0) cc_final: 0.6689 (m-30) REVERT: B 369 LYS cc_start: 0.6550 (mttt) cc_final: 0.6131 (mtpp) REVERT: B 375 LYS cc_start: 0.4806 (tttt) cc_final: 0.4483 (ttmm) REVERT: D 320 SER cc_start: 0.8259 (t) cc_final: 0.7998 (p) REVERT: D 321 LYS cc_start: 0.7452 (mtpt) cc_final: 0.7146 (mtmm) REVERT: D 345 ASP cc_start: 0.6786 (t0) cc_final: 0.6586 (p0) REVERT: D 349 ARG cc_start: 0.7661 (mtt180) cc_final: 0.6544 (mmp-170) REVERT: D 375 LYS cc_start: 0.4901 (tttt) cc_final: 0.4679 (tttm) REVERT: F 314 ASP cc_start: 0.5583 (t0) cc_final: 0.5371 (t0) REVERT: F 316 SER cc_start: 0.6735 (m) cc_final: 0.6453 (p) REVERT: F 320 SER cc_start: 0.7944 (t) cc_final: 0.7290 (p) REVERT: F 349 ARG cc_start: 0.6698 (mtt180) cc_final: 0.6472 (ptt-90) REVERT: F 375 LYS cc_start: 0.6681 (tttt) cc_final: 0.6255 (ttmm) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 3.0680 time to fit residues: 417.0458 Evaluate side-chains 94 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 307 GLN E 336 GLN E 362 HIS B 362 HIS F 362 HIS F 368 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.154028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.123166 restraints weight = 10448.068| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.54 r_work: 0.3749 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3396 Z= 0.256 Angle : 0.605 4.840 4548 Z= 0.319 Chirality : 0.051 0.135 516 Planarity : 0.003 0.034 576 Dihedral : 5.533 16.503 444 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.08 % Allowed : 11.46 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.92 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 362 PHE 0.009 0.002 PHE C 346 TYR 0.008 0.002 TYR B 310 ARG 0.004 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: C 345 ASP cc_start: 0.7617 (t0) cc_final: 0.7256 (t70) REVERT: C 349 ARG cc_start: 0.7473 (mtt180) cc_final: 0.5580 (mmp-170) REVERT: E 347 LYS cc_start: 0.7583 (mttt) cc_final: 0.6827 (pttm) REVERT: E 349 ARG cc_start: 0.7168 (mtm180) cc_final: 0.6951 (mtt180) REVERT: B 320 SER cc_start: 0.8367 (t) cc_final: 0.7982 (p) REVERT: B 321 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7927 (mttt) REVERT: B 342 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.6122 (tt0) REVERT: B 345 ASP cc_start: 0.6638 (t0) cc_final: 0.6053 (m-30) REVERT: B 349 ARG cc_start: 0.6990 (mtp85) cc_final: 0.6728 (mtp85) REVERT: B 375 LYS cc_start: 0.8124 (tttt) cc_final: 0.7800 (ttmm) REVERT: D 321 LYS cc_start: 0.8292 (mtpt) cc_final: 0.8080 (mttm) REVERT: D 345 ASP cc_start: 0.6634 (t0) cc_final: 0.6155 (p0) REVERT: D 349 ARG cc_start: 0.7300 (mtt180) cc_final: 0.6178 (mmp-170) REVERT: F 320 SER cc_start: 0.8422 (t) cc_final: 0.8109 (p) REVERT: F 375 LYS cc_start: 0.8411 (tttt) cc_final: 0.8141 (mtpp) outliers start: 8 outliers final: 3 residues processed: 96 average time/residue: 3.0982 time to fit residues: 304.1056 Evaluate side-chains 86 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN E 336 GLN E 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.149980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.119317 restraints weight = 11455.215| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.63 r_work: 0.3708 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3396 Z= 0.402 Angle : 0.660 4.499 4548 Z= 0.352 Chirality : 0.052 0.145 516 Planarity : 0.003 0.027 576 Dihedral : 5.432 16.449 444 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.12 % Allowed : 14.58 % Favored : 82.29 % 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: -2.15 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 374 PHE 0.011 0.002 PHE C 346 TYR 0.013 0.003 TYR C 310 ARG 0.004 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8224 (ttpp) cc_final: 0.7987 (mttm) REVERT: A 347 LYS cc_start: 0.7855 (mttt) cc_final: 0.7488 (mmmm) REVERT: C 321 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8396 (mttp) REVERT: C 347 LYS cc_start: 0.7913 (mmtt) cc_final: 0.7291 (mmmm) REVERT: C 349 ARG cc_start: 0.7555 (mtt180) cc_final: 0.5775 (mmp-170) REVERT: E 347 LYS cc_start: 0.7776 (mttt) cc_final: 0.7057 (pmtt) REVERT: B 320 SER cc_start: 0.8504 (t) cc_final: 0.8169 (p) REVERT: B 321 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7923 (mttt) REVERT: B 342 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6289 (tt0) REVERT: B 345 ASP cc_start: 0.6699 (t0) cc_final: 0.6421 (p0) REVERT: B 375 LYS cc_start: 0.8196 (tttt) cc_final: 0.7969 (mtpp) REVERT: D 345 ASP cc_start: 0.6645 (t0) cc_final: 0.6280 (p0) REVERT: D 349 ARG cc_start: 0.7368 (mtt180) cc_final: 0.6181 (mmp-170) REVERT: F 320 SER cc_start: 0.8399 (t) cc_final: 0.8028 (p) REVERT: F 375 LYS cc_start: 0.8395 (tttt) cc_final: 0.8158 (mtpp) outliers start: 12 outliers final: 6 residues processed: 84 average time/residue: 3.1187 time to fit residues: 268.1156 Evaluate side-chains 87 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.152627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.122263 restraints weight = 11474.387| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.64 r_work: 0.3752 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3396 Z= 0.240 Angle : 0.561 4.188 4548 Z= 0.293 Chirality : 0.051 0.139 516 Planarity : 0.002 0.015 576 Dihedral : 5.107 16.147 444 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.08 % Allowed : 15.89 % Favored : 82.03 % 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: -2.18 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.006 0.001 PHE E 378 TYR 0.009 0.002 TYR C 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.604 Fit side-chains REVERT: A 311 LYS cc_start: 0.8143 (ttpp) cc_final: 0.7900 (mttm) REVERT: A 347 LYS cc_start: 0.7816 (mttt) cc_final: 0.7446 (mmmm) REVERT: C 321 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8423 (mttp) REVERT: C 345 ASP cc_start: 0.7644 (t0) cc_final: 0.7383 (t70) REVERT: C 347 LYS cc_start: 0.7872 (mmtt) cc_final: 0.7246 (mmmm) REVERT: C 349 ARG cc_start: 0.7577 (mtt180) cc_final: 0.5776 (mmp-170) REVERT: E 347 LYS cc_start: 0.7811 (mttt) cc_final: 0.7016 (pmtt) REVERT: E 375 LYS cc_start: 0.8552 (tttp) cc_final: 0.8087 (ttmm) REVERT: B 320 SER cc_start: 0.8526 (t) cc_final: 0.8272 (p) REVERT: B 321 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7902 (mttt) REVERT: B 375 LYS cc_start: 0.8211 (tttt) cc_final: 0.7962 (mtpp) REVERT: D 349 ARG cc_start: 0.7298 (mtt180) cc_final: 0.6151 (mmp-170) REVERT: D 369 LYS cc_start: 0.8424 (ttmm) cc_final: 0.8183 (ttmt) REVERT: F 375 LYS cc_start: 0.8389 (tttt) cc_final: 0.8144 (mtpp) outliers start: 8 outliers final: 5 residues processed: 87 average time/residue: 3.2138 time to fit residues: 285.6672 Evaluate side-chains 88 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.155289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.125938 restraints weight = 11482.937| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.64 r_work: 0.3807 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3396 Z= 0.157 Angle : 0.499 4.047 4548 Z= 0.254 Chirality : 0.051 0.138 516 Planarity : 0.002 0.013 576 Dihedral : 4.650 15.400 444 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.56 % Allowed : 17.97 % Favored : 80.47 % 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: -2.11 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 362 PHE 0.004 0.001 PHE D 346 TYR 0.006 0.001 TYR C 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.616 Fit side-chains REVERT: A 347 LYS cc_start: 0.7811 (mttt) cc_final: 0.7453 (mmmm) REVERT: C 311 LYS cc_start: 0.6760 (mmtm) cc_final: 0.6500 (mmtm) REVERT: C 321 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8425 (mttp) REVERT: C 338 GLU cc_start: 0.6792 (tp30) cc_final: 0.6452 (tp30) REVERT: C 347 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7231 (mmmm) REVERT: C 349 ARG cc_start: 0.7580 (mtt180) cc_final: 0.5647 (mmp-170) REVERT: E 336 GLN cc_start: 0.7719 (tt0) cc_final: 0.7239 (tt0) REVERT: E 338 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6584 (mt-10) REVERT: E 347 LYS cc_start: 0.7802 (mttt) cc_final: 0.6903 (pmtt) REVERT: E 375 LYS cc_start: 0.8546 (tttp) cc_final: 0.8075 (ttmm) REVERT: B 321 LYS cc_start: 0.8118 (mtpt) cc_final: 0.7897 (mttt) REVERT: B 349 ARG cc_start: 0.7366 (ptp-170) cc_final: 0.6945 (ptp-110) REVERT: B 375 LYS cc_start: 0.8213 (tttt) cc_final: 0.7952 (mtpp) REVERT: D 349 ARG cc_start: 0.7315 (mtt180) cc_final: 0.6214 (mmp-170) REVERT: D 369 LYS cc_start: 0.8389 (ttmm) cc_final: 0.8169 (ttmt) REVERT: F 320 SER cc_start: 0.8314 (t) cc_final: 0.8003 (p) REVERT: F 375 LYS cc_start: 0.8364 (tttt) cc_final: 0.8107 (tttm) outliers start: 6 outliers final: 3 residues processed: 86 average time/residue: 3.2696 time to fit residues: 287.2449 Evaluate side-chains 81 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.150776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.120430 restraints weight = 11418.111| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.63 r_work: 0.3761 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3396 Z= 0.273 Angle : 0.571 4.223 4548 Z= 0.298 Chirality : 0.050 0.139 516 Planarity : 0.002 0.017 576 Dihedral : 4.864 15.995 444 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.08 % Allowed : 17.97 % Favored : 79.95 % 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: -2.25 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.008 0.002 PHE C 346 TYR 0.010 0.002 TYR B 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.584 Fit side-chains REVERT: A 347 LYS cc_start: 0.7811 (mttt) cc_final: 0.7443 (mmmm) REVERT: C 311 LYS cc_start: 0.6653 (mmtm) cc_final: 0.6385 (mmtm) REVERT: C 321 LYS cc_start: 0.8696 (mtmt) cc_final: 0.8425 (mttp) REVERT: C 349 ARG cc_start: 0.7540 (mtt180) cc_final: 0.5804 (mmp-170) REVERT: E 338 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6729 (mt-10) REVERT: E 347 LYS cc_start: 0.7839 (mttt) cc_final: 0.7064 (pmtt) REVERT: E 349 ARG cc_start: 0.7560 (mtt180) cc_final: 0.7014 (mtm180) REVERT: E 375 LYS cc_start: 0.8530 (tttp) cc_final: 0.8069 (ttmm) REVERT: B 375 LYS cc_start: 0.8229 (tttt) cc_final: 0.7985 (mtpp) REVERT: D 349 ARG cc_start: 0.7309 (mtt180) cc_final: 0.6163 (mmp-170) REVERT: D 369 LYS cc_start: 0.8398 (ttmm) cc_final: 0.8185 (ttmt) REVERT: F 320 SER cc_start: 0.8429 (t) cc_final: 0.8072 (p) REVERT: F 375 LYS cc_start: 0.8373 (tttt) cc_final: 0.8129 (mtpp) outliers start: 8 outliers final: 4 residues processed: 78 average time/residue: 3.3131 time to fit residues: 263.9837 Evaluate side-chains 77 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.150686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.120287 restraints weight = 11319.222| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.63 r_work: 0.3730 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3396 Z= 0.281 Angle : 0.581 4.248 4548 Z= 0.304 Chirality : 0.050 0.138 516 Planarity : 0.002 0.018 576 Dihedral : 4.973 16.295 444 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.56 % Allowed : 17.97 % Favored : 80.47 % 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: -2.27 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.007 0.002 PHE C 346 TYR 0.011 0.003 TYR B 310 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.562 Fit side-chains REVERT: A 347 LYS cc_start: 0.7825 (mttt) cc_final: 0.7441 (mmmm) REVERT: C 311 LYS cc_start: 0.6690 (mmtm) cc_final: 0.6431 (mmtm) REVERT: C 321 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8463 (mttp) REVERT: C 338 GLU cc_start: 0.6830 (tp30) cc_final: 0.6523 (tp30) REVERT: C 347 LYS cc_start: 0.7878 (mmtt) cc_final: 0.7263 (mmmm) REVERT: C 349 ARG cc_start: 0.7535 (mtt180) cc_final: 0.5835 (mmp-170) REVERT: E 336 GLN cc_start: 0.7594 (tt0) cc_final: 0.7078 (tt0) REVERT: E 338 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6527 (mt-10) REVERT: E 347 LYS cc_start: 0.7846 (mttt) cc_final: 0.7078 (pmtt) REVERT: B 349 ARG cc_start: 0.7426 (ptp-170) cc_final: 0.7061 (ptp-110) REVERT: B 375 LYS cc_start: 0.8246 (tttt) cc_final: 0.8022 (mtpp) REVERT: D 349 ARG cc_start: 0.7323 (mtt180) cc_final: 0.6209 (mmp-170) REVERT: D 369 LYS cc_start: 0.8412 (ttmm) cc_final: 0.8201 (ttmt) REVERT: F 320 SER cc_start: 0.8395 (t) cc_final: 0.8047 (p) REVERT: F 375 LYS cc_start: 0.8403 (tttt) cc_final: 0.8156 (mtpp) outliers start: 6 outliers final: 6 residues processed: 74 average time/residue: 3.2245 time to fit residues: 244.1282 Evaluate side-chains 78 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.155414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.125982 restraints weight = 11425.537| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.68 r_work: 0.3814 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3396 Z= 0.151 Angle : 0.496 4.161 4548 Z= 0.252 Chirality : 0.051 0.137 516 Planarity : 0.002 0.020 576 Dihedral : 4.555 14.733 444 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.56 % Allowed : 18.23 % Favored : 80.21 % 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: -2.18 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.003 0.001 PHE D 346 TYR 0.007 0.002 TYR B 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.603 Fit side-chains REVERT: A 347 LYS cc_start: 0.7807 (mttt) cc_final: 0.7373 (mmmm) REVERT: C 311 LYS cc_start: 0.6524 (mmtm) cc_final: 0.6249 (mmtm) REVERT: C 321 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8413 (mttp) REVERT: C 338 GLU cc_start: 0.6766 (tp30) cc_final: 0.6446 (tp30) REVERT: C 349 ARG cc_start: 0.7494 (mtt180) cc_final: 0.5647 (mmp-170) REVERT: E 336 GLN cc_start: 0.7548 (tt0) cc_final: 0.7019 (tt0) REVERT: E 338 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6506 (mt-10) REVERT: E 347 LYS cc_start: 0.7793 (mttt) cc_final: 0.6932 (pmtt) REVERT: E 375 LYS cc_start: 0.8502 (tttp) cc_final: 0.7991 (ttmm) REVERT: B 375 LYS cc_start: 0.8220 (tttt) cc_final: 0.7964 (mtpp) REVERT: D 349 ARG cc_start: 0.7255 (mtt180) cc_final: 0.6058 (mmp-170) REVERT: D 369 LYS cc_start: 0.8371 (ttmm) cc_final: 0.8161 (ttmt) REVERT: F 320 SER cc_start: 0.8376 (t) cc_final: 0.7988 (p) REVERT: F 375 LYS cc_start: 0.8399 (tttt) cc_final: 0.8122 (mtpp) outliers start: 6 outliers final: 4 residues processed: 75 average time/residue: 3.3587 time to fit residues: 257.7920 Evaluate side-chains 77 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.0060 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 overall best weight: 2.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.151400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.121084 restraints weight = 11417.160| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.64 r_work: 0.3775 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3396 Z= 0.247 Angle : 0.556 6.558 4548 Z= 0.291 Chirality : 0.050 0.138 516 Planarity : 0.002 0.016 576 Dihedral : 4.694 15.325 444 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.56 % Allowed : 18.49 % Favored : 79.95 % 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: -2.21 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.006 0.001 PHE C 346 TYR 0.012 0.002 TYR B 310 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.592 Fit side-chains REVERT: A 347 LYS cc_start: 0.7821 (mttt) cc_final: 0.7480 (mmmm) REVERT: C 311 LYS cc_start: 0.6650 (mmtm) cc_final: 0.6390 (mmtm) REVERT: C 321 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8443 (mttp) REVERT: C 338 GLU cc_start: 0.6803 (tp30) cc_final: 0.6498 (tp30) REVERT: C 349 ARG cc_start: 0.7535 (mtt180) cc_final: 0.5795 (mmp-170) REVERT: E 338 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6668 (mt-10) REVERT: E 347 LYS cc_start: 0.7845 (mttt) cc_final: 0.7065 (pmtt) REVERT: B 375 LYS cc_start: 0.8228 (tttt) cc_final: 0.7993 (mtpp) REVERT: D 349 ARG cc_start: 0.7316 (mtt180) cc_final: 0.6160 (mmp-170) REVERT: D 369 LYS cc_start: 0.8403 (ttmm) cc_final: 0.8196 (ttmt) REVERT: F 320 SER cc_start: 0.8405 (t) cc_final: 0.8044 (p) REVERT: F 375 LYS cc_start: 0.8376 (tttt) cc_final: 0.8130 (mtpp) outliers start: 6 outliers final: 5 residues processed: 73 average time/residue: 3.3314 time to fit residues: 248.5516 Evaluate side-chains 77 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.152063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.121875 restraints weight = 11590.563| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.65 r_work: 0.3788 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3396 Z= 0.216 Angle : 0.546 6.397 4548 Z= 0.285 Chirality : 0.050 0.136 516 Planarity : 0.002 0.017 576 Dihedral : 4.715 15.254 444 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.56 % Allowed : 18.49 % Favored : 79.95 % 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: -2.22 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.006 0.001 PHE C 346 TYR 0.011 0.002 TYR B 310 ARG 0.002 0.000 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.664 Fit side-chains REVERT: A 347 LYS cc_start: 0.7852 (mttt) cc_final: 0.7459 (mmmm) REVERT: C 311 LYS cc_start: 0.6645 (mmtm) cc_final: 0.6388 (mmtm) REVERT: C 321 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8443 (mttp) REVERT: C 338 GLU cc_start: 0.6805 (tp30) cc_final: 0.6506 (tp30) REVERT: C 347 LYS cc_start: 0.7859 (mmtt) cc_final: 0.7250 (mmmm) REVERT: C 349 ARG cc_start: 0.7520 (mtt180) cc_final: 0.5781 (mmp-170) REVERT: E 336 GLN cc_start: 0.7642 (tt0) cc_final: 0.7024 (tt0) REVERT: E 338 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6505 (mt-10) REVERT: E 347 LYS cc_start: 0.7835 (mttt) cc_final: 0.7050 (pmtt) REVERT: B 375 LYS cc_start: 0.8250 (tttt) cc_final: 0.8008 (mtpp) REVERT: D 349 ARG cc_start: 0.7324 (mtt180) cc_final: 0.6156 (mmp-170) REVERT: D 369 LYS cc_start: 0.8386 (ttmm) cc_final: 0.8176 (ttmt) REVERT: F 320 SER cc_start: 0.8397 (t) cc_final: 0.8039 (p) REVERT: F 347 LYS cc_start: 0.7022 (mttt) cc_final: 0.6615 (pmtt) REVERT: F 375 LYS cc_start: 0.8379 (tttt) cc_final: 0.8134 (mtpp) outliers start: 6 outliers final: 5 residues processed: 74 average time/residue: 3.2675 time to fit residues: 247.0965 Evaluate side-chains 78 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.150427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.119759 restraints weight = 11498.835| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.64 r_work: 0.3726 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3396 Z= 0.307 Angle : 0.593 6.232 4548 Z= 0.313 Chirality : 0.050 0.137 516 Planarity : 0.003 0.019 576 Dihedral : 4.916 15.872 444 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.56 % Allowed : 18.75 % Favored : 79.69 % 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: -2.27 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.008 0.002 PHE C 346 TYR 0.013 0.003 TYR B 310 ARG 0.002 0.001 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7296.65 seconds wall clock time: 128 minutes 41.77 seconds (7721.77 seconds total)