Starting phenix.real_space_refine on Fri Oct 10 14:55:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9g_18280/10_2025/8q9g_18280.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9g_18280/10_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_18280/10_2025/8q9g_18280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9g_18280/10_2025/8q9g_18280.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9g_18280/10_2025/8q9g_18280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9g_18280/10_2025/8q9g_18280.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.39, per 1000 atoms: 0.20 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: 0.62 Conformation dependent library (CDL) restraints added in 281.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.18 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: 1.25 Time building geometry restraints manager: 0.89 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.220 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: 0.050 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.460 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.580 ------------------------------------------------------------------------------- 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= 0.693 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.006 0.001 ARG C 349 TYR 0.082 0.024 TYR D 310 PHE 0.043 0.014 PHE C 346 HIS 0.017 0.005 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.01121 ( 3396) covalent geometry : angle 1.94730 ( 4548) hydrogen bonds : bond 0.11102 ( 83) hydrogen bonds : angle 7.46844 ( 249) *********************** 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 : 0.201 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: 0.7607 (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: 0.5433 (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: 0.6549 (mmp-170) REVERT: D 375 LYS cc_start: 0.4901 (tttt) cc_final: 0.4678 (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: 0.6474 (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: 1.4874 time to fit residues: 201.8983 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 : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.4177 r_free = 0.4177 target = 0.154436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.123836 restraints weight = 10642.658| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.58 r_work: 0.3760 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3396 Z= 0.142 Angle : 0.586 4.742 4548 Z= 0.307 Chirality : 0.051 0.133 516 Planarity : 0.003 0.033 576 Dihedral : 5.555 16.426 444 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.56 % Allowed : 11.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (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 ARG 0.003 0.001 ARG E 349 TYR 0.007 0.002 TYR F 310 PHE 0.007 0.001 PHE C 346 HIS 0.004 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 3396) covalent geometry : angle 0.58647 ( 4548) hydrogen bonds : bond 0.02378 ( 83) hydrogen bonds : angle 4.76110 ( 249) *********************** 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 100 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: C 345 ASP cc_start: 0.7618 (t0) cc_final: 0.7289 (t70) REVERT: C 349 ARG cc_start: 0.7499 (mtt180) cc_final: 0.5581 (mmp-170) REVERT: E 347 LYS cc_start: 0.7589 (mttt) cc_final: 0.6844 (pttm) REVERT: B 320 SER cc_start: 0.8362 (t) cc_final: 0.7989 (p) REVERT: B 321 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7942 (mttt) REVERT: B 342 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.6108 (tt0) REVERT: B 345 ASP cc_start: 0.6653 (t0) cc_final: 0.6082 (m-30) REVERT: B 349 ARG cc_start: 0.6991 (mtp85) cc_final: 0.6730 (mtp85) REVERT: D 321 LYS cc_start: 0.8297 (mtpt) cc_final: 0.8090 (mttm) REVERT: D 345 ASP cc_start: 0.6625 (t0) cc_final: 0.6158 (p0) REVERT: D 349 ARG cc_start: 0.7321 (mtt180) cc_final: 0.6188 (mmp-170) REVERT: F 320 SER cc_start: 0.8430 (t) cc_final: 0.8134 (p) REVERT: F 375 LYS cc_start: 0.8398 (tttt) cc_final: 0.8138 (mtpp) outliers start: 6 outliers final: 3 residues processed: 94 average time/residue: 1.5048 time to fit residues: 144.3690 Evaluate side-chains 85 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 30 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 13 optimal weight: 0.0060 chunk 37 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.8198 ------------------------------------------------------------------------------- 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 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.155614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.125797 restraints weight = 10713.542| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.59 r_work: 0.3801 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3396 Z= 0.087 Angle : 0.511 5.333 4548 Z= 0.258 Chirality : 0.051 0.137 516 Planarity : 0.002 0.014 576 Dihedral : 4.717 15.176 444 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.60 % Allowed : 15.62 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (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 ARG 0.002 0.000 ARG F 349 TYR 0.006 0.001 TYR C 310 PHE 0.004 0.001 PHE D 346 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 3396) covalent geometry : angle 0.51070 ( 4548) hydrogen bonds : bond 0.01728 ( 83) hydrogen bonds : angle 4.12973 ( 249) *********************** 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 99 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8018 (ttpp) cc_final: 0.7813 (mttm) REVERT: C 347 LYS cc_start: 0.7919 (mmtt) cc_final: 0.7379 (mmmm) REVERT: C 349 ARG cc_start: 0.7497 (mtt180) cc_final: 0.5676 (mmp-170) REVERT: E 336 GLN cc_start: 0.7877 (tt0) cc_final: 0.7256 (tt0) REVERT: E 338 GLU cc_start: 0.6987 (tt0) cc_final: 0.6374 (mt-10) REVERT: E 347 LYS cc_start: 0.7687 (mttt) cc_final: 0.6892 (pttm) REVERT: B 320 SER cc_start: 0.8428 (t) cc_final: 0.8124 (p) REVERT: B 321 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7950 (mttt) REVERT: B 375 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7807 (ttmm) REVERT: D 341 SER cc_start: 0.6475 (m) cc_final: 0.6264 (t) REVERT: D 349 ARG cc_start: 0.7324 (mtt180) cc_final: 0.6141 (mmp-170) REVERT: D 369 LYS cc_start: 0.8121 (mtpp) cc_final: 0.7811 (mttt) REVERT: F 320 SER cc_start: 0.8423 (t) cc_final: 0.8075 (p) REVERT: F 349 ARG cc_start: 0.6007 (ptt-90) cc_final: 0.5725 (pmt-80) outliers start: 10 outliers final: 2 residues processed: 91 average time/residue: 1.4983 time to fit residues: 139.2857 Evaluate side-chains 86 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain B residue 375 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 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 = 0.153060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.122910 restraints weight = 10724.514| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.59 r_work: 0.3752 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3396 Z= 0.122 Angle : 0.515 3.929 4548 Z= 0.268 Chirality : 0.051 0.139 516 Planarity : 0.002 0.012 576 Dihedral : 4.620 15.464 444 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.60 % Allowed : 18.23 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.001 0.000 ARG B 349 TYR 0.009 0.002 TYR C 310 PHE 0.006 0.001 PHE F 346 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3396) covalent geometry : angle 0.51514 ( 4548) hydrogen bonds : bond 0.01717 ( 83) hydrogen bonds : angle 4.11415 ( 249) *********************** 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 93 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.123 Fit side-chains REVERT: A 311 LYS cc_start: 0.8091 (ttpp) cc_final: 0.7888 (mttm) REVERT: A 347 LYS cc_start: 0.7791 (mttt) cc_final: 0.7448 (mmmm) REVERT: C 321 LYS cc_start: 0.8654 (mtmt) cc_final: 0.8348 (mttp) REVERT: C 349 ARG cc_start: 0.7511 (mtt180) cc_final: 0.5673 (mmp-170) REVERT: E 336 GLN cc_start: 0.7935 (tt0) cc_final: 0.7211 (tt0) REVERT: E 338 GLU cc_start: 0.7030 (tt0) cc_final: 0.6384 (mt-10) REVERT: E 347 LYS cc_start: 0.7736 (mttt) cc_final: 0.6904 (pttm) REVERT: B 320 SER cc_start: 0.8472 (t) cc_final: 0.8125 (p) REVERT: B 321 LYS cc_start: 0.8150 (mtpt) cc_final: 0.7901 (mttt) REVERT: B 336 GLN cc_start: 0.6875 (tt0) cc_final: 0.6580 (tt0) REVERT: B 375 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7897 (ttmm) REVERT: D 341 SER cc_start: 0.6586 (m) cc_final: 0.6362 (t) REVERT: D 349 ARG cc_start: 0.7299 (mtt180) cc_final: 0.6152 (mmp-170) REVERT: F 320 SER cc_start: 0.8412 (t) cc_final: 0.8013 (p) REVERT: F 349 ARG cc_start: 0.6002 (ptt-90) cc_final: 0.5672 (pmt-80) outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 1.5639 time to fit residues: 135.6191 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 : 0.211 ------------------------------------------------------------------------------- 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 345 ASP Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain D residue 345 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN E 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.150182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.119764 restraints weight = 11562.655| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.64 r_work: 0.3745 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3396 Z= 0.230 Angle : 0.612 4.480 4548 Z= 0.322 Chirality : 0.051 0.138 516 Planarity : 0.003 0.014 576 Dihedral : 5.037 16.706 444 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.60 % Allowed : 17.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.33), 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 ARG 0.004 0.001 ARG C 349 TYR 0.012 0.003 TYR C 310 PHE 0.008 0.002 PHE E 346 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 3396) covalent geometry : angle 0.61212 ( 4548) hydrogen bonds : bond 0.02316 ( 83) hydrogen bonds : angle 4.63954 ( 249) *********************** 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 90 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7431 (mtt180) cc_final: 0.7142 (mtt180) REVERT: C 321 LYS cc_start: 0.8699 (mttt) cc_final: 0.8423 (mttp) REVERT: C 347 LYS cc_start: 0.7814 (mmpt) cc_final: 0.7597 (mmtt) REVERT: C 349 ARG cc_start: 0.7540 (mtt180) cc_final: 0.5782 (mmp-170) REVERT: E 336 GLN cc_start: 0.7917 (tt0) cc_final: 0.7290 (tt0) REVERT: E 338 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6343 (mt-10) REVERT: E 347 LYS cc_start: 0.7811 (mttt) cc_final: 0.6974 (pmtt) REVERT: E 375 LYS cc_start: 0.8500 (tttp) cc_final: 0.8022 (ttmm) REVERT: B 320 SER cc_start: 0.8485 (t) cc_final: 0.8120 (p) REVERT: B 321 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7941 (mttt) REVERT: B 336 GLN cc_start: 0.6851 (tt0) cc_final: 0.6629 (tt0) REVERT: B 375 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8005 (mtpp) REVERT: D 349 ARG cc_start: 0.7341 (mtt180) cc_final: 0.6195 (mmp-170) REVERT: D 369 LYS cc_start: 0.8357 (ttmm) cc_final: 0.8030 (ttmt) REVERT: F 349 ARG cc_start: 0.5972 (ptt-90) cc_final: 0.5673 (pmt-80) outliers start: 10 outliers final: 4 residues processed: 81 average time/residue: 1.6215 time to fit residues: 134.0752 Evaluate side-chains 85 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 338 GLU Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain D residue 345 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.151360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.121210 restraints weight = 11562.462| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.65 r_work: 0.3737 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4910 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= 0.169 Angle : 0.555 4.147 4548 Z= 0.290 Chirality : 0.050 0.137 516 Planarity : 0.002 0.016 576 Dihedral : 4.945 17.145 444 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.82 % Allowed : 17.45 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (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 ARG 0.002 0.000 ARG C 349 TYR 0.010 0.002 TYR B 310 PHE 0.006 0.002 PHE E 378 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 3396) covalent geometry : angle 0.55486 ( 4548) hydrogen bonds : bond 0.02011 ( 83) hydrogen bonds : angle 4.38748 ( 249) *********************** 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 90 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 347 LYS cc_start: 0.7826 (mttt) cc_final: 0.7469 (mmmm) REVERT: A 349 ARG cc_start: 0.7468 (mtt180) cc_final: 0.7145 (mtt180) REVERT: C 311 LYS cc_start: 0.6849 (mmtm) cc_final: 0.6606 (mmtm) REVERT: C 321 LYS cc_start: 0.8758 (mttt) cc_final: 0.8478 (mttp) REVERT: C 349 ARG cc_start: 0.7549 (mtt180) cc_final: 0.5794 (mmp-170) REVERT: E 336 GLN cc_start: 0.7825 (tt0) cc_final: 0.7213 (tt0) REVERT: E 338 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6396 (mt-10) REVERT: E 347 LYS cc_start: 0.7831 (mttt) cc_final: 0.7069 (pmtt) REVERT: B 320 SER cc_start: 0.8532 (t) cc_final: 0.8238 (p) REVERT: B 321 LYS cc_start: 0.8155 (mtpt) cc_final: 0.7948 (mttt) REVERT: B 375 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8025 (mtpp) REVERT: D 349 ARG cc_start: 0.7304 (mtt180) cc_final: 0.6180 (mmp-170) REVERT: D 369 LYS cc_start: 0.8364 (ttmm) cc_final: 0.8144 (ttmt) REVERT: F 349 ARG cc_start: 0.6067 (ptt-90) cc_final: 0.5677 (pmt-80) outliers start: 7 outliers final: 4 residues processed: 84 average time/residue: 1.6755 time to fit residues: 143.5824 Evaluate side-chains 85 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 338 GLU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain B residue 375 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.152970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.123166 restraints weight = 11352.102| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.64 r_work: 0.3801 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3396 Z= 0.118 Angle : 0.519 4.617 4548 Z= 0.267 Chirality : 0.050 0.137 516 Planarity : 0.002 0.016 576 Dihedral : 4.709 16.576 444 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (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 ARG 0.001 0.000 ARG C 349 TYR 0.009 0.002 TYR B 310 PHE 0.004 0.001 PHE C 346 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3396) covalent geometry : angle 0.51935 ( 4548) hydrogen bonds : bond 0.01703 ( 83) hydrogen bonds : angle 4.09272 ( 249) *********************** 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 85 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 347 LYS cc_start: 0.7797 (mttt) cc_final: 0.7438 (mmmm) REVERT: A 349 ARG cc_start: 0.7479 (mtt180) cc_final: 0.7184 (mtt180) REVERT: C 311 LYS cc_start: 0.6747 (mmtm) cc_final: 0.6506 (mmtm) REVERT: C 321 LYS cc_start: 0.8731 (mttt) cc_final: 0.8455 (mttp) REVERT: C 349 ARG cc_start: 0.7539 (mtt180) cc_final: 0.5722 (mmp-170) REVERT: E 336 GLN cc_start: 0.7820 (tt0) cc_final: 0.7229 (tt0) REVERT: E 338 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6381 (mt-10) REVERT: E 347 LYS cc_start: 0.7810 (mttt) cc_final: 0.7046 (pmtt) REVERT: B 320 SER cc_start: 0.8508 (t) cc_final: 0.8245 (p) REVERT: B 321 LYS cc_start: 0.8141 (mtpt) cc_final: 0.7923 (mttt) REVERT: B 375 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7964 (mtpp) REVERT: D 349 ARG cc_start: 0.7301 (mtt180) cc_final: 0.6187 (mmp-170) REVERT: D 369 LYS cc_start: 0.8345 (ttmm) cc_final: 0.8131 (ttmt) REVERT: F 349 ARG cc_start: 0.6082 (ptt-90) cc_final: 0.5684 (pmt-80) outliers start: 8 outliers final: 4 residues processed: 78 average time/residue: 1.6968 time to fit residues: 135.0651 Evaluate side-chains 83 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 338 GLU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain B residue 375 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.150693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.120274 restraints weight = 11542.525| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.65 r_work: 0.3760 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3396 Z= 0.190 Angle : 0.578 4.724 4548 Z= 0.304 Chirality : 0.050 0.137 516 Planarity : 0.002 0.019 576 Dihedral : 4.916 17.135 444 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.08 % Allowed : 18.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 349 TYR 0.011 0.003 TYR B 310 PHE 0.007 0.002 PHE E 346 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 3396) covalent geometry : angle 0.57801 ( 4548) hydrogen bonds : bond 0.02041 ( 83) hydrogen bonds : angle 4.42515 ( 249) *********************** 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 83 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7457 (mtt180) cc_final: 0.7232 (mtt180) REVERT: C 311 LYS cc_start: 0.6585 (mmtm) cc_final: 0.6333 (mmtm) REVERT: C 321 LYS cc_start: 0.8729 (mttt) cc_final: 0.8466 (mttp) REVERT: C 347 LYS cc_start: 0.7815 (mmpt) cc_final: 0.7601 (mmpt) REVERT: C 349 ARG cc_start: 0.7524 (mtt180) cc_final: 0.5809 (mmp-170) REVERT: E 336 GLN cc_start: 0.7842 (tt0) cc_final: 0.7243 (tt0) REVERT: E 338 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6393 (mt-10) REVERT: E 347 LYS cc_start: 0.7833 (mttt) cc_final: 0.7083 (pmtt) REVERT: B 320 SER cc_start: 0.8540 (t) cc_final: 0.8229 (p) REVERT: B 321 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7931 (mttt) REVERT: B 345 ASP cc_start: 0.6515 (p0) cc_final: 0.6103 (p0) REVERT: B 375 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8016 (mtpp) REVERT: D 349 ARG cc_start: 0.7328 (mtt180) cc_final: 0.6187 (mmp-170) REVERT: F 349 ARG cc_start: 0.6078 (ptt-90) cc_final: 0.5689 (pmt-80) outliers start: 8 outliers final: 4 residues processed: 76 average time/residue: 1.5419 time to fit residues: 119.6663 Evaluate side-chains 81 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 338 GLU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain B residue 375 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.154607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.125067 restraints weight = 11395.005| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.64 r_work: 0.3824 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3396 Z= 0.099 Angle : 0.508 5.100 4548 Z= 0.260 Chirality : 0.050 0.136 516 Planarity : 0.002 0.016 576 Dihedral : 4.598 16.044 444 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.56 % Allowed : 17.71 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (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 ARG 0.001 0.000 ARG F 349 TYR 0.008 0.002 TYR B 310 PHE 0.004 0.001 PHE C 346 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 3396) covalent geometry : angle 0.50780 ( 4548) hydrogen bonds : bond 0.01581 ( 83) hydrogen bonds : angle 3.99519 ( 249) *********************** 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 82 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 347 LYS cc_start: 0.7806 (mttt) cc_final: 0.7441 (mmmm) REVERT: A 349 ARG cc_start: 0.7443 (mtt180) cc_final: 0.7148 (mtt180) REVERT: C 311 LYS cc_start: 0.6574 (mmtm) cc_final: 0.6323 (mmtm) REVERT: C 321 LYS cc_start: 0.8740 (mttt) cc_final: 0.8487 (mttp) REVERT: C 331 LYS cc_start: 0.8384 (mtpt) cc_final: 0.8068 (mtmt) REVERT: C 349 ARG cc_start: 0.7544 (mtt180) cc_final: 0.5793 (mmp-170) REVERT: E 336 GLN cc_start: 0.7829 (tt0) cc_final: 0.7240 (tt0) REVERT: E 338 GLU cc_start: 0.6999 (tt0) cc_final: 0.6407 (mt-10) REVERT: E 347 LYS cc_start: 0.7800 (mttt) cc_final: 0.7066 (pmtt) REVERT: E 375 LYS cc_start: 0.8482 (tttp) cc_final: 0.8037 (ttmm) REVERT: B 311 LYS cc_start: 0.8254 (ttpt) cc_final: 0.8050 (pttt) REVERT: B 320 SER cc_start: 0.8506 (t) cc_final: 0.8272 (p) REVERT: B 321 LYS cc_start: 0.8131 (mtpt) cc_final: 0.7927 (mttt) REVERT: B 375 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7959 (mtpp) REVERT: D 349 ARG cc_start: 0.7305 (mtt180) cc_final: 0.6265 (mmp-170) REVERT: D 369 LYS cc_start: 0.8333 (ttmm) cc_final: 0.8132 (ttmt) REVERT: F 349 ARG cc_start: 0.6099 (ptt-90) cc_final: 0.5716 (pmt-80) outliers start: 6 outliers final: 4 residues processed: 77 average time/residue: 1.6040 time to fit residues: 126.0808 Evaluate side-chains 81 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 375 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.0980 chunk 41 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 0.0980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.157295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.128041 restraints weight = 11449.641| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.63 r_work: 0.3869 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3396 Z= 0.086 Angle : 0.484 4.385 4548 Z= 0.244 Chirality : 0.051 0.137 516 Planarity : 0.002 0.017 576 Dihedral : 4.199 14.864 444 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.30 % Allowed : 18.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.005 0.001 TYR B 310 PHE 0.003 0.001 PHE C 346 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 3396) covalent geometry : angle 0.48375 ( 4548) hydrogen bonds : bond 0.01399 ( 83) hydrogen bonds : angle 3.69789 ( 249) ********************** 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 83 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 347 LYS cc_start: 0.7806 (mttt) cc_final: 0.7450 (mmmm) REVERT: A 349 ARG cc_start: 0.7435 (mtt180) cc_final: 0.7080 (mtt180) REVERT: C 311 LYS cc_start: 0.6557 (mmtm) cc_final: 0.6141 (mmtm) REVERT: C 321 LYS cc_start: 0.8745 (mttt) cc_final: 0.8502 (mttp) REVERT: C 331 LYS cc_start: 0.8365 (mtpt) cc_final: 0.8073 (mtmt) REVERT: C 347 LYS cc_start: 0.7797 (mmpt) cc_final: 0.7596 (mmpt) REVERT: C 349 ARG cc_start: 0.7535 (mtt180) cc_final: 0.5801 (mmp-170) REVERT: E 336 GLN cc_start: 0.7846 (tt0) cc_final: 0.7236 (tt0) REVERT: E 338 GLU cc_start: 0.6986 (tt0) cc_final: 0.6402 (mt-10) REVERT: E 347 LYS cc_start: 0.7787 (mttt) cc_final: 0.6934 (pmtt) REVERT: E 375 LYS cc_start: 0.8456 (tttp) cc_final: 0.8016 (ttmm) REVERT: B 320 SER cc_start: 0.8531 (t) cc_final: 0.8260 (p) REVERT: B 321 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7897 (mttt) REVERT: B 375 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7886 (ttmm) REVERT: D 311 LYS cc_start: 0.8554 (ttpt) cc_final: 0.7748 (mmtm) REVERT: D 349 ARG cc_start: 0.7287 (mtt180) cc_final: 0.6255 (mmp-170) REVERT: F 349 ARG cc_start: 0.6169 (ptt-90) cc_final: 0.5797 (pmt-80) outliers start: 5 outliers final: 4 residues processed: 79 average time/residue: 1.6704 time to fit residues: 134.4914 Evaluate side-chains 82 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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 375 LYS 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 19 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.4177 r_free = 0.4177 target = 0.153512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.123442 restraints weight = 11423.514| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.66 r_work: 0.3803 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3396 Z= 0.125 Angle : 0.527 6.606 4548 Z= 0.273 Chirality : 0.050 0.136 516 Planarity : 0.002 0.017 576 Dihedral : 4.393 15.597 444 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.30 % Allowed : 19.27 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.33), 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 ARG 0.002 0.000 ARG C 349 TYR 0.008 0.002 TYR A 310 PHE 0.005 0.001 PHE D 346 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 3396) covalent geometry : angle 0.52663 ( 4548) hydrogen bonds : bond 0.01621 ( 83) hydrogen bonds : angle 3.92225 ( 249) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3916.21 seconds wall clock time: 67 minutes 1.36 seconds (4021.36 seconds total)