Starting phenix.real_space_refine on Tue Feb 11 16:41:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9k_18284/02_2025/8q9k_18284.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9k_18284/02_2025/8q9k_18284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q9k_18284/02_2025/8q9k_18284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9k_18284/02_2025/8q9k_18284.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9k_18284/02_2025/8q9k_18284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9k_18284/02_2025/8q9k_18284.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 1932 2.51 5 N 570 2.21 5 O 582 1.98 5 H 3216 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 6306 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "C" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "D" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "B" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "F" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Time building chain proxies: 4.20, per 1000 atoms: 0.67 Number of scatterers: 6306 At special positions: 0 Unit cell: (139.256, 84.048, 41.2, 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 582 8.00 N 570 7.00 C 1932 6.00 H 3216 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: 1.56 Conformation dependent library (CDL) restraints added in 431.1 milliseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 708 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 45.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 309 through 310 removed outlier: 6.552A pdb=" N VAL A 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.837A pdb=" N VAL A 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 317 through 322 removed outlier: 6.415A pdb=" N LYS A 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N SER F 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR A 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N CYS F 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS A 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 325 through 330 removed outlier: 6.913A pdb=" N GLY A 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN E 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY F 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN A 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 337 through 341 removed outlier: 6.613A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.648A pdb=" N ASP A 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 350 through 354 removed outlier: 6.381A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 357 through 362 removed outlier: 6.440A pdb=" N ASP A 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N THR F 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 360 " --> pdb=" O THR F 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 369 through 374 removed outlier: 6.568A pdb=" N LYS A 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLU F 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE A 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N HIS F 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR A 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 309 through 310 removed outlier: 6.488A pdb=" N VAL C 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL D 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.753A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL D 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.424A pdb=" N LYS C 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N SER D 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR C 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N CYS D 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS C 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS D 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N SER B 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR D 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N CYS B 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LYS D 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 325 through 330 removed outlier: 8.850A pdb=" N LEU C 325 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N ILE D 328 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN C 327 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N HIS D 330 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS C 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N LEU D 325 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N ILE B 328 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN D 327 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N HIS B 330 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N HIS D 329 " --> pdb=" O HIS B 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 337 through 340 Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.564A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP D 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 354 Processing sheet with id=AB8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.440A pdb=" N ASP C 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N THR D 361 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE C 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP D 358 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR B 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE D 360 " --> pdb=" O THR B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 369 through 374 removed outlier: 6.501A pdb=" N LYS C 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLU D 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE C 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N HIS D 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR C 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS D 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLU B 372 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE D 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N HIS B 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR D 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 47 hydrogen bonds defined for protein. 141 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: 1.94 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3210 1.12 - 1.29: 522 1.29 - 1.46: 891 1.46 - 1.63: 1725 1.63 - 1.81: 6 Bond restraints: 6354 Sorted by residual: bond pdb=" N SER C 324 " pdb=" H SER C 324 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE ARG A 349 " pdb=" HE ARG A 349 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CD2 PHE E 346 " pdb=" HD2 PHE E 346 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLU F 338 " pdb=" H GLU F 338 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LYS C 311 " pdb=" H LYS C 311 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 6349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 10214 3.10 - 6.19: 1247 6.19 - 9.29: 133 9.29 - 12.38: 6 12.38 - 15.48: 4 Bond angle restraints: 11604 Sorted by residual: angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 110.69 117.98 -7.29 1.33e+00 5.65e-01 3.00e+01 angle pdb=" C LYS C 340 " pdb=" N SER C 341 " pdb=" H SER C 341 " ideal model delta sigma weight residual 123.83 108.35 15.48 3.00e+00 1.11e-01 2.66e+01 angle pdb=" C LYS B 340 " pdb=" N SER B 341 " pdb=" H SER B 341 " ideal model delta sigma weight residual 123.83 108.63 15.20 3.00e+00 1.11e-01 2.57e+01 angle pdb=" N ARG D 349 " pdb=" CA ARG D 349 " pdb=" C ARG D 349 " ideal model delta sigma weight residual 110.35 117.23 -6.88 1.36e+00 5.41e-01 2.56e+01 angle pdb=" C LYS D 340 " pdb=" N SER D 341 " pdb=" H SER D 341 " ideal model delta sigma weight residual 123.83 108.95 14.88 3.00e+00 1.11e-01 2.46e+01 ... (remaining 11599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.63: 2579 13.63 - 27.26: 156 27.26 - 40.89: 58 40.89 - 54.52: 42 54.52 - 68.15: 87 Dihedral angle restraints: 2922 sinusoidal: 1680 harmonic: 1242 Sorted by residual: dihedral pdb=" C ARG B 349 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " pdb=" CB ARG B 349 " ideal model delta harmonic sigma weight residual -122.60 -133.04 10.44 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" C ARG F 349 " pdb=" N ARG F 349 " pdb=" CA ARG F 349 " pdb=" CB ARG F 349 " ideal model delta harmonic sigma weight residual -122.60 -132.63 10.03 0 2.50e+00 1.60e-01 1.61e+01 dihedral pdb=" N ARG B 349 " pdb=" C ARG B 349 " pdb=" CA ARG B 349 " pdb=" CB ARG B 349 " ideal model delta harmonic sigma weight residual 122.80 131.83 -9.03 0 2.50e+00 1.60e-01 1.31e+01 ... (remaining 2919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 323 0.085 - 0.169: 124 0.169 - 0.254: 16 0.254 - 0.338: 2 0.338 - 0.423: 3 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA ARG B 349 " pdb=" N ARG B 349 " pdb=" C ARG B 349 " pdb=" CB ARG B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CA ARG F 349 " pdb=" N ARG F 349 " pdb=" C ARG F 349 " pdb=" CB ARG F 349 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA ARG D 349 " pdb=" N ARG D 349 " pdb=" C ARG D 349 " pdb=" CB ARG D 349 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.38 2.00e-01 2.50e+01 3.52e+00 ... (remaining 465 not shown) Planarity restraints: 918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 340 " 0.046 2.00e-02 2.50e+03 8.41e-02 7.07e+01 pdb=" N SER B 341 " -0.145 2.00e-02 2.50e+03 pdb=" CA SER B 341 " 0.045 2.00e-02 2.50e+03 pdb=" H SER B 341 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 340 " 0.044 2.00e-02 2.50e+03 7.88e-02 6.21e+01 pdb=" N SER C 341 " -0.136 2.00e-02 2.50e+03 pdb=" CA SER C 341 " 0.042 2.00e-02 2.50e+03 pdb=" H SER C 341 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 340 " 0.041 2.00e-02 2.50e+03 7.42e-02 5.51e+01 pdb=" N SER D 341 " -0.128 2.00e-02 2.50e+03 pdb=" CA SER D 341 " 0.039 2.00e-02 2.50e+03 pdb=" H SER D 341 " 0.048 2.00e-02 2.50e+03 ... (remaining 915 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 475 2.18 - 2.78: 10985 2.78 - 3.39: 16438 3.39 - 3.99: 21542 3.99 - 4.60: 30268 Nonbonded interactions: 79708 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.571 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.573 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.579 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.583 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.597 2.450 ... (remaining 79703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.460 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 3138 Z= 0.741 Angle : 1.997 7.291 4194 Z= 1.327 Chirality : 0.088 0.423 468 Planarity : 0.011 0.092 534 Dihedral : 9.094 65.306 1212 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.94 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.003 HIS B 330 PHE 0.037 0.018 PHE D 346 TYR 0.049 0.014 TYR D 310 ARG 0.007 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 317 LYS cc_start: 0.8756 (pttt) cc_final: 0.7914 (mmmt) REVERT: C 317 LYS cc_start: 0.8615 (pttt) cc_final: 0.7747 (mmtt) REVERT: C 345 ASP cc_start: 0.7730 (t0) cc_final: 0.7432 (t70) REVERT: F 340 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7594 (tttm) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.6125 time to fit residues: 102.1452 Evaluate side-chains 90 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.169548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.133572 restraints weight = 10684.165| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.40 r_work: 0.4105 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4007 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3138 Z= 0.170 Angle : 0.549 4.293 4194 Z= 0.288 Chirality : 0.052 0.135 468 Planarity : 0.004 0.032 534 Dihedral : 5.534 19.103 414 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.13 % Allowed : 7.63 % Favored : 91.24 % 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: -1.78 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 330 PHE 0.006 0.002 PHE D 346 TYR 0.003 0.001 TYR E 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 THR cc_start: 0.8675 (m) cc_final: 0.8443 (p) REVERT: E 317 LYS cc_start: 0.8825 (pttt) cc_final: 0.7041 (mmmt) REVERT: E 340 LYS cc_start: 0.8294 (ttmt) cc_final: 0.8041 (tttt) REVERT: E 372 GLU cc_start: 0.5918 (pm20) cc_final: 0.5673 (pm20) REVERT: C 317 LYS cc_start: 0.8771 (pttt) cc_final: 0.6970 (mmmt) REVERT: C 345 ASP cc_start: 0.8345 (t0) cc_final: 0.8005 (t0) REVERT: C 347 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8249 (mmtm) REVERT: D 331 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7457 (tptt) REVERT: D 345 ASP cc_start: 0.8336 (t70) cc_final: 0.7575 (t0) REVERT: D 347 LYS cc_start: 0.8766 (mmtp) cc_final: 0.8194 (mmtt) REVERT: D 372 GLU cc_start: 0.8265 (tt0) cc_final: 0.7747 (tp30) REVERT: B 345 ASP cc_start: 0.8237 (t70) cc_final: 0.7964 (t0) REVERT: F 369 LYS cc_start: 0.8854 (mtmt) cc_final: 0.8375 (mtmm) outliers start: 4 outliers final: 4 residues processed: 106 average time/residue: 0.4648 time to fit residues: 56.2321 Evaluate side-chains 97 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.163986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.127761 restraints weight = 11030.796| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.40 r_work: 0.4028 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3932 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3138 Z= 0.257 Angle : 0.540 4.097 4194 Z= 0.282 Chirality : 0.052 0.132 468 Planarity : 0.004 0.036 534 Dihedral : 5.283 18.495 414 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.26 % Allowed : 7.63 % Favored : 90.11 % 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: -1.73 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 329 PHE 0.006 0.001 PHE E 346 TYR 0.005 0.001 TYR E 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 THR cc_start: 0.8739 (m) cc_final: 0.8520 (p) REVERT: A 373 THR cc_start: 0.8882 (m) cc_final: 0.8412 (p) REVERT: E 317 LYS cc_start: 0.8865 (pttt) cc_final: 0.7079 (mmmt) REVERT: E 369 LYS cc_start: 0.8859 (mtpt) cc_final: 0.8411 (mtmt) REVERT: C 317 LYS cc_start: 0.8824 (pttt) cc_final: 0.7022 (mmmt) REVERT: C 345 ASP cc_start: 0.8317 (t0) cc_final: 0.7936 (t0) REVERT: C 347 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8300 (mmtm) REVERT: C 369 LYS cc_start: 0.8968 (mtmt) cc_final: 0.8688 (mtmt) REVERT: D 345 ASP cc_start: 0.8372 (t70) cc_final: 0.7704 (t0) REVERT: D 347 LYS cc_start: 0.8781 (mmtp) cc_final: 0.8220 (mmtt) REVERT: D 372 GLU cc_start: 0.8323 (tt0) cc_final: 0.7822 (tp30) REVERT: B 345 ASP cc_start: 0.8327 (t70) cc_final: 0.8102 (t0) outliers start: 8 outliers final: 8 residues processed: 93 average time/residue: 0.4962 time to fit residues: 52.1195 Evaluate side-chains 90 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 309 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.164517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.128437 restraints weight = 11020.126| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.38 r_work: 0.4023 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3928 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3138 Z= 0.247 Angle : 0.519 4.384 4194 Z= 0.272 Chirality : 0.052 0.130 468 Planarity : 0.004 0.037 534 Dihedral : 5.196 17.433 414 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.69 % Allowed : 9.32 % Favored : 88.98 % 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: -1.82 (0.33), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 329 PHE 0.004 0.001 PHE E 346 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 THR cc_start: 0.8637 (m) cc_final: 0.8420 (p) REVERT: E 317 LYS cc_start: 0.8804 (pttt) cc_final: 0.7027 (mmmt) REVERT: E 348 ASP cc_start: 0.8657 (t0) cc_final: 0.8417 (t0) REVERT: E 349 ARG cc_start: 0.7873 (ptp-170) cc_final: 0.5096 (mmm-85) REVERT: C 317 LYS cc_start: 0.8783 (pttt) cc_final: 0.6969 (mmmt) REVERT: C 345 ASP cc_start: 0.8276 (t0) cc_final: 0.7861 (t0) REVERT: C 347 LYS cc_start: 0.8725 (mmtt) cc_final: 0.8266 (mmtm) REVERT: C 349 ARG cc_start: 0.7962 (ptp-170) cc_final: 0.5061 (mmm-85) REVERT: D 345 ASP cc_start: 0.8344 (t70) cc_final: 0.7641 (t0) REVERT: D 347 LYS cc_start: 0.8790 (mmtp) cc_final: 0.8186 (mmtt) REVERT: D 372 GLU cc_start: 0.8325 (tt0) cc_final: 0.7788 (tp30) REVERT: B 345 ASP cc_start: 0.8349 (t70) cc_final: 0.8105 (t0) outliers start: 6 outliers final: 6 residues processed: 89 average time/residue: 0.5102 time to fit residues: 51.1214 Evaluate side-chains 92 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.168761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.132658 restraints weight = 10799.663| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 2.43 r_work: 0.4078 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3982 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3138 Z= 0.164 Angle : 0.477 4.048 4194 Z= 0.245 Chirality : 0.051 0.133 468 Planarity : 0.004 0.039 534 Dihedral : 4.817 17.072 414 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.98 % Allowed : 10.17 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 329 PHE 0.002 0.001 PHE E 346 TYR 0.004 0.001 TYR E 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 THR cc_start: 0.8617 (m) cc_final: 0.8405 (p) REVERT: A 372 GLU cc_start: 0.8381 (tt0) cc_final: 0.7893 (tp30) REVERT: E 317 LYS cc_start: 0.8762 (pttt) cc_final: 0.6961 (mmmt) REVERT: E 340 LYS cc_start: 0.8258 (ttmt) cc_final: 0.8006 (tttt) REVERT: E 348 ASP cc_start: 0.8591 (t0) cc_final: 0.8377 (t0) REVERT: E 349 ARG cc_start: 0.7884 (ptp-170) cc_final: 0.5042 (mmm-85) REVERT: E 369 LYS cc_start: 0.8782 (mtpt) cc_final: 0.8164 (mtmm) REVERT: C 317 LYS cc_start: 0.8757 (pttt) cc_final: 0.6957 (mmmt) REVERT: C 345 ASP cc_start: 0.8272 (t0) cc_final: 0.7867 (t0) REVERT: C 347 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8283 (mmtm) REVERT: C 349 ARG cc_start: 0.7907 (ptp-170) cc_final: 0.5050 (mmm-85) REVERT: D 345 ASP cc_start: 0.8326 (t70) cc_final: 0.7627 (t0) REVERT: D 347 LYS cc_start: 0.8728 (mmtp) cc_final: 0.8095 (mmtt) REVERT: D 372 GLU cc_start: 0.8328 (tt0) cc_final: 0.7786 (tp30) REVERT: B 345 ASP cc_start: 0.8314 (t70) cc_final: 0.8035 (t0) REVERT: F 345 ASP cc_start: 0.8297 (t0) cc_final: 0.7779 (t0) REVERT: F 347 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8509 (mmtt) outliers start: 7 outliers final: 7 residues processed: 95 average time/residue: 0.5404 time to fit residues: 57.7174 Evaluate side-chains 94 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 28 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.164495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.128177 restraints weight = 10835.171| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.39 r_work: 0.4026 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3928 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3138 Z= 0.237 Angle : 0.497 4.393 4194 Z= 0.259 Chirality : 0.051 0.131 468 Planarity : 0.004 0.040 534 Dihedral : 4.955 16.325 414 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.26 % Allowed : 10.73 % Favored : 87.01 % 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: -1.77 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 329 PHE 0.005 0.001 PHE E 346 TYR 0.004 0.001 TYR E 310 ARG 0.003 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 THR cc_start: 0.8629 (m) cc_final: 0.8416 (p) REVERT: A 372 GLU cc_start: 0.8414 (tt0) cc_final: 0.7979 (tp30) REVERT: E 317 LYS cc_start: 0.8778 (pttt) cc_final: 0.6979 (mmmt) REVERT: E 348 ASP cc_start: 0.8742 (t0) cc_final: 0.8497 (t0) REVERT: E 349 ARG cc_start: 0.7929 (ptp-170) cc_final: 0.5180 (mmm-85) REVERT: E 369 LYS cc_start: 0.8759 (mtpt) cc_final: 0.8147 (mtmm) REVERT: C 317 LYS cc_start: 0.8756 (pttt) cc_final: 0.6924 (mmmt) REVERT: C 345 ASP cc_start: 0.8234 (t0) cc_final: 0.7806 (t0) REVERT: C 347 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8252 (mmtm) REVERT: D 345 ASP cc_start: 0.8291 (t70) cc_final: 0.7586 (t0) REVERT: D 347 LYS cc_start: 0.8791 (mmtp) cc_final: 0.8155 (mmtt) REVERT: D 372 GLU cc_start: 0.8293 (tt0) cc_final: 0.7807 (tp30) REVERT: B 345 ASP cc_start: 0.8338 (t70) cc_final: 0.8077 (t0) outliers start: 8 outliers final: 8 residues processed: 89 average time/residue: 0.5033 time to fit residues: 50.9992 Evaluate side-chains 89 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.167759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.131636 restraints weight = 10913.038| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.42 r_work: 0.4068 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3969 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.6199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3138 Z= 0.172 Angle : 0.468 4.245 4194 Z= 0.239 Chirality : 0.051 0.131 468 Planarity : 0.004 0.038 534 Dihedral : 4.695 16.268 414 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.98 % Allowed : 11.30 % Favored : 86.72 % 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: -1.64 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 329 PHE 0.002 0.001 PHE E 346 TYR 0.004 0.001 TYR E 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 317 LYS cc_start: 0.8764 (pttt) cc_final: 0.6972 (mmmt) REVERT: E 340 LYS cc_start: 0.8269 (ttmt) cc_final: 0.8043 (tttt) REVERT: E 349 ARG cc_start: 0.7922 (ptp-170) cc_final: 0.5077 (mmm-85) REVERT: E 369 LYS cc_start: 0.8757 (mtpt) cc_final: 0.8152 (mtmm) REVERT: C 317 LYS cc_start: 0.8771 (pttt) cc_final: 0.6982 (mmmt) REVERT: C 345 ASP cc_start: 0.8236 (t0) cc_final: 0.7821 (t0) REVERT: C 347 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8288 (mmtm) REVERT: D 345 ASP cc_start: 0.8291 (t70) cc_final: 0.7591 (t0) REVERT: D 347 LYS cc_start: 0.8778 (mmtp) cc_final: 0.8156 (mmtt) REVERT: D 372 GLU cc_start: 0.8283 (tt0) cc_final: 0.7721 (tp30) REVERT: B 345 ASP cc_start: 0.8353 (t70) cc_final: 0.8084 (t0) REVERT: B 372 GLU cc_start: 0.7992 (mm-30) cc_final: 0.6788 (mm-30) REVERT: F 345 ASP cc_start: 0.8313 (t0) cc_final: 0.8032 (t0) REVERT: F 347 LYS cc_start: 0.8820 (mmtt) cc_final: 0.8606 (mmtt) outliers start: 7 outliers final: 7 residues processed: 92 average time/residue: 0.5077 time to fit residues: 53.2735 Evaluate side-chains 92 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.161799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.125607 restraints weight = 10962.419| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.39 r_work: 0.3990 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3893 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.6277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3138 Z= 0.318 Angle : 0.529 4.567 4194 Z= 0.276 Chirality : 0.051 0.130 468 Planarity : 0.004 0.036 534 Dihedral : 5.161 16.032 414 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.26 % Allowed : 11.58 % Favored : 86.16 % 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: -1.84 (0.33), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 329 PHE 0.005 0.001 PHE D 346 TYR 0.004 0.001 TYR A 310 ARG 0.003 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8346 (tt0) cc_final: 0.7992 (tp30) REVERT: E 317 LYS cc_start: 0.8802 (pttt) cc_final: 0.7034 (mmmt) REVERT: E 349 ARG cc_start: 0.8015 (ptp-170) cc_final: 0.5191 (mmm-85) REVERT: C 317 LYS cc_start: 0.8779 (pttt) cc_final: 0.7012 (mmmt) REVERT: C 345 ASP cc_start: 0.8257 (t0) cc_final: 0.7832 (t0) REVERT: C 347 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8349 (mmtm) REVERT: C 348 ASP cc_start: 0.8840 (t70) cc_final: 0.8628 (t0) REVERT: D 331 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7728 (mttp) REVERT: D 345 ASP cc_start: 0.8302 (t70) cc_final: 0.7844 (t0) REVERT: D 372 GLU cc_start: 0.8279 (tt0) cc_final: 0.7771 (tp30) REVERT: B 314 ASP cc_start: 0.8518 (t0) cc_final: 0.8314 (t0) REVERT: B 345 ASP cc_start: 0.8384 (t70) cc_final: 0.8142 (t0) REVERT: F 345 ASP cc_start: 0.8383 (t0) cc_final: 0.8167 (t0) REVERT: F 347 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8558 (mmtt) REVERT: F 358 ASP cc_start: 0.8496 (t0) cc_final: 0.8276 (t0) outliers start: 8 outliers final: 8 residues processed: 86 average time/residue: 0.4262 time to fit residues: 42.5806 Evaluate side-chains 85 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.168623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.132502 restraints weight = 10830.005| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 2.44 r_work: 0.4081 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3983 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.6378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3138 Z= 0.155 Angle : 0.467 4.249 4194 Z= 0.237 Chirality : 0.051 0.133 468 Planarity : 0.004 0.041 534 Dihedral : 4.629 16.077 414 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.98 % Allowed : 12.15 % Favored : 85.88 % 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: -1.68 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 330 PHE 0.002 0.001 PHE C 346 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8271 (tt0) cc_final: 0.8033 (tp30) REVERT: E 317 LYS cc_start: 0.8780 (pttt) cc_final: 0.7007 (mmmt) REVERT: E 340 LYS cc_start: 0.8299 (ttmt) cc_final: 0.8091 (tttt) REVERT: E 349 ARG cc_start: 0.7965 (ptp-170) cc_final: 0.5310 (mmm160) REVERT: C 317 LYS cc_start: 0.8790 (pttt) cc_final: 0.6985 (mmmt) REVERT: C 345 ASP cc_start: 0.8247 (t0) cc_final: 0.7824 (t0) REVERT: C 347 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8295 (mmtm) REVERT: C 369 LYS cc_start: 0.8888 (mtmt) cc_final: 0.8505 (mtmm) REVERT: D 345 ASP cc_start: 0.8248 (t70) cc_final: 0.7605 (t0) REVERT: D 347 LYS cc_start: 0.8758 (mmtp) cc_final: 0.8146 (mmtt) REVERT: D 372 GLU cc_start: 0.8268 (tt0) cc_final: 0.7753 (tp30) REVERT: B 314 ASP cc_start: 0.8596 (t0) cc_final: 0.8318 (t0) REVERT: B 345 ASP cc_start: 0.8357 (t70) cc_final: 0.8087 (t0) REVERT: B 372 GLU cc_start: 0.7942 (mm-30) cc_final: 0.6743 (mm-30) REVERT: F 358 ASP cc_start: 0.8442 (t0) cc_final: 0.8206 (t0) outliers start: 7 outliers final: 7 residues processed: 98 average time/residue: 0.4912 time to fit residues: 54.8727 Evaluate side-chains 96 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 0.0770 chunk 14 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 25 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.168338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.132087 restraints weight = 10944.488| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.44 r_work: 0.4077 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3974 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.6418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3138 Z= 0.190 Angle : 0.482 4.585 4194 Z= 0.246 Chirality : 0.051 0.132 468 Planarity : 0.004 0.036 534 Dihedral : 4.599 15.543 414 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.98 % Allowed : 11.58 % Favored : 86.44 % 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: -1.66 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.002 0.001 PHE A 346 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.000 ARG D 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8320 (tt0) cc_final: 0.8029 (tp30) REVERT: E 317 LYS cc_start: 0.8786 (pttt) cc_final: 0.7015 (mmmt) REVERT: E 349 ARG cc_start: 0.8007 (ptp-170) cc_final: 0.5331 (mmm160) REVERT: C 317 LYS cc_start: 0.8805 (pttt) cc_final: 0.7082 (mmmt) REVERT: C 349 ARG cc_start: 0.8207 (ptp-170) cc_final: 0.5355 (mmm160) REVERT: C 369 LYS cc_start: 0.8893 (mtmt) cc_final: 0.8509 (mtmm) REVERT: D 345 ASP cc_start: 0.8275 (t70) cc_final: 0.7658 (t0) REVERT: D 347 LYS cc_start: 0.8787 (mmtp) cc_final: 0.8177 (mmtt) REVERT: B 314 ASP cc_start: 0.8595 (t0) cc_final: 0.8345 (t0) REVERT: B 345 ASP cc_start: 0.8364 (t70) cc_final: 0.8109 (t0) REVERT: B 372 GLU cc_start: 0.7948 (mm-30) cc_final: 0.6940 (mm-30) REVERT: F 358 ASP cc_start: 0.8454 (t0) cc_final: 0.8233 (t0) outliers start: 7 outliers final: 7 residues processed: 91 average time/residue: 0.4852 time to fit residues: 50.1144 Evaluate side-chains 93 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.168441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.132105 restraints weight = 11080.708| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.46 r_work: 0.4078 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3976 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.6447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3138 Z= 0.191 Angle : 0.479 4.394 4194 Z= 0.244 Chirality : 0.051 0.131 468 Planarity : 0.004 0.037 534 Dihedral : 4.590 15.511 414 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.98 % Allowed : 11.86 % Favored : 86.16 % 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: -1.66 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.002 0.001 PHE E 346 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.000 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4708.83 seconds wall clock time: 83 minutes 33.70 seconds (5013.70 seconds total)