Starting phenix.real_space_refine on Tue Mar 3 11:28:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qk2_14029/03_2026/7qk2_14029.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qk2_14029/03_2026/7qk2_14029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qk2_14029/03_2026/7qk2_14029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qk2_14029/03_2026/7qk2_14029.map" model { file = "/net/cci-nas-00/data/ceres_data/7qk2_14029/03_2026/7qk2_14029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qk2_14029/03_2026/7qk2_14029.cif" } resolution = 2.61 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= 0.004 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2046 2.51 5 N 588 2.21 5 O 606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3246 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "B" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "C" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "D" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "E" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "F" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Time building chain proxies: 0.85, per 1000 atoms: 0.26 Number of scatterers: 3246 At special positions: 0 Unit cell: (114.502, 110.14, 49.0725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 606 8.00 N 588 7.00 C 2046 6.00 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: 0.19 Conformation dependent library (CDL) restraints added in 127.5 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 47.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 309 through 310 removed outlier: 6.556A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.804A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 325 removed outlier: 6.418A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N SER B 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR A 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N CYS B 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS A 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER B 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLY A 323 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.403A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 341 removed outlier: 6.495A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.699A pdb=" N ASP A 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 350 through 354 removed outlier: 6.571A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.676A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 377 removed outlier: 6.404A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASN A 368 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE C 371 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N THR C 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU A 372 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LYS C 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N HIS A 374 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N THR C 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 309 through 310 removed outlier: 6.589A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.834A pdb=" N VAL D 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 317 through 325 removed outlier: 6.533A pdb=" N LYS D 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N SER E 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR D 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N CYS E 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LYS D 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N SER E 324 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLY D 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 328 through 330 removed outlier: 6.371A pdb=" N ILE D 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 336 through 341 removed outlier: 6.494A pdb=" N VAL D 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LYS F 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL D 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.675A pdb=" N ASP D 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 350 through 354 removed outlier: 6.622A pdb=" N GLN D 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE E 354 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS D 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 359 through 362 Processing sheet with id=AB9, first strand: chain 'E' and resid 368 through 377 removed outlier: 6.440A pdb=" N ASN D 368 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE F 371 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS D 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N THR F 373 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLU D 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N LYS F 375 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N HIS D 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N THR F 377 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU D 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) 62 hydrogen bonds defined for protein. 186 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: 0.30 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 937 1.33 - 1.45: 377 1.45 - 1.57: 1980 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3300 Sorted by residual: bond pdb=" CZ ARG B 349 " pdb=" NH2 ARG B 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 7.00e+00 bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.93e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.87e+00 bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.62e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.57e+00 ... (remaining 3295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 2518 1.37 - 2.74: 1298 2.74 - 4.11: 445 4.11 - 5.48: 120 5.48 - 6.85: 35 Bond angle restraints: 4416 Sorted by residual: angle pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " pdb=" CG ASP E 358 " ideal model delta sigma weight residual 112.60 118.08 -5.48 1.00e+00 1.00e+00 3.00e+01 angle pdb=" OE1 GLN F 351 " pdb=" CD GLN F 351 " pdb=" NE2 GLN F 351 " ideal model delta sigma weight residual 122.60 117.24 5.36 1.00e+00 1.00e+00 2.87e+01 angle pdb=" N SER D 356 " pdb=" CA SER D 356 " pdb=" C SER D 356 " ideal model delta sigma weight residual 111.14 116.87 -5.73 1.08e+00 8.57e-01 2.81e+01 angle pdb=" OE1 GLN D 351 " pdb=" CD GLN D 351 " pdb=" NE2 GLN D 351 " ideal model delta sigma weight residual 122.60 117.41 5.19 1.00e+00 1.00e+00 2.69e+01 angle pdb=" N SER A 356 " pdb=" CA SER A 356 " pdb=" C SER A 356 " ideal model delta sigma weight residual 111.07 116.46 -5.39 1.07e+00 8.73e-01 2.54e+01 ... (remaining 4411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.68: 1726 10.68 - 21.36: 208 21.36 - 32.04: 42 32.04 - 42.71: 18 42.71 - 53.39: 10 Dihedral angle restraints: 2004 sinusoidal: 834 harmonic: 1170 Sorted by residual: dihedral pdb=" CA HIS C 374 " pdb=" C HIS C 374 " pdb=" N LYS C 375 " pdb=" CA LYS C 375 " ideal model delta harmonic sigma weight residual 180.00 153.77 26.23 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA LYS D 369 " pdb=" C LYS D 369 " pdb=" N LYS D 370 " pdb=" CA LYS D 370 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA LYS E 369 " pdb=" C LYS E 369 " pdb=" N LYS E 370 " pdb=" CA LYS E 370 " ideal model delta harmonic sigma weight residual 180.00 156.69 23.31 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 2001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 310 0.077 - 0.153: 129 0.153 - 0.230: 32 0.230 - 0.307: 21 0.307 - 0.383: 6 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA LYS A 375 " pdb=" N LYS A 375 " pdb=" C LYS A 375 " pdb=" CB LYS A 375 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA LYS F 347 " pdb=" N LYS F 347 " pdb=" C LYS F 347 " pdb=" CB LYS F 347 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CA GLN A 351 " pdb=" N GLN A 351 " pdb=" C GLN A 351 " pdb=" CB GLN A 351 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 495 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 346 " -0.048 2.00e-02 2.50e+03 2.92e-02 1.50e+01 pdb=" CG PHE F 346 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE F 346 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE F 346 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE F 346 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE F 346 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE F 346 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " -0.050 2.00e-02 2.50e+03 2.66e-02 1.42e+01 pdb=" CG TYR F 310 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 346 " -0.044 2.00e-02 2.50e+03 2.70e-02 1.28e+01 pdb=" CG PHE D 346 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE D 346 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE D 346 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE D 346 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE D 346 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE D 346 " -0.026 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1431 2.98 - 3.46: 2496 3.46 - 3.94: 5222 3.94 - 4.42: 5015 4.42 - 4.90: 9837 Nonbonded interactions: 24001 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.499 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.508 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.508 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.514 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.531 3.040 ... (remaining 23996 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: 0.620 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.920 Find NCS groups from input model: 0.030 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:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 0.034 3300 Z= 0.696 Angle : 1.864 6.853 4416 Z= 1.222 Chirality : 0.106 0.383 498 Planarity : 0.009 0.062 558 Dihedral : 10.807 53.393 1260 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Cbeta Deviations : 2.69 % 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 are not related in a simple way. whole: -1.51 (0.33), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 349 TYR 0.050 0.011 TYR F 310 PHE 0.048 0.013 PHE F 346 HIS 0.018 0.003 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.01103 ( 3300) covalent geometry : angle 1.86421 ( 4416) hydrogen bonds : bond 0.06082 ( 62) hydrogen bonds : angle 7.98926 ( 186) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8252 (mt-10) cc_final: 0.8051 (mt-10) REVERT: B 347 LYS cc_start: 0.8626 (mttp) cc_final: 0.7982 (pptt) REVERT: C 311 LYS cc_start: 0.7880 (mttt) cc_final: 0.7630 (mttm) REVERT: C 349 ARG cc_start: 0.8493 (mtt180) cc_final: 0.7029 (mmp-170) REVERT: D 340 LYS cc_start: 0.8417 (mmmm) cc_final: 0.8141 (mptp) REVERT: E 336 GLN cc_start: 0.8745 (tt0) cc_final: 0.8500 (tt0) REVERT: F 336 GLN cc_start: 0.8542 (tt0) cc_final: 0.8279 (tt0) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.6903 time to fit residues: 107.5874 Evaluate side-chains 109 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.080 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN C 336 GLN D 359 ASN E 330 HIS E 359 ASN F 351 GLN F 359 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.121180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.108531 restraints weight = 4078.512| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.58 r_work: 0.3443 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3300 Z= 0.105 Angle : 0.609 5.270 4416 Z= 0.301 Chirality : 0.049 0.123 498 Planarity : 0.003 0.018 558 Dihedral : 5.449 13.233 432 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.57 % Allowed : 19.62 % Favored : 75.81 % 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 are not related in a simple way. whole: -1.36 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 349 TYR 0.007 0.001 TYR F 310 PHE 0.011 0.002 PHE D 346 HIS 0.001 0.000 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 3300) covalent geometry : angle 0.60910 ( 4416) hydrogen bonds : bond 0.02128 ( 62) hydrogen bonds : angle 5.26362 ( 186) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8234 (mptm) cc_final: 0.7820 (mtpt) REVERT: A 351 GLN cc_start: 0.8609 (pt0) cc_final: 0.8307 (mt0) REVERT: B 347 LYS cc_start: 0.8147 (mttp) cc_final: 0.7627 (pptt) REVERT: B 359 ASN cc_start: 0.9207 (m110) cc_final: 0.8982 (m-40) REVERT: C 311 LYS cc_start: 0.8651 (mttt) cc_final: 0.8006 (mtpp) REVERT: C 345 ASP cc_start: 0.8296 (t0) cc_final: 0.7797 (t70) REVERT: C 347 LYS cc_start: 0.8796 (mmtp) cc_final: 0.8267 (mmtp) REVERT: C 348 ASP cc_start: 0.8639 (t70) cc_final: 0.8390 (t70) REVERT: C 349 ARG cc_start: 0.8328 (mtt180) cc_final: 0.6643 (mmp-170) REVERT: C 351 GLN cc_start: 0.8562 (pt0) cc_final: 0.8237 (pt0) REVERT: D 343 LYS cc_start: 0.7851 (ptmt) cc_final: 0.7643 (ptmt) REVERT: E 340 LYS cc_start: 0.8405 (tppt) cc_final: 0.8176 (mmtm) REVERT: F 336 GLN cc_start: 0.8249 (tt0) cc_final: 0.7973 (mt0) REVERT: F 338 GLU cc_start: 0.8292 (tt0) cc_final: 0.7828 (tm-30) outliers start: 17 outliers final: 2 residues processed: 141 average time/residue: 0.6620 time to fit residues: 95.1910 Evaluate side-chains 108 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN D 359 ASN E 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.111498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.099237 restraints weight = 4203.308| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.58 r_work: 0.3307 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3300 Z= 0.266 Angle : 0.702 5.728 4416 Z= 0.351 Chirality : 0.051 0.134 498 Planarity : 0.004 0.030 558 Dihedral : 5.876 16.328 432 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.11 % Allowed : 22.31 % Favored : 72.58 % 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 are not related in a simple way. whole: -1.62 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 349 TYR 0.014 0.003 TYR F 310 PHE 0.016 0.003 PHE F 378 HIS 0.003 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00636 ( 3300) covalent geometry : angle 0.70243 ( 4416) hydrogen bonds : bond 0.02344 ( 62) hydrogen bonds : angle 4.86785 ( 186) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8273 (mptm) cc_final: 0.7937 (mtpt) REVERT: A 351 GLN cc_start: 0.8712 (pt0) cc_final: 0.8416 (mt0) REVERT: B 347 LYS cc_start: 0.8403 (mttp) cc_final: 0.7758 (pptt) REVERT: C 311 LYS cc_start: 0.8679 (mttt) cc_final: 0.8058 (mttm) REVERT: C 348 ASP cc_start: 0.8763 (t70) cc_final: 0.8461 (t70) REVERT: C 349 ARG cc_start: 0.8362 (mtt180) cc_final: 0.6743 (mmp-170) REVERT: C 351 GLN cc_start: 0.8754 (pt0) cc_final: 0.8336 (pt0) REVERT: D 369 LYS cc_start: 0.8592 (mtpm) cc_final: 0.8357 (ttpt) REVERT: E 336 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8375 (mt0) REVERT: E 349 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8060 (mtp180) REVERT: E 369 LYS cc_start: 0.8879 (mtpm) cc_final: 0.8609 (tttp) REVERT: F 336 GLN cc_start: 0.8360 (tt0) cc_final: 0.8068 (mt0) REVERT: F 338 GLU cc_start: 0.8328 (tt0) cc_final: 0.7379 (tm-30) REVERT: F 340 LYS cc_start: 0.8251 (mmmm) cc_final: 0.8033 (mttm) outliers start: 19 outliers final: 9 residues processed: 113 average time/residue: 0.6721 time to fit residues: 77.4118 Evaluate side-chains 105 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 375 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.111518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.099346 restraints weight = 4199.791| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.57 r_work: 0.3306 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3300 Z= 0.261 Angle : 0.669 4.873 4416 Z= 0.334 Chirality : 0.049 0.131 498 Planarity : 0.004 0.031 558 Dihedral : 5.764 16.450 432 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 6.18 % Allowed : 22.04 % Favored : 71.77 % 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 are not related in a simple way. whole: -1.81 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 349 TYR 0.014 0.003 TYR F 310 PHE 0.018 0.003 PHE F 378 HIS 0.003 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00622 ( 3300) covalent geometry : angle 0.66912 ( 4416) hydrogen bonds : bond 0.02296 ( 62) hydrogen bonds : angle 4.72469 ( 186) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8403 (mptm) cc_final: 0.8018 (mtpt) REVERT: A 351 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8529 (mt0) REVERT: B 347 LYS cc_start: 0.8527 (mttp) cc_final: 0.7908 (pptt) REVERT: B 351 GLN cc_start: 0.9047 (mt0) cc_final: 0.8696 (mt0) REVERT: C 311 LYS cc_start: 0.8694 (mttt) cc_final: 0.8068 (mttm) REVERT: C 348 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8570 (t70) REVERT: C 349 ARG cc_start: 0.8360 (mtt180) cc_final: 0.6735 (mmp-170) REVERT: C 375 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8221 (ttpt) REVERT: D 369 LYS cc_start: 0.8562 (mtpm) cc_final: 0.8323 (ttmt) REVERT: E 336 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8346 (mt0) REVERT: E 349 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8111 (mtp180) REVERT: F 311 LYS cc_start: 0.6692 (mttm) cc_final: 0.6212 (mttm) REVERT: F 336 GLN cc_start: 0.8375 (tt0) cc_final: 0.8031 (mt0) REVERT: F 338 GLU cc_start: 0.8341 (tt0) cc_final: 0.7811 (tm-30) REVERT: F 340 LYS cc_start: 0.8288 (mmmm) cc_final: 0.8061 (mttm) outliers start: 23 outliers final: 12 residues processed: 111 average time/residue: 0.6449 time to fit residues: 73.0521 Evaluate side-chains 108 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 375 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.0000 chunk 11 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN D 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.112224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.100329 restraints weight = 4166.377| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.57 r_work: 0.3320 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3300 Z= 0.213 Angle : 0.634 5.526 4416 Z= 0.311 Chirality : 0.048 0.122 498 Planarity : 0.003 0.033 558 Dihedral : 5.529 15.382 432 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.65 % Allowed : 22.31 % Favored : 72.04 % 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 are not related in a simple way. whole: -1.85 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 349 TYR 0.012 0.002 TYR F 310 PHE 0.014 0.002 PHE F 378 HIS 0.002 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 3300) covalent geometry : angle 0.63440 ( 4416) hydrogen bonds : bond 0.02121 ( 62) hydrogen bonds : angle 4.62223 ( 186) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8370 (mptm) cc_final: 0.8019 (mtpt) REVERT: B 347 LYS cc_start: 0.8619 (mttp) cc_final: 0.7937 (pptt) REVERT: C 311 LYS cc_start: 0.8671 (mttt) cc_final: 0.8035 (mttm) REVERT: C 343 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8385 (ptpt) REVERT: C 345 ASP cc_start: 0.8243 (t0) cc_final: 0.7791 (m-30) REVERT: C 348 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8522 (t70) REVERT: C 349 ARG cc_start: 0.8415 (mtt180) cc_final: 0.6817 (mmp-170) REVERT: D 369 LYS cc_start: 0.8542 (mtpm) cc_final: 0.8310 (ttmt) REVERT: E 349 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8129 (mtp180) REVERT: F 311 LYS cc_start: 0.6501 (OUTLIER) cc_final: 0.5823 (mttm) REVERT: F 336 GLN cc_start: 0.8454 (tt0) cc_final: 0.8067 (mt0) REVERT: F 338 GLU cc_start: 0.8334 (tt0) cc_final: 0.7826 (tm-30) REVERT: F 340 LYS cc_start: 0.8292 (mmmm) cc_final: 0.8017 (mttm) REVERT: F 348 ASP cc_start: 0.8858 (OUTLIER) cc_final: 0.8615 (t0) REVERT: F 369 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8451 (ttmt) outliers start: 21 outliers final: 11 residues processed: 109 average time/residue: 0.6313 time to fit residues: 70.2355 Evaluate side-chains 111 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 369 LYS Chi-restraints excluded: chain F residue 375 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 2 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN D 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.113518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.101721 restraints weight = 4150.081| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.55 r_work: 0.3346 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3300 Z= 0.155 Angle : 0.582 6.309 4416 Z= 0.283 Chirality : 0.048 0.117 498 Planarity : 0.003 0.032 558 Dihedral : 5.183 14.316 432 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.38 % Allowed : 22.58 % Favored : 72.04 % 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 are not related in a simple way. whole: -1.85 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 349 TYR 0.010 0.002 TYR F 310 PHE 0.014 0.002 PHE D 378 HIS 0.002 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 3300) covalent geometry : angle 0.58231 ( 4416) hydrogen bonds : bond 0.01926 ( 62) hydrogen bonds : angle 4.42893 ( 186) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8337 (mptm) cc_final: 0.8008 (mtpt) REVERT: A 353 LYS cc_start: 0.8741 (mttm) cc_final: 0.8343 (mtpm) REVERT: B 343 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8094 (ptpt) REVERT: B 347 LYS cc_start: 0.8605 (mttp) cc_final: 0.7945 (pptt) REVERT: B 375 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8502 (ttmt) REVERT: C 311 LYS cc_start: 0.8631 (mttt) cc_final: 0.8011 (mttm) REVERT: C 343 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8341 (ptpt) REVERT: C 345 ASP cc_start: 0.8289 (t0) cc_final: 0.7798 (m-30) REVERT: C 348 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8489 (t70) REVERT: C 349 ARG cc_start: 0.8344 (mtt180) cc_final: 0.6750 (mmp-170) REVERT: D 369 LYS cc_start: 0.8509 (mtpm) cc_final: 0.8232 (tttt) REVERT: F 311 LYS cc_start: 0.6496 (mttm) cc_final: 0.5808 (mttm) REVERT: F 336 GLN cc_start: 0.8350 (tt0) cc_final: 0.8025 (mt0) REVERT: F 338 GLU cc_start: 0.8336 (tt0) cc_final: 0.7845 (tm-30) REVERT: F 340 LYS cc_start: 0.8281 (mmmm) cc_final: 0.7923 (mttm) outliers start: 20 outliers final: 9 residues processed: 111 average time/residue: 0.6170 time to fit residues: 69.9767 Evaluate side-chains 111 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 375 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.111525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.099753 restraints weight = 4206.238| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.57 r_work: 0.3319 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3300 Z= 0.221 Angle : 0.626 7.114 4416 Z= 0.308 Chirality : 0.048 0.124 498 Planarity : 0.003 0.033 558 Dihedral : 5.400 15.454 432 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.65 % Allowed : 22.58 % Favored : 71.77 % 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 are not related in a simple way. whole: -1.91 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 349 TYR 0.013 0.002 TYR F 310 PHE 0.017 0.002 PHE D 378 HIS 0.002 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00524 ( 3300) covalent geometry : angle 0.62586 ( 4416) hydrogen bonds : bond 0.02130 ( 62) hydrogen bonds : angle 4.51337 ( 186) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8339 (mptm) cc_final: 0.8003 (mtpt) REVERT: B 347 LYS cc_start: 0.8590 (mttp) cc_final: 0.8028 (pptt) REVERT: B 375 LYS cc_start: 0.8844 (ttpt) cc_final: 0.8501 (ttmt) REVERT: C 311 LYS cc_start: 0.8690 (mttt) cc_final: 0.8059 (mttm) REVERT: C 343 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8443 (ptpt) REVERT: C 345 ASP cc_start: 0.8302 (t0) cc_final: 0.7813 (m-30) REVERT: C 348 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8506 (t70) REVERT: C 349 ARG cc_start: 0.8405 (mtt180) cc_final: 0.6848 (mmp-170) REVERT: D 369 LYS cc_start: 0.8540 (mtpm) cc_final: 0.8224 (tttt) REVERT: F 311 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.5849 (mttm) REVERT: F 336 GLN cc_start: 0.8420 (tt0) cc_final: 0.8064 (mt0) REVERT: F 338 GLU cc_start: 0.8327 (tt0) cc_final: 0.7845 (tm-30) REVERT: F 340 LYS cc_start: 0.8282 (mmmm) cc_final: 0.8018 (mttm) REVERT: F 348 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8508 (t70) REVERT: F 349 ARG cc_start: 0.8418 (mtp180) cc_final: 0.8019 (mtt180) REVERT: F 369 LYS cc_start: 0.8703 (tttm) cc_final: 0.8464 (ttpt) outliers start: 21 outliers final: 13 residues processed: 107 average time/residue: 0.6452 time to fit residues: 70.4659 Evaluate side-chains 107 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 375 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 29 optimal weight: 0.0040 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 overall best weight: 1.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN D 351 GLN F 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.115090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.103089 restraints weight = 4244.108| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.61 r_work: 0.3360 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3300 Z= 0.119 Angle : 0.581 7.957 4416 Z= 0.275 Chirality : 0.048 0.117 498 Planarity : 0.003 0.031 558 Dihedral : 4.916 12.455 432 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.57 % Allowed : 23.66 % Favored : 71.77 % 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 are not related in a simple way. whole: -1.82 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 349 TYR 0.009 0.002 TYR F 310 PHE 0.015 0.002 PHE D 378 HIS 0.001 0.000 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 3300) covalent geometry : angle 0.58145 ( 4416) hydrogen bonds : bond 0.01775 ( 62) hydrogen bonds : angle 4.29372 ( 186) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8291 (mptm) cc_final: 0.7985 (mtpt) REVERT: B 347 LYS cc_start: 0.8603 (mttp) cc_final: 0.7977 (pptt) REVERT: B 375 LYS cc_start: 0.8815 (ttpt) cc_final: 0.8473 (ttmt) REVERT: C 311 LYS cc_start: 0.8633 (mttt) cc_final: 0.8033 (mttm) REVERT: C 343 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8311 (ptpt) REVERT: C 345 ASP cc_start: 0.8305 (t0) cc_final: 0.7805 (m-30) REVERT: C 348 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8506 (t70) REVERT: C 349 ARG cc_start: 0.8342 (mtt180) cc_final: 0.6766 (mmp-170) REVERT: D 369 LYS cc_start: 0.8490 (mtpm) cc_final: 0.8259 (tttt) REVERT: F 311 LYS cc_start: 0.6515 (mttm) cc_final: 0.5807 (mttm) REVERT: F 336 GLN cc_start: 0.8318 (tt0) cc_final: 0.8079 (mt0) REVERT: F 338 GLU cc_start: 0.8341 (tt0) cc_final: 0.7832 (tm-30) REVERT: F 340 LYS cc_start: 0.8245 (mmmm) cc_final: 0.7958 (mttm) REVERT: F 348 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8546 (t0) REVERT: F 369 LYS cc_start: 0.8707 (tttm) cc_final: 0.8470 (ttpt) outliers start: 17 outliers final: 9 residues processed: 108 average time/residue: 0.5997 time to fit residues: 66.1898 Evaluate side-chains 106 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 375 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 40 optimal weight: 0.2980 chunk 14 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN C 359 ASN D 351 GLN F 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.117590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.105769 restraints weight = 4116.469| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.56 r_work: 0.3406 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3300 Z= 0.086 Angle : 0.568 9.771 4416 Z= 0.261 Chirality : 0.048 0.119 498 Planarity : 0.003 0.030 558 Dihedral : 4.499 11.574 432 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.03 % Allowed : 24.73 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.009 0.002 TYR D 310 PHE 0.014 0.001 PHE D 378 HIS 0.001 0.000 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 3300) covalent geometry : angle 0.56841 ( 4416) hydrogen bonds : bond 0.01504 ( 62) hydrogen bonds : angle 4.00816 ( 186) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8302 (mptm) cc_final: 0.7967 (mtpt) REVERT: B 343 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8026 (ptpt) REVERT: B 347 LYS cc_start: 0.8646 (mttp) cc_final: 0.8013 (pptt) REVERT: B 375 LYS cc_start: 0.8795 (ttpt) cc_final: 0.8453 (ttmt) REVERT: C 311 LYS cc_start: 0.8608 (mttt) cc_final: 0.7892 (mtpp) REVERT: C 343 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8108 (ptpt) REVERT: C 345 ASP cc_start: 0.8305 (t0) cc_final: 0.7826 (m-30) REVERT: C 348 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8429 (t70) REVERT: C 349 ARG cc_start: 0.8348 (mtt180) cc_final: 0.6726 (mmp-170) REVERT: F 311 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.5838 (mttm) REVERT: F 348 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8418 (t0) REVERT: F 349 ARG cc_start: 0.8323 (mtp180) cc_final: 0.6632 (mtp180) outliers start: 15 outliers final: 8 residues processed: 111 average time/residue: 0.5927 time to fit residues: 67.3625 Evaluate side-chains 109 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 375 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 9.9990 chunk 30 optimal weight: 0.0040 chunk 39 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN D 351 GLN F 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.112666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.100693 restraints weight = 4207.229| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.59 r_work: 0.3327 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3300 Z= 0.174 Angle : 0.627 9.181 4416 Z= 0.297 Chirality : 0.048 0.116 498 Planarity : 0.003 0.033 558 Dihedral : 5.034 13.852 432 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.76 % Allowed : 25.27 % Favored : 70.97 % 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 are not related in a simple way. whole: -1.72 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 349 TYR 0.011 0.002 TYR F 310 PHE 0.016 0.002 PHE D 378 HIS 0.002 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 3300) covalent geometry : angle 0.62689 ( 4416) hydrogen bonds : bond 0.01946 ( 62) hydrogen bonds : angle 4.26504 ( 186) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8286 (mptm) cc_final: 0.7980 (mtpt) REVERT: B 343 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8138 (ptpt) REVERT: B 347 LYS cc_start: 0.8702 (mttp) cc_final: 0.8116 (pptt) REVERT: B 375 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8457 (ttmt) REVERT: C 311 LYS cc_start: 0.8653 (mttt) cc_final: 0.8045 (mttm) REVERT: C 340 LYS cc_start: 0.8528 (mtpp) cc_final: 0.8170 (mtpt) REVERT: C 345 ASP cc_start: 0.8306 (t0) cc_final: 0.7873 (m-30) REVERT: C 348 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8486 (t70) REVERT: C 349 ARG cc_start: 0.8397 (mtt180) cc_final: 0.6821 (mmp-170) REVERT: F 311 LYS cc_start: 0.6560 (OUTLIER) cc_final: 0.5836 (mttm) REVERT: F 338 GLU cc_start: 0.8412 (tt0) cc_final: 0.7985 (tm-30) REVERT: F 348 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8476 (t70) outliers start: 14 outliers final: 9 residues processed: 101 average time/residue: 0.6378 time to fit residues: 65.8238 Evaluate side-chains 105 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 375 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN D 351 GLN F 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.114486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.102412 restraints weight = 4146.173| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.57 r_work: 0.3350 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3300 Z= 0.131 Angle : 0.599 9.148 4416 Z= 0.281 Chirality : 0.048 0.117 498 Planarity : 0.003 0.028 558 Dihedral : 4.866 14.086 432 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.23 % Allowed : 25.00 % Favored : 71.77 % 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 are not related in a simple way. whole: -1.71 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 349 TYR 0.010 0.002 TYR F 310 PHE 0.017 0.002 PHE D 378 HIS 0.001 0.000 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3300) covalent geometry : angle 0.59897 ( 4416) hydrogen bonds : bond 0.01733 ( 62) hydrogen bonds : angle 4.19290 ( 186) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1826.23 seconds wall clock time: 31 minutes 48.31 seconds (1908.31 seconds total)