Starting phenix.real_space_refine on Wed Jun 4 14:30:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qk2_14029/06_2025/7qk2_14029.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qk2_14029/06_2025/7qk2_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_14029/06_2025/7qk2_14029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qk2_14029/06_2025/7qk2_14029.map" model { file = "/net/cci-nas-00/data/ceres_data/7qk2_14029/06_2025/7qk2_14029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qk2_14029/06_2025/7qk2_14029.cif" } resolution = 2.61 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= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 2.72, per 1000 atoms: 0.84 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: 0.74 Conformation dependent library (CDL) restraints added in 405.3 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: 0.59 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: 0.69 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 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: 0.01 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: 0.940 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.950 Find NCS groups from input model: 0.100 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:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.590 ------------------------------------------------------------------------------- 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 (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: -1.51 (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 HIS 0.018 0.003 HIS E 374 PHE 0.048 0.013 PHE F 346 TYR 0.050 0.011 TYR F 310 ARG 0.007 0.001 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.06082 ( 62) hydrogen bonds : angle 7.98926 ( 186) covalent geometry : bond 0.01103 ( 3300) covalent geometry : angle 1.86421 ( 4416) *********************** 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 : 0.487 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: 0.7629 (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: 1.4297 time to fit residues: 223.2404 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 : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 327 ASN E 330 HIS E 359 ASN F 351 GLN F 359 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.121160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.108598 restraints weight = 4021.856| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.57 r_work: 0.3443 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3300 Z= 0.110 Angle : 0.607 5.425 4416 Z= 0.301 Chirality : 0.049 0.123 498 Planarity : 0.003 0.019 558 Dihedral : 5.402 13.049 432 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.84 % Allowed : 19.35 % 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 (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: -1.34 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 330 PHE 0.010 0.002 PHE D 346 TYR 0.008 0.001 TYR F 310 ARG 0.002 0.001 ARG F 349 Details of bonding type rmsd hydrogen bonds : bond 0.02138 ( 62) hydrogen bonds : angle 5.21262 ( 186) covalent geometry : bond 0.00252 ( 3300) covalent geometry : angle 0.60661 ( 4416) *********************** 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 155 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.9451 (p) cc_final: 0.9218 (p) REVERT: A 340 LYS cc_start: 0.8190 (mptm) cc_final: 0.7804 (mtpt) REVERT: A 351 GLN cc_start: 0.8596 (pt0) cc_final: 0.8334 (mt0) REVERT: B 347 LYS cc_start: 0.8127 (mttp) cc_final: 0.7628 (pptt) REVERT: B 359 ASN cc_start: 0.9234 (m110) cc_final: 0.9016 (m-40) REVERT: C 311 LYS cc_start: 0.8599 (mttt) cc_final: 0.7940 (mtpp) REVERT: C 345 ASP cc_start: 0.8290 (t0) cc_final: 0.7811 (t70) REVERT: C 347 LYS cc_start: 0.8680 (mmtm) cc_final: 0.8118 (mmtp) REVERT: C 348 ASP cc_start: 0.8637 (t70) cc_final: 0.8387 (t70) REVERT: C 349 ARG cc_start: 0.8310 (mtt180) cc_final: 0.6651 (mmp-170) REVERT: C 351 GLN cc_start: 0.8562 (pt0) cc_final: 0.8301 (pt0) REVERT: F 336 GLN cc_start: 0.8243 (tt0) cc_final: 0.8006 (mt0) REVERT: F 338 GLU cc_start: 0.8292 (tt0) cc_final: 0.7826 (tm-30) outliers start: 18 outliers final: 3 residues processed: 145 average time/residue: 1.3926 time to fit residues: 206.2321 Evaluate side-chains 109 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 363 VAL 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 35 optimal weight: 0.1980 chunk 2 optimal weight: 0.0770 chunk 1 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 overall best weight: 3.4342 ------------------------------------------------------------------------------- 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 D 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.114029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.101641 restraints weight = 4091.476| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.59 r_work: 0.3347 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3326 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= 0.191 Angle : 0.653 5.930 4416 Z= 0.320 Chirality : 0.049 0.121 498 Planarity : 0.003 0.027 558 Dihedral : 5.544 14.205 432 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.57 % Allowed : 22.31 % Favored : 73.12 % 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: -1.53 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.014 0.002 PHE F 378 TYR 0.012 0.002 TYR F 310 ARG 0.003 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02091 ( 62) hydrogen bonds : angle 4.74062 ( 186) covalent geometry : bond 0.00459 ( 3300) covalent geometry : angle 0.65277 ( 4416) *********************** 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 123 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8254 (mptm) cc_final: 0.7944 (mtpt) REVERT: A 351 GLN cc_start: 0.8736 (pt0) cc_final: 0.8468 (mt0) REVERT: B 347 LYS cc_start: 0.8393 (mttp) cc_final: 0.7806 (pptt) REVERT: B 359 ASN cc_start: 0.9255 (m110) cc_final: 0.8967 (m-40) REVERT: C 311 LYS cc_start: 0.8636 (mttt) cc_final: 0.8019 (mttm) REVERT: C 348 ASP cc_start: 0.8732 (t70) cc_final: 0.8441 (t70) REVERT: C 349 ARG cc_start: 0.8347 (mtt180) cc_final: 0.6744 (mmp-170) REVERT: C 351 GLN cc_start: 0.8655 (pt0) cc_final: 0.8245 (pt0) REVERT: D 369 LYS cc_start: 0.8554 (mtpm) cc_final: 0.8211 (tttt) REVERT: E 340 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8259 (mmtp) REVERT: E 369 LYS cc_start: 0.8853 (mtpm) cc_final: 0.8631 (tttp) REVERT: F 336 GLN cc_start: 0.8369 (tt0) cc_final: 0.8077 (mt0) REVERT: F 338 GLU cc_start: 0.8360 (tt0) cc_final: 0.7884 (tm-30) outliers start: 17 outliers final: 10 residues processed: 117 average time/residue: 1.4045 time to fit residues: 167.9730 Evaluate side-chains 112 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 352 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 340 LYS 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 341 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN C 336 GLN D 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.114096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.101805 restraints weight = 4167.544| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.58 r_work: 0.3353 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3492 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= 0.161 Angle : 0.605 4.889 4416 Z= 0.293 Chirality : 0.048 0.118 498 Planarity : 0.003 0.028 558 Dihedral : 5.248 13.844 432 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % 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 (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: -1.65 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.015 0.002 PHE F 378 TYR 0.011 0.002 TYR F 310 ARG 0.002 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.01925 ( 62) hydrogen bonds : angle 4.45983 ( 186) covalent geometry : bond 0.00383 ( 3300) covalent geometry : angle 0.60465 ( 4416) *********************** 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 125 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8354 (mptm) cc_final: 0.7959 (mtpt) REVERT: B 347 LYS cc_start: 0.8524 (mttp) cc_final: 0.7954 (pptt) REVERT: B 359 ASN cc_start: 0.9264 (m110) cc_final: 0.8981 (m-40) REVERT: C 311 LYS cc_start: 0.8633 (mttt) cc_final: 0.7991 (mttm) REVERT: C 348 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8544 (t70) REVERT: C 349 ARG cc_start: 0.8359 (mtt180) cc_final: 0.6734 (mmp-170) REVERT: D 336 GLN cc_start: 0.8427 (mt0) cc_final: 0.8051 (mt0) REVERT: D 340 LYS cc_start: 0.8276 (mttp) cc_final: 0.8036 (mttp) REVERT: D 369 LYS cc_start: 0.8530 (mtpm) cc_final: 0.8215 (tttt) REVERT: F 311 LYS cc_start: 0.6802 (mttm) cc_final: 0.6418 (pttt) REVERT: F 336 GLN cc_start: 0.8299 (tt0) cc_final: 0.8049 (mt0) REVERT: F 338 GLU cc_start: 0.8371 (tt0) cc_final: 0.7911 (tm-30) REVERT: F 369 LYS cc_start: 0.8620 (mtpm) cc_final: 0.8390 (tttt) outliers start: 23 outliers final: 10 residues processed: 117 average time/residue: 1.3770 time to fit residues: 164.7064 Evaluate side-chains 110 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 352 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 363 VAL Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN C 336 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 = 0.112112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.100109 restraints weight = 4408.474| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.58 r_work: 0.3310 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3578 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= 0.259 Angle : 0.653 5.289 4416 Z= 0.324 Chirality : 0.049 0.128 498 Planarity : 0.003 0.031 558 Dihedral : 5.599 15.969 432 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.84 % Allowed : 23.12 % 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 (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: -1.83 (0.35), 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 HIS 0.003 0.001 HIS E 330 PHE 0.017 0.002 PHE F 378 TYR 0.014 0.003 TYR F 310 ARG 0.003 0.001 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02280 ( 62) hydrogen bonds : angle 4.52702 ( 186) covalent geometry : bond 0.00615 ( 3300) covalent geometry : angle 0.65258 ( 4416) *********************** 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 119 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8417 (mptm) cc_final: 0.8026 (mtpt) REVERT: B 347 LYS cc_start: 0.8631 (mttp) cc_final: 0.7968 (pptt) REVERT: C 311 LYS cc_start: 0.8665 (mttt) cc_final: 0.8043 (mttm) REVERT: C 343 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8537 (ptpt) REVERT: C 348 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8572 (t70) REVERT: C 349 ARG cc_start: 0.8375 (mtt180) cc_final: 0.6845 (mmp-170) REVERT: D 336 GLN cc_start: 0.8476 (mt0) cc_final: 0.8157 (mt0) REVERT: D 340 LYS cc_start: 0.8302 (mttm) cc_final: 0.8087 (mttp) REVERT: D 369 LYS cc_start: 0.8551 (mtpm) cc_final: 0.8197 (tttt) REVERT: F 311 LYS cc_start: 0.6503 (mttm) cc_final: 0.6042 (pttt) REVERT: F 336 GLN cc_start: 0.8435 (tt0) cc_final: 0.8127 (mt0) REVERT: F 338 GLU cc_start: 0.8371 (tt0) cc_final: 0.7867 (tm-30) REVERT: F 340 LYS cc_start: 0.8291 (mmmm) cc_final: 0.8051 (mttm) REVERT: F 348 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8506 (t70) REVERT: F 349 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8253 (mtt180) outliers start: 18 outliers final: 11 residues processed: 113 average time/residue: 1.3997 time to fit residues: 161.5969 Evaluate side-chains 107 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 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 341 SER Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 349 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.115724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.103630 restraints weight = 4384.026| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.60 r_work: 0.3363 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3769 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= 0.123 Angle : 0.584 7.642 4416 Z= 0.275 Chirality : 0.047 0.118 498 Planarity : 0.003 0.030 558 Dihedral : 4.958 12.801 432 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.38 % Allowed : 23.12 % Favored : 71.51 % 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: -1.75 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 330 PHE 0.011 0.001 PHE F 378 TYR 0.011 0.002 TYR D 310 ARG 0.002 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.01747 ( 62) hydrogen bonds : angle 4.20610 ( 186) covalent geometry : bond 0.00291 ( 3300) covalent geometry : angle 0.58447 ( 4416) *********************** 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 122 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8304 (mptm) cc_final: 0.7964 (mtpt) REVERT: B 347 LYS cc_start: 0.8614 (mttp) cc_final: 0.7976 (pptt) REVERT: B 359 ASN cc_start: 0.9259 (m110) cc_final: 0.8971 (m-40) REVERT: C 311 LYS cc_start: 0.8621 (mttt) cc_final: 0.8017 (mttm) REVERT: C 343 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8288 (ptpt) REVERT: C 345 ASP cc_start: 0.8222 (t0) cc_final: 0.7741 (m-30) REVERT: C 348 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8515 (t70) REVERT: C 349 ARG cc_start: 0.8320 (mtt180) cc_final: 0.6741 (mmp-170) REVERT: D 340 LYS cc_start: 0.8184 (mttm) cc_final: 0.7970 (mttp) REVERT: D 369 LYS cc_start: 0.8504 (mtpm) cc_final: 0.8248 (tttt) REVERT: F 311 LYS cc_start: 0.6461 (mttm) cc_final: 0.6016 (pttt) REVERT: F 338 GLU cc_start: 0.8393 (tt0) cc_final: 0.7870 (tm-30) REVERT: F 340 LYS cc_start: 0.8236 (mmmm) cc_final: 0.7914 (mttm) REVERT: F 348 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8565 (t0) outliers start: 20 outliers final: 13 residues processed: 114 average time/residue: 1.3290 time to fit residues: 154.9852 Evaluate side-chains 111 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 315 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 352 SER 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 363 VAL Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 352 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 28 optimal weight: 0.0570 chunk 23 optimal weight: 0.4980 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 overall best weight: 1.9104 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.115795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.103727 restraints weight = 4300.591| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.59 r_work: 0.3383 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3814 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= 0.121 Angle : 0.577 9.279 4416 Z= 0.270 Chirality : 0.047 0.117 498 Planarity : 0.003 0.029 558 Dihedral : 4.804 12.016 432 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.57 % Allowed : 24.46 % 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 (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: -1.72 (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 HIS 0.001 0.000 HIS E 329 PHE 0.012 0.001 PHE F 378 TYR 0.013 0.002 TYR D 310 ARG 0.002 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.01722 ( 62) hydrogen bonds : angle 4.10290 ( 186) covalent geometry : bond 0.00285 ( 3300) covalent geometry : angle 0.57677 ( 4416) *********************** 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 117 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8305 (mptm) cc_final: 0.7969 (mtpt) REVERT: B 347 LYS cc_start: 0.8713 (mttp) cc_final: 0.8017 (pptt) REVERT: C 311 LYS cc_start: 0.8604 (mttt) cc_final: 0.7954 (mtpp) REVERT: C 343 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8309 (ptpt) REVERT: C 345 ASP cc_start: 0.8244 (t0) cc_final: 0.7744 (m-30) REVERT: C 348 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8487 (t70) REVERT: C 349 ARG cc_start: 0.8327 (mtt180) cc_final: 0.6734 (mmp-170) REVERT: D 311 LYS cc_start: 0.8667 (pttt) cc_final: 0.8384 (ptmt) REVERT: D 369 LYS cc_start: 0.8476 (mtpm) cc_final: 0.8264 (tttt) REVERT: F 311 LYS cc_start: 0.6477 (mttm) cc_final: 0.5802 (mttm) REVERT: F 338 GLU cc_start: 0.8448 (tt0) cc_final: 0.7939 (tm-30) REVERT: F 340 LYS cc_start: 0.8260 (mmmm) cc_final: 0.8004 (mttm) outliers start: 17 outliers final: 11 residues processed: 112 average time/residue: 1.3214 time to fit residues: 151.3914 Evaluate side-chains 111 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 352 SER 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 352 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.2980 chunk 5 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 23 optimal weight: 0.4980 chunk 8 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN C 351 GLN C 359 ASN D 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.114124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.102116 restraints weight = 4424.959| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.58 r_work: 0.3349 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3300 Z= 0.157 Angle : 0.613 8.429 4416 Z= 0.289 Chirality : 0.048 0.118 498 Planarity : 0.003 0.030 558 Dihedral : 5.018 14.289 432 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.11 % Allowed : 24.19 % Favored : 70.70 % 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: -1.76 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.013 0.002 PHE F 378 TYR 0.012 0.002 TYR D 310 ARG 0.003 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.01906 ( 62) hydrogen bonds : angle 4.18357 ( 186) covalent geometry : bond 0.00373 ( 3300) covalent geometry : angle 0.61281 ( 4416) *********************** 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 116 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8325 (mptm) cc_final: 0.7978 (mtpt) REVERT: B 340 LYS cc_start: 0.8668 (mtpm) cc_final: 0.8461 (mtpt) REVERT: B 347 LYS cc_start: 0.8709 (mttp) cc_final: 0.8138 (pptt) REVERT: C 311 LYS cc_start: 0.8601 (mttt) cc_final: 0.7995 (mttm) REVERT: C 343 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8366 (ptpt) REVERT: C 345 ASP cc_start: 0.8256 (t0) cc_final: 0.7758 (m-30) REVERT: C 348 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8501 (t70) REVERT: C 349 ARG cc_start: 0.8363 (mtt180) cc_final: 0.6825 (mmp-170) REVERT: D 311 LYS cc_start: 0.8740 (pttt) cc_final: 0.8473 (ptmt) REVERT: D 338 GLU cc_start: 0.8250 (tt0) cc_final: 0.7991 (tm-30) REVERT: D 340 LYS cc_start: 0.8270 (mttp) cc_final: 0.7927 (mttp) REVERT: D 369 LYS cc_start: 0.8474 (mtpm) cc_final: 0.8232 (tttt) REVERT: F 311 LYS cc_start: 0.6514 (OUTLIER) cc_final: 0.5823 (mttm) REVERT: F 338 GLU cc_start: 0.8426 (tt0) cc_final: 0.7933 (tm-30) REVERT: F 340 LYS cc_start: 0.8276 (mmmm) cc_final: 0.8023 (mttm) outliers start: 19 outliers final: 13 residues processed: 111 average time/residue: 1.3660 time to fit residues: 154.9930 Evaluate side-chains 112 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 352 SER 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 363 VAL Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 352 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.111403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.099457 restraints weight = 4472.311| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.58 r_work: 0.3310 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3760 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= 0.268 Angle : 0.684 9.324 4416 Z= 0.332 Chirality : 0.049 0.128 498 Planarity : 0.003 0.033 558 Dihedral : 5.464 16.345 432 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.11 % Allowed : 24.46 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.87 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 329 PHE 0.014 0.002 PHE F 378 TYR 0.014 0.003 TYR F 310 ARG 0.003 0.001 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02308 ( 62) hydrogen bonds : angle 4.45730 ( 186) covalent geometry : bond 0.00636 ( 3300) covalent geometry : angle 0.68371 ( 4416) *********************** 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 114 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8400 (mptm) cc_final: 0.8029 (mtpt) REVERT: B 340 LYS cc_start: 0.8700 (mtpm) cc_final: 0.8498 (mtpt) REVERT: B 343 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.7258 (pptt) REVERT: B 347 LYS cc_start: 0.8719 (mttp) cc_final: 0.8128 (pptt) REVERT: C 311 LYS cc_start: 0.8669 (mttt) cc_final: 0.8052 (mttm) REVERT: C 343 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8491 (ptpt) REVERT: C 345 ASP cc_start: 0.8293 (t0) cc_final: 0.7859 (m-30) REVERT: C 348 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8554 (t70) REVERT: C 349 ARG cc_start: 0.8373 (mtt180) cc_final: 0.6901 (mmp-170) REVERT: D 311 LYS cc_start: 0.8766 (pttt) cc_final: 0.8502 (ptmt) REVERT: D 369 LYS cc_start: 0.8527 (mtpm) cc_final: 0.8209 (tttt) REVERT: F 311 LYS cc_start: 0.6597 (OUTLIER) cc_final: 0.5906 (mttm) REVERT: F 338 GLU cc_start: 0.8455 (tt0) cc_final: 0.7995 (tm-30) REVERT: F 348 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8501 (t70) outliers start: 19 outliers final: 13 residues processed: 110 average time/residue: 1.3414 time to fit residues: 150.9786 Evaluate side-chains 108 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 352 SER 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 352 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.112412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.100484 restraints weight = 4377.780| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.57 r_work: 0.3321 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 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 : 0.005 0.034 3300 Z= 0.211 Angle : 0.658 9.154 4416 Z= 0.314 Chirality : 0.048 0.119 498 Planarity : 0.003 0.032 558 Dihedral : 5.327 15.345 432 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.11 % Allowed : 24.73 % Favored : 70.16 % 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: -1.88 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 330 PHE 0.013 0.002 PHE F 378 TYR 0.012 0.002 TYR D 310 ARG 0.004 0.001 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02124 ( 62) hydrogen bonds : angle 4.40580 ( 186) covalent geometry : bond 0.00500 ( 3300) covalent geometry : angle 0.65808 ( 4416) ********************** 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 114 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8358 (mptm) cc_final: 0.7989 (mtpt) REVERT: B 343 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.7222 (pptt) REVERT: B 347 LYS cc_start: 0.8701 (mttp) cc_final: 0.8117 (pptt) REVERT: C 311 LYS cc_start: 0.8660 (mttt) cc_final: 0.8048 (mttm) REVERT: C 343 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8431 (ptpt) REVERT: C 345 ASP cc_start: 0.8265 (t0) cc_final: 0.7795 (m-30) REVERT: C 348 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8522 (t70) REVERT: C 349 ARG cc_start: 0.8369 (mtt180) cc_final: 0.6852 (mmp-170) REVERT: D 311 LYS cc_start: 0.8753 (pttt) cc_final: 0.8488 (ptmt) REVERT: D 369 LYS cc_start: 0.8510 (mtpm) cc_final: 0.8215 (tttt) REVERT: F 311 LYS cc_start: 0.6560 (OUTLIER) cc_final: 0.5854 (mttm) REVERT: F 338 GLU cc_start: 0.8441 (tt0) cc_final: 0.8022 (tm-30) REVERT: F 348 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8627 (t0) outliers start: 19 outliers final: 12 residues processed: 108 average time/residue: 1.3302 time to fit residues: 147.0696 Evaluate side-chains 110 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 352 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 8 optimal weight: 0.0980 chunk 30 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.113805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.101766 restraints weight = 4310.387| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.56 r_work: 0.3356 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3300 Z= 0.163 Angle : 0.625 9.066 4416 Z= 0.296 Chirality : 0.048 0.116 498 Planarity : 0.003 0.031 558 Dihedral : 5.129 14.096 432 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.57 % Allowed : 25.00 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.86 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 330 PHE 0.020 0.002 PHE D 378 TYR 0.011 0.002 TYR D 310 ARG 0.003 0.001 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.01961 ( 62) hydrogen bonds : angle 4.26268 ( 186) covalent geometry : bond 0.00385 ( 3300) covalent geometry : angle 0.62541 ( 4416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3931.20 seconds wall clock time: 67 minutes 43.57 seconds (4063.57 seconds total)