Starting phenix.real_space_refine on Fri Dec 27 06:46:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qk2_14029/12_2024/7qk2_14029.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qk2_14029/12_2024/7qk2_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_14029/12_2024/7qk2_14029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qk2_14029/12_2024/7qk2_14029.map" model { file = "/net/cci-nas-00/data/ceres_data/7qk2_14029/12_2024/7qk2_14029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qk2_14029/12_2024/7qk2_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-5532/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: 2.55, per 1000 atoms: 0.79 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: 0.70 Conformation dependent library (CDL) restraints added in 430.1 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: 0.52 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: 0.73 Time building geometry restraints manager: 0.83 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: 0.690 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: 0.040 Process input model: 12.130 Find NCS groups from input model: 0.110 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:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.660 ------------------------------------------------------------------------------- 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= 0.740 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 *********************** 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 : 0.407 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: 1.4906 time to fit residues: 232.6938 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 : 0.410 ------------------------------------------------------------------------------- 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: 0.8980 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: 1.3786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3071 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= 0.172 Angle : 0.605 5.362 4416 Z= 0.300 Chirality : 0.049 0.122 498 Planarity : 0.003 0.019 558 Dihedral : 5.412 13.029 432 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.27 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: -1.36 (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 HIS 0.001 0.000 HIS D 330 PHE 0.010 0.002 PHE D 346 TYR 0.007 0.002 TYR F 310 ARG 0.002 0.001 ARG F 349 *********************** 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 156 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8160 (mptm) cc_final: 0.7899 (mtpt) REVERT: A 351 GLN cc_start: 0.8748 (pt0) cc_final: 0.8531 (mt0) REVERT: B 347 LYS cc_start: 0.8474 (mttp) cc_final: 0.7877 (pptt) REVERT: C 311 LYS cc_start: 0.7807 (mttt) cc_final: 0.7538 (mtpp) REVERT: C 345 ASP cc_start: 0.8803 (t0) cc_final: 0.8510 (t70) REVERT: C 347 LYS cc_start: 0.9050 (mmtm) cc_final: 0.8668 (mmtp) REVERT: C 349 ARG cc_start: 0.8554 (mtt180) cc_final: 0.6961 (mmp-170) REVERT: C 351 GLN cc_start: 0.8761 (pt0) cc_final: 0.8558 (pt0) REVERT: D 308 ILE cc_start: 0.7870 (mt) cc_final: 0.7657 (mt) REVERT: F 336 GLN cc_start: 0.8573 (tt0) cc_final: 0.8304 (mt0) REVERT: F 338 GLU cc_start: 0.8369 (tt0) cc_final: 0.7946 (tm-30) outliers start: 18 outliers final: 3 residues processed: 146 average time/residue: 1.4080 time to fit residues: 209.9474 Evaluate side-chains 108 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 105 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 31 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 0.0870 chunk 19 optimal weight: 5.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3300 Z= 0.306 Angle : 0.656 5.968 4416 Z= 0.321 Chirality : 0.049 0.120 498 Planarity : 0.003 0.026 558 Dihedral : 5.537 14.209 432 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.11 % Allowed : 22.58 % Favored : 72.31 % 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: -1.55 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 330 PHE 0.014 0.002 PHE F 378 TYR 0.012 0.002 TYR F 310 ARG 0.003 0.000 ARG E 349 *********************** 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 129 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 GLN cc_start: 0.8855 (pt0) cc_final: 0.8635 (mt0) REVERT: B 347 LYS cc_start: 0.8730 (mttp) cc_final: 0.8083 (pptt) REVERT: C 311 LYS cc_start: 0.7926 (mttt) cc_final: 0.7625 (mttm) REVERT: C 345 ASP cc_start: 0.8871 (t0) cc_final: 0.8620 (t70) REVERT: C 347 LYS cc_start: 0.9092 (mmtm) cc_final: 0.8879 (mmtp) REVERT: C 349 ARG cc_start: 0.8540 (mtt180) cc_final: 0.6998 (mmp-170) REVERT: C 351 GLN cc_start: 0.8826 (pt0) cc_final: 0.8505 (pt0) REVERT: D 369 LYS cc_start: 0.8163 (mtpm) cc_final: 0.7941 (tttt) REVERT: E 340 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8133 (mmtp) REVERT: F 336 GLN cc_start: 0.8643 (tt0) cc_final: 0.8346 (mt0) REVERT: F 338 GLU cc_start: 0.8402 (tt0) cc_final: 0.7978 (tm-30) outliers start: 19 outliers final: 11 residues processed: 121 average time/residue: 1.4989 time to fit residues: 185.1009 Evaluate side-chains 118 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3473 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= 0.351 Angle : 0.640 4.814 4416 Z= 0.317 Chirality : 0.049 0.121 498 Planarity : 0.003 0.030 558 Dihedral : 5.543 15.149 432 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 6.18 % Allowed : 21.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.016 0.002 PHE F 378 TYR 0.013 0.003 TYR D 310 ARG 0.002 0.001 ARG E 349 *********************** 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 : 0.404 Fit side-chains revert: symmetry clash REVERT: B 347 LYS cc_start: 0.8864 (mttp) cc_final: 0.8197 (pptt) REVERT: C 311 LYS cc_start: 0.7991 (mttt) cc_final: 0.7665 (mttm) REVERT: C 349 ARG cc_start: 0.8540 (mtt180) cc_final: 0.7068 (mmp-170) REVERT: D 336 GLN cc_start: 0.8631 (mt0) cc_final: 0.8373 (mt0) REVERT: D 369 LYS cc_start: 0.8155 (mtpm) cc_final: 0.7934 (tttt) REVERT: F 311 LYS cc_start: 0.6726 (mttm) cc_final: 0.6291 (mttm) REVERT: F 336 GLN cc_start: 0.8641 (tt0) cc_final: 0.8342 (mt0) REVERT: F 338 GLU cc_start: 0.8428 (tt0) cc_final: 0.7910 (tm-30) outliers start: 23 outliers final: 12 residues processed: 111 average time/residue: 1.3889 time to fit residues: 157.6673 Evaluate side-chains 100 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 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 343 LYS 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 30 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 0.0270 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 overall best weight: 4.4046 ------------------------------------------------------------------------------- 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 F 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3300 Z= 0.385 Angle : 0.647 5.362 4416 Z= 0.320 Chirality : 0.048 0.125 498 Planarity : 0.003 0.031 558 Dihedral : 5.559 15.844 432 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.11 % Allowed : 21.77 % 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: -1.84 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 329 PHE 0.017 0.002 PHE F 378 TYR 0.013 0.003 TYR F 310 ARG 0.003 0.001 ARG E 349 *********************** 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 109 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: B 347 LYS cc_start: 0.8949 (mttp) cc_final: 0.8232 (pptt) REVERT: C 311 LYS cc_start: 0.8017 (mttt) cc_final: 0.7676 (mttm) REVERT: C 349 ARG cc_start: 0.8529 (mtt180) cc_final: 0.7070 (mmp-170) REVERT: D 336 GLN cc_start: 0.8596 (mt0) cc_final: 0.8349 (mt0) REVERT: D 369 LYS cc_start: 0.8149 (mtpm) cc_final: 0.7935 (tttt) REVERT: F 311 LYS cc_start: 0.6523 (mttm) cc_final: 0.6012 (mttm) REVERT: F 336 GLN cc_start: 0.8633 (tt0) cc_final: 0.8306 (mt0) REVERT: F 338 GLU cc_start: 0.8401 (tt0) cc_final: 0.8023 (tm-30) outliers start: 19 outliers final: 13 residues processed: 103 average time/residue: 1.3353 time to fit residues: 140.8133 Evaluate side-chains 100 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 341 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3775 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= 0.186 Angle : 0.574 6.189 4416 Z= 0.273 Chirality : 0.047 0.117 498 Planarity : 0.003 0.029 558 Dihedral : 4.905 12.379 432 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.49 % Allowed : 24.19 % Favored : 72.31 % 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: -1.80 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (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 0.009 0.002 TYR D 310 ARG 0.004 0.001 ARG A 349 *********************** 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 109 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: B 347 LYS cc_start: 0.8947 (mttp) cc_final: 0.8222 (pptt) REVERT: B 375 LYS cc_start: 0.8276 (ttpt) cc_final: 0.8072 (ttmt) REVERT: C 311 LYS cc_start: 0.7975 (mttt) cc_final: 0.7619 (mtpp) REVERT: C 345 ASP cc_start: 0.8794 (t0) cc_final: 0.8363 (m-30) REVERT: C 349 ARG cc_start: 0.8524 (mtt180) cc_final: 0.7013 (mmp-170) REVERT: F 311 LYS cc_start: 0.6489 (mttm) cc_final: 0.5957 (mttm) REVERT: F 336 GLN cc_start: 0.8552 (tt0) cc_final: 0.8305 (mt0) REVERT: F 338 GLU cc_start: 0.8447 (tt0) cc_final: 0.8110 (tm-30) REVERT: F 348 ASP cc_start: 0.8851 (t70) cc_final: 0.8573 (t0) outliers start: 13 outliers final: 9 residues processed: 106 average time/residue: 1.2817 time to fit residues: 139.3136 Evaluate side-chains 103 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU 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 375 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3300 Z= 0.154 Angle : 0.559 7.319 4416 Z= 0.263 Chirality : 0.047 0.118 498 Planarity : 0.002 0.026 558 Dihedral : 4.622 11.056 432 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.03 % Allowed : 23.12 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.36), 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 HIS 0.001 0.000 HIS D 374 PHE 0.012 0.001 PHE D 378 TYR 0.009 0.002 TYR D 310 ARG 0.003 0.001 ARG A 349 *********************** 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 112 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: B 347 LYS cc_start: 0.8952 (mttp) cc_final: 0.8251 (pptt) REVERT: B 375 LYS cc_start: 0.8324 (ttpt) cc_final: 0.8118 (ttmt) REVERT: C 311 LYS cc_start: 0.7876 (mttt) cc_final: 0.7589 (mtpp) REVERT: C 345 ASP cc_start: 0.8800 (t0) cc_final: 0.8374 (m-30) REVERT: C 349 ARG cc_start: 0.8512 (mtt180) cc_final: 0.6982 (mmp-170) REVERT: F 311 LYS cc_start: 0.6560 (OUTLIER) cc_final: 0.6025 (mttm) REVERT: F 336 GLN cc_start: 0.8465 (tt0) cc_final: 0.8252 (mt0) REVERT: F 338 GLU cc_start: 0.8421 (tt0) cc_final: 0.8123 (tm-30) REVERT: F 348 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8508 (t0) outliers start: 15 outliers final: 10 residues processed: 106 average time/residue: 1.2961 time to fit residues: 140.7774 Evaluate side-chains 101 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3864 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= 0.206 Angle : 0.596 7.963 4416 Z= 0.281 Chirality : 0.047 0.118 498 Planarity : 0.003 0.026 558 Dihedral : 4.793 12.115 432 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.03 % Allowed : 23.92 % 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: -1.74 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 330 PHE 0.014 0.002 PHE D 378 TYR 0.009 0.002 TYR D 310 ARG 0.005 0.001 ARG B 349 *********************** 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 106 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: B 340 LYS cc_start: 0.8632 (mtpm) cc_final: 0.8430 (mtpt) REVERT: B 347 LYS cc_start: 0.9037 (mttp) cc_final: 0.8308 (pptt) REVERT: B 375 LYS cc_start: 0.8336 (ttpt) cc_final: 0.8129 (ttmt) REVERT: C 311 LYS cc_start: 0.7923 (mttt) cc_final: 0.7604 (mtpp) REVERT: C 345 ASP cc_start: 0.8813 (t0) cc_final: 0.8371 (m-30) REVERT: C 349 ARG cc_start: 0.8481 (mtt180) cc_final: 0.6938 (mmp-170) REVERT: F 311 LYS cc_start: 0.6552 (OUTLIER) cc_final: 0.5998 (mttm) REVERT: F 336 GLN cc_start: 0.8498 (tt0) cc_final: 0.8265 (mt0) REVERT: F 338 GLU cc_start: 0.8412 (tt0) cc_final: 0.8076 (tm-30) outliers start: 15 outliers final: 11 residues processed: 103 average time/residue: 1.3370 time to fit residues: 140.9999 Evaluate side-chains 100 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 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 375 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3300 Z= 0.232 Angle : 0.614 8.191 4416 Z= 0.290 Chirality : 0.047 0.117 498 Planarity : 0.003 0.026 558 Dihedral : 4.902 12.745 432 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.03 % Allowed : 24.46 % 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: -1.76 (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 330 PHE 0.015 0.002 PHE D 378 TYR 0.010 0.002 TYR F 310 ARG 0.006 0.001 ARG A 349 *********************** 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 107 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: B 340 LYS cc_start: 0.8637 (mtpm) cc_final: 0.8433 (mtpt) REVERT: B 347 LYS cc_start: 0.9033 (mttp) cc_final: 0.8368 (pptt) REVERT: B 375 LYS cc_start: 0.8338 (ttpt) cc_final: 0.8128 (ttmt) REVERT: C 311 LYS cc_start: 0.7899 (mttt) cc_final: 0.7586 (mtpp) REVERT: C 345 ASP cc_start: 0.8814 (t0) cc_final: 0.8374 (m-30) REVERT: C 349 ARG cc_start: 0.8476 (mtt180) cc_final: 0.6960 (mmp-170) REVERT: F 311 LYS cc_start: 0.6574 (OUTLIER) cc_final: 0.6015 (mttm) REVERT: F 336 GLN cc_start: 0.8491 (tt0) cc_final: 0.8261 (mt0) REVERT: F 338 GLU cc_start: 0.8440 (tt0) cc_final: 0.8091 (tm-30) REVERT: F 348 ASP cc_start: 0.8851 (t70) cc_final: 0.8591 (t0) outliers start: 15 outliers final: 12 residues processed: 104 average time/residue: 1.2965 time to fit residues: 138.1811 Evaluate side-chains 102 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 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 375 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 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 : 0.005 0.032 3300 Z= 0.318 Angle : 0.658 10.172 4416 Z= 0.315 Chirality : 0.048 0.116 498 Planarity : 0.003 0.027 558 Dihedral : 5.195 14.674 432 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.76 % Allowed : 24.73 % 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: -1.83 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 329 PHE 0.018 0.002 PHE D 378 TYR 0.012 0.002 TYR F 310 ARG 0.006 0.001 ARG A 349 ********************** 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 103 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: B 340 LYS cc_start: 0.8614 (mtpm) cc_final: 0.8409 (mtpt) REVERT: B 343 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.7593 (pptt) REVERT: B 347 LYS cc_start: 0.9037 (mttp) cc_final: 0.8396 (pptt) REVERT: B 375 LYS cc_start: 0.8360 (ttpt) cc_final: 0.8143 (ttmt) REVERT: C 311 LYS cc_start: 0.7977 (mttt) cc_final: 0.7664 (mttm) REVERT: C 345 ASP cc_start: 0.8816 (t0) cc_final: 0.8395 (m-30) REVERT: C 349 ARG cc_start: 0.8465 (mtt180) cc_final: 0.7035 (mmp-170) REVERT: F 311 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.6090 (mttm) REVERT: F 336 GLN cc_start: 0.8519 (tt0) cc_final: 0.8247 (mt0) REVERT: F 338 GLU cc_start: 0.8440 (tt0) cc_final: 0.8067 (tm-30) outliers start: 14 outliers final: 11 residues processed: 100 average time/residue: 1.2938 time to fit residues: 132.5798 Evaluate side-chains 101 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 375 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.0270 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 overall best weight: 0.7642 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.119293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.106942 restraints weight = 4071.846| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.58 r_work: 0.3416 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4006 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= 0.124 Angle : 0.580 8.612 4416 Z= 0.267 Chirality : 0.048 0.119 498 Planarity : 0.003 0.028 558 Dihedral : 4.390 11.152 432 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.69 % Allowed : 26.08 % 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 (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 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 374 PHE 0.017 0.001 PHE D 378 TYR 0.008 0.001 TYR D 310 ARG 0.007 0.001 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2626.07 seconds wall clock time: 47 minutes 49.75 seconds (2869.75 seconds total)