Starting phenix.real_space_refine on Fri Aug 22 19:00:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qjj_18448/08_2025/8qjj_18448.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qjj_18448/08_2025/8qjj_18448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qjj_18448/08_2025/8qjj_18448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qjj_18448/08_2025/8qjj_18448.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qjj_18448/08_2025/8qjj_18448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qjj_18448/08_2025/8qjj_18448.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 H 3588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7032 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 1.55, per 1000 atoms: 0.22 Number of scatterers: 7032 At special positions: 0 Unit cell: (151.616, 97.232, 37.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 642 8.00 N 636 7.00 C 2160 6.00 H 3588 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 317.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 19 sheets defined 0.0% alpha, 44.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.561A pdb=" N VAL A 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N VAL C 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.739A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 318 removed outlier: 6.634A pdb=" N LYS A 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 321 through 322 removed outlier: 6.574A pdb=" N LYS A 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 325 through 330 removed outlier: 5.857A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN A 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 337 through 342 Processing sheet with id=AA7, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.438A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 350 through 357 removed outlier: 6.720A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N SER E 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY A 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.485A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 369 through 374 removed outlier: 6.451A pdb=" N ASN A 368 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ILE C 371 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N THR C 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU A 372 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLY A 367 " --> pdb=" O ASN E 368 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N LYS E 370 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.583A pdb=" N VAL B 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL D 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE B 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN B 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N TYR F 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.666A pdb=" N VAL B 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 317 through 322 removed outlier: 6.546A pdb=" N LYS B 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N SER F 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N CYS F 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS B 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 325 through 330 removed outlier: 5.817A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY F 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN B 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.640A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N GLU D 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER B 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.478A pdb=" N ASP B 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 350 through 357 Processing sheet with id=AB9, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.497A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 369 through 374 removed outlier: 6.597A pdb=" N LYS B 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) 66 hydrogen bonds defined for protein. 198 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 3582 1.11 - 1.29: 570 1.29 - 1.46: 881 1.46 - 1.63: 2047 1.63 - 1.80: 6 Bond restraints: 7086 Sorted by residual: bond pdb=" CE2 TYR A 310 " pdb=" HE2 TYR A 310 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N ILE B 354 " pdb=" H ILE B 354 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N GLN C 351 " pdb=" H GLN C 351 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N ILE C 371 " pdb=" H ILE C 371 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" CD2 HIS D 374 " pdb=" HD2 HIS D 374 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.64e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 10585 2.46 - 4.91: 1805 4.91 - 7.37: 478 7.37 - 9.83: 38 9.83 - 12.28: 6 Bond angle restraints: 12912 Sorted by residual: angle pdb=" CA THR A 319 " pdb=" CB THR A 319 " pdb=" CG2 THR A 319 " ideal model delta sigma weight residual 110.50 119.20 -8.70 1.70e+00 3.46e-01 2.62e+01 angle pdb=" N SER A 316 " pdb=" CA SER A 316 " pdb=" C SER A 316 " ideal model delta sigma weight residual 110.43 116.97 -6.54 1.31e+00 5.83e-01 2.49e+01 angle pdb=" CA THR C 319 " pdb=" CB THR C 319 " pdb=" CG2 THR C 319 " ideal model delta sigma weight residual 110.50 118.44 -7.94 1.70e+00 3.46e-01 2.18e+01 angle pdb=" CA ASP F 345 " pdb=" CB ASP F 345 " pdb=" CG ASP F 345 " ideal model delta sigma weight residual 112.60 117.15 -4.55 1.00e+00 1.00e+00 2.07e+01 angle pdb=" CA ASP F 348 " pdb=" CB ASP F 348 " pdb=" CG ASP F 348 " ideal model delta sigma weight residual 112.60 117.13 -4.53 1.00e+00 1.00e+00 2.05e+01 ... (remaining 12907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.48: 2834 14.48 - 28.96: 198 28.96 - 43.44: 103 43.44 - 57.92: 61 57.92 - 72.41: 68 Dihedral angle restraints: 3264 sinusoidal: 1866 harmonic: 1398 Sorted by residual: dihedral pdb=" CA GLY A 365 " pdb=" C GLY A 365 " pdb=" N GLY A 366 " pdb=" CA GLY A 366 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA GLY F 365 " pdb=" C GLY F 365 " pdb=" N GLY F 366 " pdb=" CA GLY F 366 " ideal model delta harmonic sigma weight residual 180.00 150.83 29.17 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA GLY B 365 " pdb=" C GLY B 365 " pdb=" N GLY B 366 " pdb=" CA GLY B 366 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 249 0.061 - 0.121: 163 0.121 - 0.181: 87 0.181 - 0.241: 18 0.241 - 0.301: 11 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS F 370 " pdb=" N LYS F 370 " pdb=" C LYS F 370 " pdb=" CB LYS F 370 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA ASP F 348 " pdb=" N ASP F 348 " pdb=" C ASP F 348 " pdb=" CB ASP F 348 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA LYS C 343 " pdb=" N LYS C 343 " pdb=" C LYS C 343 " pdb=" CB LYS C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 525 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 330 " 0.088 2.00e-02 2.50e+03 4.87e-02 5.34e+01 pdb=" CG HIS C 330 " -0.079 2.00e-02 2.50e+03 pdb=" ND1 HIS C 330 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS C 330 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 HIS C 330 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS C 330 " 0.019 2.00e-02 2.50e+03 pdb=" HD1 HIS C 330 " -0.017 2.00e-02 2.50e+03 pdb=" HD2 HIS C 330 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 HIS C 330 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 330 " -0.079 2.00e-02 2.50e+03 4.49e-02 4.53e+01 pdb=" CG HIS D 330 " 0.076 2.00e-02 2.50e+03 pdb=" ND1 HIS D 330 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 HIS D 330 " 0.044 2.00e-02 2.50e+03 pdb=" CE1 HIS D 330 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS D 330 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 HIS D 330 " 0.014 2.00e-02 2.50e+03 pdb=" HD2 HIS D 330 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 HIS D 330 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 374 " -0.034 2.00e-02 2.50e+03 6.28e-02 3.94e+01 pdb=" N LYS A 375 " 0.108 2.00e-02 2.50e+03 pdb=" CA LYS A 375 " -0.031 2.00e-02 2.50e+03 pdb=" H LYS A 375 " -0.043 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 531 2.19 - 2.79: 12402 2.79 - 3.39: 18577 3.39 - 4.00: 24104 4.00 - 4.60: 34365 Nonbonded interactions: 89979 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.583 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.595 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.630 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.631 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.659 2.450 ... (remaining 89974 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: 4.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.340 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 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 : 0.012 0.037 3498 Z= 0.757 Angle : 1.984 8.700 4680 Z= 1.309 Chirality : 0.097 0.301 528 Planarity : 0.011 0.061 594 Dihedral : 12.602 72.406 1344 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 379 TYR 0.057 0.017 TYR A 310 PHE 0.056 0.019 PHE F 346 HIS 0.018 0.004 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.01179 ( 3498) covalent geometry : angle 1.98366 ( 4680) hydrogen bonds : bond 0.13251 ( 66) hydrogen bonds : angle 6.26912 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 VAL cc_start: 0.7828 (t) cc_final: 0.6780 (t) REVERT: A 308 ILE cc_start: 0.7138 (mt) cc_final: 0.6647 (mp) REVERT: A 340 LYS cc_start: 0.8686 (ttpt) cc_final: 0.8080 (mtmt) REVERT: A 372 GLU cc_start: 0.7162 (tt0) cc_final: 0.5891 (mt-10) REVERT: B 340 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8162 (mttt) REVERT: B 372 GLU cc_start: 0.6598 (tt0) cc_final: 0.6313 (mt-10) REVERT: C 308 ILE cc_start: 0.7399 (mt) cc_final: 0.7109 (mp) REVERT: C 340 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8077 (mttt) REVERT: C 349 ARG cc_start: 0.8343 (mtt180) cc_final: 0.7189 (mmp-170) REVERT: C 370 LYS cc_start: 0.8030 (tttt) cc_final: 0.7159 (mttt) REVERT: D 340 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8078 (mttt) REVERT: D 349 ARG cc_start: 0.8501 (mtt180) cc_final: 0.7625 (mmp-170) REVERT: D 370 LYS cc_start: 0.8360 (tttt) cc_final: 0.7930 (mttt) REVERT: D 376 LEU cc_start: 0.7819 (tp) cc_final: 0.7421 (mt) REVERT: E 306 VAL cc_start: 0.6987 (t) cc_final: 0.6752 (t) REVERT: E 308 ILE cc_start: 0.6794 (mt) cc_final: 0.6464 (mt) REVERT: E 340 LYS cc_start: 0.8886 (ttpt) cc_final: 0.8344 (mttt) REVERT: E 349 ARG cc_start: 0.8120 (mtt180) cc_final: 0.6694 (pmt-80) REVERT: E 358 ASP cc_start: 0.9229 (m-30) cc_final: 0.8986 (m-30) REVERT: E 372 GLU cc_start: 0.6815 (tt0) cc_final: 0.6087 (mp0) REVERT: F 340 LYS cc_start: 0.8836 (ttpt) cc_final: 0.8338 (mtmt) REVERT: F 370 LYS cc_start: 0.7598 (tttt) cc_final: 0.7047 (ptpt) REVERT: F 372 GLU cc_start: 0.6433 (tt0) cc_final: 0.5783 (mt-10) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.3057 time to fit residues: 48.9857 Evaluate side-chains 95 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 362 HIS B 362 HIS ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS D 362 HIS ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 HIS F 359 ASN F 362 HIS ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.191181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.169520 restraints weight = 13397.793| |-----------------------------------------------------------------------------| r_work (start): 0.4528 rms_B_bonded: 2.24 r_work: 0.4443 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4362 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3498 Z= 0.143 Angle : 0.637 6.965 4680 Z= 0.335 Chirality : 0.052 0.151 528 Planarity : 0.003 0.023 594 Dihedral : 6.254 21.034 462 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.77 % Allowed : 11.62 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.26), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.20), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 379 TYR 0.008 0.002 TYR C 310 PHE 0.015 0.002 PHE B 378 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3498) covalent geometry : angle 0.63684 ( 4680) hydrogen bonds : bond 0.02431 ( 66) hydrogen bonds : angle 4.22613 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.8799 (mt) cc_final: 0.8545 (mp) REVERT: A 340 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8169 (mttt) REVERT: B 340 LYS cc_start: 0.8480 (ttpt) cc_final: 0.7893 (mttt) REVERT: B 347 LYS cc_start: 0.8044 (mttt) cc_final: 0.7796 (mttm) REVERT: B 372 GLU cc_start: 0.6869 (tt0) cc_final: 0.6418 (mt-10) REVERT: C 308 ILE cc_start: 0.8659 (mt) cc_final: 0.8415 (mp) REVERT: C 340 LYS cc_start: 0.8502 (ttpt) cc_final: 0.7997 (mttt) REVERT: C 349 ARG cc_start: 0.8199 (mtt180) cc_final: 0.7220 (mmp-170) REVERT: D 340 LYS cc_start: 0.8473 (ttpt) cc_final: 0.8002 (mttp) REVERT: D 349 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7393 (mmm160) REVERT: D 370 LYS cc_start: 0.8367 (tttt) cc_final: 0.7923 (mttt) REVERT: D 376 LEU cc_start: 0.8155 (tp) cc_final: 0.7769 (mt) REVERT: E 340 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8446 (mttt) REVERT: E 349 ARG cc_start: 0.7841 (mtt180) cc_final: 0.6695 (pmt-80) REVERT: E 370 LYS cc_start: 0.7126 (ptmt) cc_final: 0.5951 (tppt) REVERT: F 340 LYS cc_start: 0.8775 (ttpt) cc_final: 0.8295 (mttt) REVERT: F 379 ARG cc_start: 0.4685 (pmt-80) cc_final: 0.3719 (mtm180) outliers start: 7 outliers final: 5 residues processed: 94 average time/residue: 0.2773 time to fit residues: 29.2246 Evaluate side-chains 89 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 ASN ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.190802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.169291 restraints weight = 13326.862| |-----------------------------------------------------------------------------| r_work (start): 0.4501 rms_B_bonded: 2.25 r_work: 0.4422 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4340 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3498 Z= 0.106 Angle : 0.540 4.241 4680 Z= 0.285 Chirality : 0.051 0.146 528 Planarity : 0.002 0.022 594 Dihedral : 5.538 16.561 462 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.27 % Allowed : 13.38 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.26), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.20), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 379 TYR 0.007 0.002 TYR C 310 PHE 0.009 0.001 PHE E 378 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 3498) covalent geometry : angle 0.53974 ( 4680) hydrogen bonds : bond 0.02167 ( 66) hydrogen bonds : angle 3.90533 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.8740 (mt) cc_final: 0.8485 (mp) REVERT: A 340 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8115 (mttt) REVERT: B 340 LYS cc_start: 0.8464 (ttpt) cc_final: 0.7859 (mttp) REVERT: B 347 LYS cc_start: 0.7710 (mttt) cc_final: 0.7446 (mttm) REVERT: B 348 ASP cc_start: 0.7545 (m-30) cc_final: 0.7288 (m-30) REVERT: C 307 GLN cc_start: 0.7666 (mp10) cc_final: 0.6706 (tp40) REVERT: C 340 LYS cc_start: 0.8511 (ttpt) cc_final: 0.7991 (mttt) REVERT: C 349 ARG cc_start: 0.8263 (mtt180) cc_final: 0.7281 (mmp-170) REVERT: D 340 LYS cc_start: 0.8476 (ttpt) cc_final: 0.7982 (mttp) REVERT: D 349 ARG cc_start: 0.8214 (mtt180) cc_final: 0.7444 (mmm160) REVERT: E 340 LYS cc_start: 0.8764 (ttpt) cc_final: 0.8412 (mttt) REVERT: E 349 ARG cc_start: 0.7842 (mtt180) cc_final: 0.6717 (pmt-80) REVERT: E 370 LYS cc_start: 0.7120 (ptmt) cc_final: 0.5607 (tppt) REVERT: F 340 LYS cc_start: 0.8819 (ttpt) cc_final: 0.8305 (mtmt) outliers start: 9 outliers final: 7 residues processed: 90 average time/residue: 0.2759 time to fit residues: 27.8754 Evaluate side-chains 90 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 40 optimal weight: 0.0000 overall best weight: 3.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.184707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.162980 restraints weight = 13727.268| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 2.21 r_work: 0.4332 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.4252 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3498 Z= 0.195 Angle : 0.589 4.001 4680 Z= 0.315 Chirality : 0.053 0.154 528 Planarity : 0.003 0.021 594 Dihedral : 5.899 15.716 462 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.27 % Allowed : 12.88 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.26), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.20), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.011 0.002 TYR C 310 PHE 0.025 0.002 PHE B 378 HIS 0.006 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 3498) covalent geometry : angle 0.58882 ( 4680) hydrogen bonds : bond 0.02244 ( 66) hydrogen bonds : angle 4.01130 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.212 Fit side-chains REVERT: A 308 ILE cc_start: 0.8811 (mt) cc_final: 0.8559 (mp) REVERT: A 340 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8157 (mttt) REVERT: B 340 LYS cc_start: 0.8509 (ttpt) cc_final: 0.7928 (mtmt) REVERT: B 347 LYS cc_start: 0.7750 (mttt) cc_final: 0.7480 (mttm) REVERT: B 348 ASP cc_start: 0.7601 (m-30) cc_final: 0.7304 (m-30) REVERT: C 307 GLN cc_start: 0.7837 (mp10) cc_final: 0.6806 (tp40) REVERT: C 340 LYS cc_start: 0.8536 (ttpt) cc_final: 0.7964 (mttt) REVERT: C 349 ARG cc_start: 0.8244 (mtt180) cc_final: 0.7307 (mmp-170) REVERT: D 340 LYS cc_start: 0.8568 (mtpt) cc_final: 0.7969 (mttp) REVERT: D 349 ARG cc_start: 0.8156 (mtt180) cc_final: 0.7454 (mmm160) REVERT: E 340 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8439 (mttt) REVERT: E 349 ARG cc_start: 0.7942 (mtt180) cc_final: 0.6874 (pmt-80) REVERT: E 370 LYS cc_start: 0.7185 (ptmt) cc_final: 0.6074 (tppt) REVERT: E 372 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7301 (tm-30) REVERT: F 340 LYS cc_start: 0.8865 (ttpt) cc_final: 0.8343 (mtmt) outliers start: 9 outliers final: 8 residues processed: 91 average time/residue: 0.2736 time to fit residues: 27.9586 Evaluate side-chains 94 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.184010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.162356 restraints weight = 13713.454| |-----------------------------------------------------------------------------| r_work (start): 0.4432 rms_B_bonded: 2.13 r_work: 0.4355 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4273 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3498 Z= 0.166 Angle : 0.540 3.637 4680 Z= 0.287 Chirality : 0.052 0.145 528 Planarity : 0.003 0.019 594 Dihedral : 5.742 15.089 462 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.28 % Allowed : 12.63 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.26), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.20), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.008 0.002 TYR C 310 PHE 0.008 0.001 PHE E 378 HIS 0.004 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 3498) covalent geometry : angle 0.54006 ( 4680) hydrogen bonds : bond 0.02003 ( 66) hydrogen bonds : angle 3.94819 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 308 ILE cc_start: 0.8830 (mt) cc_final: 0.8563 (mp) REVERT: A 340 LYS cc_start: 0.8592 (ttpt) cc_final: 0.8189 (mttt) REVERT: B 340 LYS cc_start: 0.8577 (mtpt) cc_final: 0.7978 (mttp) REVERT: B 347 LYS cc_start: 0.7762 (mttt) cc_final: 0.7493 (mttm) REVERT: B 348 ASP cc_start: 0.7556 (m-30) cc_final: 0.7313 (m-30) REVERT: C 307 GLN cc_start: 0.7702 (mp10) cc_final: 0.6814 (tp40) REVERT: C 308 ILE cc_start: 0.8894 (mt) cc_final: 0.8469 (mm) REVERT: C 340 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8044 (mtmt) REVERT: C 349 ARG cc_start: 0.8253 (mtt180) cc_final: 0.7326 (mmp-170) REVERT: D 340 LYS cc_start: 0.8600 (mtpt) cc_final: 0.8008 (mttp) REVERT: D 349 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7462 (mmm160) REVERT: E 340 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8456 (mttt) REVERT: E 349 ARG cc_start: 0.7910 (mtt180) cc_final: 0.6847 (pmt-80) REVERT: E 370 LYS cc_start: 0.7319 (ptmt) cc_final: 0.5868 (tptt) REVERT: E 372 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7153 (tm-30) REVERT: F 340 LYS cc_start: 0.8905 (ttpt) cc_final: 0.8356 (mtmt) REVERT: F 370 LYS cc_start: 0.8471 (tttt) cc_final: 0.7651 (mttt) REVERT: F 372 GLU cc_start: 0.6993 (mp0) cc_final: 0.6786 (mp0) outliers start: 13 outliers final: 7 residues processed: 86 average time/residue: 0.2864 time to fit residues: 27.6256 Evaluate side-chains 88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.190346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.168799 restraints weight = 13465.188| |-----------------------------------------------------------------------------| r_work (start): 0.4485 rms_B_bonded: 2.18 r_work: 0.4408 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4326 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.6760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3498 Z= 0.080 Angle : 0.477 3.538 4680 Z= 0.251 Chirality : 0.051 0.141 528 Planarity : 0.002 0.023 594 Dihedral : 5.000 14.554 462 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.02 % Allowed : 13.64 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.27), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.006 0.001 TYR C 310 PHE 0.016 0.001 PHE F 378 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 3498) covalent geometry : angle 0.47652 ( 4680) hydrogen bonds : bond 0.01502 ( 66) hydrogen bonds : angle 3.57337 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.218 Fit side-chains REVERT: A 308 ILE cc_start: 0.8745 (mt) cc_final: 0.8517 (mp) REVERT: A 340 LYS cc_start: 0.8570 (ttpt) cc_final: 0.8148 (mttt) REVERT: B 340 LYS cc_start: 0.8553 (mtpt) cc_final: 0.7949 (mttp) REVERT: C 307 GLN cc_start: 0.7673 (mp10) cc_final: 0.6832 (tp40) REVERT: C 308 ILE cc_start: 0.8892 (mt) cc_final: 0.8457 (mm) REVERT: C 340 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8011 (mtmt) REVERT: C 349 ARG cc_start: 0.8260 (mtt180) cc_final: 0.7369 (mmp-170) REVERT: D 340 LYS cc_start: 0.8521 (mtpt) cc_final: 0.7949 (mttp) REVERT: D 349 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7494 (mmm160) REVERT: E 340 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8476 (mttt) REVERT: E 349 ARG cc_start: 0.7878 (mtt180) cc_final: 0.6820 (pmt-80) REVERT: E 370 LYS cc_start: 0.7284 (ptmt) cc_final: 0.5827 (tptt) REVERT: E 372 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7078 (tm-30) REVERT: F 340 LYS cc_start: 0.8892 (mtpt) cc_final: 0.8340 (mtmt) REVERT: F 370 LYS cc_start: 0.8476 (tttt) cc_final: 0.7638 (mttt) REVERT: F 372 GLU cc_start: 0.6949 (mp0) cc_final: 0.6649 (mp0) outliers start: 8 outliers final: 5 residues processed: 80 average time/residue: 0.2840 time to fit residues: 25.4252 Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 340 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.193932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.172222 restraints weight = 13281.228| |-----------------------------------------------------------------------------| r_work (start): 0.4531 rms_B_bonded: 2.19 r_work: 0.4458 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4377 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.6985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3498 Z= 0.074 Angle : 0.450 3.291 4680 Z= 0.236 Chirality : 0.051 0.136 528 Planarity : 0.002 0.024 594 Dihedral : 4.574 13.051 462 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.02 % Allowed : 13.64 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 349 TYR 0.006 0.001 TYR C 310 PHE 0.016 0.001 PHE A 378 HIS 0.002 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00174 ( 3498) covalent geometry : angle 0.44956 ( 4680) hydrogen bonds : bond 0.01359 ( 66) hydrogen bonds : angle 3.29886 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 308 ILE cc_start: 0.8654 (mt) cc_final: 0.8420 (mp) REVERT: A 340 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8126 (mttt) REVERT: C 307 GLN cc_start: 0.7618 (mp10) cc_final: 0.6867 (tp40) REVERT: C 308 ILE cc_start: 0.8858 (mt) cc_final: 0.8430 (mm) REVERT: C 340 LYS cc_start: 0.8462 (ttpt) cc_final: 0.7978 (mtmt) REVERT: C 349 ARG cc_start: 0.8216 (mtt180) cc_final: 0.7311 (mmp-170) REVERT: D 340 LYS cc_start: 0.8493 (mtpt) cc_final: 0.7909 (mttp) REVERT: D 349 ARG cc_start: 0.8211 (mtt180) cc_final: 0.7559 (mmm160) REVERT: E 340 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8452 (mttt) REVERT: E 349 ARG cc_start: 0.7872 (mtt180) cc_final: 0.6716 (pmt-80) REVERT: E 372 GLU cc_start: 0.7375 (tm-30) cc_final: 0.6980 (tm-30) REVERT: F 340 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8315 (mtmt) REVERT: F 370 LYS cc_start: 0.8501 (tttt) cc_final: 0.7679 (mttt) REVERT: F 372 GLU cc_start: 0.6856 (mp0) cc_final: 0.6631 (mp0) outliers start: 8 outliers final: 4 residues processed: 80 average time/residue: 0.2955 time to fit residues: 26.5102 Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain F residue 338 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 0.0070 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.184639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.162854 restraints weight = 13706.465| |-----------------------------------------------------------------------------| r_work (start): 0.4429 rms_B_bonded: 2.14 r_work: 0.4355 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4274 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.7025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3498 Z= 0.178 Angle : 0.522 3.666 4680 Z= 0.279 Chirality : 0.052 0.144 528 Planarity : 0.003 0.018 594 Dihedral : 5.236 13.870 462 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.77 % Allowed : 14.14 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 349 TYR 0.008 0.002 TYR C 310 PHE 0.013 0.002 PHE F 378 HIS 0.004 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 3498) covalent geometry : angle 0.52238 ( 4680) hydrogen bonds : bond 0.01790 ( 66) hydrogen bonds : angle 3.65745 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 308 ILE cc_start: 0.8752 (mt) cc_final: 0.8517 (mp) REVERT: A 340 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8150 (mttt) REVERT: B 340 LYS cc_start: 0.8553 (mtpt) cc_final: 0.7910 (mttp) REVERT: C 307 GLN cc_start: 0.7685 (mp10) cc_final: 0.6949 (tp40) REVERT: C 308 ILE cc_start: 0.8970 (mt) cc_final: 0.8563 (mm) REVERT: C 340 LYS cc_start: 0.8511 (ttpt) cc_final: 0.7997 (mttt) REVERT: C 349 ARG cc_start: 0.8208 (mtt180) cc_final: 0.7275 (mmp-170) REVERT: D 340 LYS cc_start: 0.8582 (mtpt) cc_final: 0.7948 (mttp) REVERT: D 349 ARG cc_start: 0.8218 (mtt180) cc_final: 0.7554 (mmm160) REVERT: E 340 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8430 (mttt) REVERT: E 349 ARG cc_start: 0.8009 (mtt180) cc_final: 0.6892 (pmt-80) REVERT: E 372 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7188 (tm-30) REVERT: F 340 LYS cc_start: 0.8921 (mtpt) cc_final: 0.8314 (mtmt) REVERT: F 372 GLU cc_start: 0.6983 (mp0) cc_final: 0.6640 (mp0) outliers start: 7 outliers final: 3 residues processed: 82 average time/residue: 0.2963 time to fit residues: 27.2052 Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 340 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.189196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.167491 restraints weight = 13488.879| |-----------------------------------------------------------------------------| r_work (start): 0.4464 rms_B_bonded: 2.27 r_work: 0.4383 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4300 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.7140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3498 Z= 0.095 Angle : 0.476 3.357 4680 Z= 0.252 Chirality : 0.051 0.139 528 Planarity : 0.002 0.019 594 Dihedral : 4.890 13.489 462 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.26 % Allowed : 15.15 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.018 0.002 TYR A 310 PHE 0.015 0.001 PHE A 378 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 3498) covalent geometry : angle 0.47557 ( 4680) hydrogen bonds : bond 0.01517 ( 66) hydrogen bonds : angle 3.48770 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8093 (mttt) REVERT: B 340 LYS cc_start: 0.8549 (mtpt) cc_final: 0.7869 (mttp) REVERT: C 307 GLN cc_start: 0.7666 (mp10) cc_final: 0.6973 (tp40) REVERT: C 308 ILE cc_start: 0.8917 (mt) cc_final: 0.8479 (mm) REVERT: C 340 LYS cc_start: 0.8465 (ttpt) cc_final: 0.7931 (mtmt) REVERT: C 349 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7227 (mmp-170) REVERT: D 340 LYS cc_start: 0.8502 (mtpt) cc_final: 0.7850 (mttp) REVERT: D 349 ARG cc_start: 0.8292 (mtt180) cc_final: 0.7510 (mmm160) REVERT: E 307 GLN cc_start: 0.7237 (tp-100) cc_final: 0.6610 (pp30) REVERT: E 340 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8404 (mttt) REVERT: E 349 ARG cc_start: 0.7973 (mtt180) cc_final: 0.6791 (pmt-80) REVERT: E 372 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7137 (tm-30) REVERT: F 340 LYS cc_start: 0.8911 (mtpt) cc_final: 0.8271 (mtmt) REVERT: F 372 GLU cc_start: 0.6922 (mp0) cc_final: 0.6589 (mp0) outliers start: 5 outliers final: 4 residues processed: 79 average time/residue: 0.3519 time to fit residues: 30.7671 Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 340 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.190837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.169392 restraints weight = 13501.487| |-----------------------------------------------------------------------------| r_work (start): 0.4489 rms_B_bonded: 2.19 r_work: 0.4418 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4340 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.7300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3498 Z= 0.084 Angle : 0.475 4.388 4680 Z= 0.252 Chirality : 0.051 0.136 528 Planarity : 0.003 0.042 594 Dihedral : 4.704 12.897 462 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.01 % Allowed : 15.15 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 349 TYR 0.012 0.002 TYR A 310 PHE 0.015 0.001 PHE F 378 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 3498) covalent geometry : angle 0.47518 ( 4680) hydrogen bonds : bond 0.01404 ( 66) hydrogen bonds : angle 3.34140 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8610 (ttpt) cc_final: 0.8185 (mttt) REVERT: B 340 LYS cc_start: 0.8575 (mtpt) cc_final: 0.7978 (mttp) REVERT: C 307 GLN cc_start: 0.7685 (mp10) cc_final: 0.7073 (tp40) REVERT: C 308 ILE cc_start: 0.8892 (mt) cc_final: 0.8487 (mm) REVERT: C 340 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8019 (mtmt) REVERT: C 349 ARG cc_start: 0.8209 (mtt180) cc_final: 0.7344 (mmp-170) REVERT: D 340 LYS cc_start: 0.8502 (mtpt) cc_final: 0.7921 (mttp) REVERT: D 349 ARG cc_start: 0.8244 (mtt180) cc_final: 0.7594 (mmm160) REVERT: E 307 GLN cc_start: 0.7377 (tp-100) cc_final: 0.6671 (pp30) REVERT: E 340 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8442 (mttt) REVERT: E 349 ARG cc_start: 0.7877 (mtt180) cc_final: 0.6855 (pmt-80) REVERT: E 372 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7183 (tm-30) REVERT: F 340 LYS cc_start: 0.8895 (mtpt) cc_final: 0.8311 (mtmt) REVERT: F 372 GLU cc_start: 0.6919 (mp0) cc_final: 0.6608 (mp0) outliers start: 4 outliers final: 3 residues processed: 77 average time/residue: 0.2999 time to fit residues: 25.8282 Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 340 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.192035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.170404 restraints weight = 13243.759| |-----------------------------------------------------------------------------| r_work (start): 0.4498 rms_B_bonded: 2.20 r_work: 0.4424 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4342 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.4342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.7363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3498 Z= 0.081 Angle : 0.466 3.931 4680 Z= 0.245 Chirality : 0.051 0.136 528 Planarity : 0.003 0.036 594 Dihedral : 4.563 12.530 462 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.26 % Allowed : 14.90 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 349 TYR 0.012 0.002 TYR A 310 PHE 0.013 0.001 PHE A 378 HIS 0.003 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 3498) covalent geometry : angle 0.46604 ( 4680) hydrogen bonds : bond 0.01439 ( 66) hydrogen bonds : angle 3.28872 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2534.64 seconds wall clock time: 43 minutes 56.51 seconds (2636.51 seconds total)