Starting phenix.real_space_refine on Sat May 10 23:18:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qjj_18448/05_2025/8qjj_18448.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qjj_18448/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qjj_18448/05_2025/8qjj_18448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qjj_18448/05_2025/8qjj_18448.map" model { file = "/net/cci-nas-00/data/ceres_data/8qjj_18448/05_2025/8qjj_18448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qjj_18448/05_2025/8qjj_18448.cif" } resolution = 3.35 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= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.29, per 1000 atoms: 0.61 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: 1.72 Conformation dependent library (CDL) restraints added in 617.0 milliseconds 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: 0.71 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: 2.23 Time building geometry restraints manager: 2.07 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.770 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.700 ------------------------------------------------------------------------------- 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 : 0.43 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 (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: -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 HIS 0.018 0.004 HIS E 330 PHE 0.056 0.019 PHE F 346 TYR 0.057 0.017 TYR A 310 ARG 0.003 0.001 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.13251 ( 66) hydrogen bonds : angle 6.26912 ( 198) covalent geometry : bond 0.01179 ( 3498) covalent geometry : angle 1.98366 ( 4680) *********************** 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 : 0.537 Fit side-chains 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: 0.8160 (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: 0.7197 (mmp-170) REVERT: C 370 LYS cc_start: 0.8030 (tttt) cc_final: 0.7158 (mttt) REVERT: D 340 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8076 (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: 0.7931 (mttt) REVERT: D 376 LEU cc_start: 0.7819 (tp) cc_final: 0.7422 (mt) REVERT: E 306 VAL cc_start: 0.6987 (t) cc_final: 0.6753 (t) REVERT: E 308 ILE cc_start: 0.6794 (mt) cc_final: 0.6466 (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: 0.6685 (pmt-80) REVERT: E 370 LYS cc_start: 0.7637 (tttt) cc_final: 0.7420 (ptpt) 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: 0.5818 time to fit residues: 93.8048 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 : 0.608 ------------------------------------------------------------------------------- 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: 7.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.4738 r_free = 0.4738 target = 0.191410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.169692 restraints weight = 13297.782| |-----------------------------------------------------------------------------| r_work (start): 0.4530 rms_B_bonded: 2.24 r_work: 0.4447 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4365 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3498 Z= 0.142 Angle : 0.633 7.024 4680 Z= 0.333 Chirality : 0.053 0.151 528 Planarity : 0.003 0.023 594 Dihedral : 6.261 21.135 462 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.02 % Allowed : 11.11 % Favored : 86.87 % 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: -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 HIS 0.003 0.001 HIS B 330 PHE 0.014 0.002 PHE B 378 TYR 0.008 0.002 TYR C 310 ARG 0.003 0.000 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.02331 ( 66) hydrogen bonds : angle 4.21644 ( 198) covalent geometry : bond 0.00321 ( 3498) covalent geometry : angle 0.63328 ( 4680) *********************** 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 99 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.8797 (mt) cc_final: 0.8543 (mp) REVERT: A 340 LYS cc_start: 0.8578 (ttpt) cc_final: 0.8167 (mttt) REVERT: B 340 LYS cc_start: 0.8473 (ttpt) cc_final: 0.7886 (mttt) REVERT: B 347 LYS cc_start: 0.8022 (mttt) cc_final: 0.7771 (mttm) REVERT: B 372 GLU cc_start: 0.6855 (tt0) cc_final: 0.6412 (mt-10) REVERT: C 308 ILE cc_start: 0.8656 (mt) cc_final: 0.8415 (mp) REVERT: C 340 LYS cc_start: 0.8494 (ttpt) cc_final: 0.7978 (mttt) REVERT: C 349 ARG cc_start: 0.8186 (mtt180) cc_final: 0.7208 (mmp-170) REVERT: D 340 LYS cc_start: 0.8473 (ttpt) cc_final: 0.7995 (mttp) REVERT: D 349 ARG cc_start: 0.8199 (mtt180) cc_final: 0.7389 (mmm160) REVERT: D 370 LYS cc_start: 0.8387 (tttt) cc_final: 0.7950 (mttt) REVERT: D 376 LEU cc_start: 0.8156 (tp) cc_final: 0.7768 (mt) REVERT: E 340 LYS cc_start: 0.8787 (ttpt) cc_final: 0.8446 (mttt) REVERT: E 349 ARG cc_start: 0.7826 (mtt180) cc_final: 0.6689 (pmt-80) REVERT: E 370 LYS cc_start: 0.7663 (tttt) cc_final: 0.7155 (ptpt) REVERT: F 340 LYS cc_start: 0.8776 (ttpt) cc_final: 0.8294 (mttt) REVERT: F 379 ARG cc_start: 0.4668 (pmt-80) cc_final: 0.3678 (mtm180) outliers start: 8 outliers final: 5 residues processed: 94 average time/residue: 0.5465 time to fit residues: 58.1269 Evaluate side-chains 88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 20 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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** E 359 ASN ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.188842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.167295 restraints weight = 13523.924| |-----------------------------------------------------------------------------| r_work (start): 0.4479 rms_B_bonded: 2.24 r_work: 0.4405 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4325 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5710 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= 0.139 Angle : 0.568 4.431 4680 Z= 0.302 Chirality : 0.052 0.149 528 Planarity : 0.003 0.022 594 Dihedral : 5.778 16.716 462 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.53 % Allowed : 12.37 % Favored : 85.10 % 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: -2.17 (0.26), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.20), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 362 PHE 0.009 0.001 PHE E 378 TYR 0.009 0.002 TYR C 310 ARG 0.002 0.000 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.02299 ( 66) hydrogen bonds : angle 3.99549 ( 198) covalent geometry : bond 0.00320 ( 3498) covalent geometry : angle 0.56763 ( 4680) *********************** 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 97 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 308 ILE cc_start: 0.8785 (mt) cc_final: 0.8525 (mp) REVERT: A 340 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8131 (mttt) REVERT: B 340 LYS cc_start: 0.8514 (ttpt) cc_final: 0.7887 (mttt) REVERT: B 347 LYS cc_start: 0.7720 (mttt) cc_final: 0.7447 (mttm) REVERT: B 348 ASP cc_start: 0.7570 (m-30) cc_final: 0.7285 (m-30) REVERT: C 307 GLN cc_start: 0.7709 (mp10) cc_final: 0.6587 (tp40) REVERT: C 340 LYS cc_start: 0.8503 (ttpt) cc_final: 0.7973 (mttt) REVERT: C 349 ARG cc_start: 0.8230 (mtt180) cc_final: 0.7260 (mmp-170) REVERT: D 340 LYS cc_start: 0.8529 (ttpt) cc_final: 0.7997 (mttp) REVERT: D 349 ARG cc_start: 0.8214 (mtt180) cc_final: 0.7440 (mmm160) REVERT: E 340 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8399 (mttt) REVERT: E 349 ARG cc_start: 0.7865 (mtt180) cc_final: 0.6780 (pmt-80) REVERT: E 370 LYS cc_start: 0.7648 (tttt) cc_final: 0.7124 (ptpt) REVERT: F 340 LYS cc_start: 0.8824 (ttpt) cc_final: 0.8303 (mtmt) outliers start: 10 outliers final: 8 residues processed: 90 average time/residue: 0.6400 time to fit residues: 65.7003 Evaluate side-chains 87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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** ** E 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 = 0.4673 r_free = 0.4673 target = 0.184038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.162519 restraints weight = 13743.964| |-----------------------------------------------------------------------------| r_work (start): 0.4434 rms_B_bonded: 2.15 r_work: 0.4358 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4275 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.6276 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= 0.172 Angle : 0.562 3.817 4680 Z= 0.300 Chirality : 0.053 0.154 528 Planarity : 0.003 0.022 594 Dihedral : 5.813 15.108 462 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.27 % Allowed : 13.13 % Favored : 84.60 % 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: -2.35 (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 HIS 0.005 0.001 HIS E 362 PHE 0.028 0.002 PHE B 378 TYR 0.010 0.002 TYR C 310 ARG 0.002 0.000 ARG B 379 Details of bonding type rmsd hydrogen bonds : bond 0.02111 ( 66) hydrogen bonds : angle 3.97973 ( 198) covalent geometry : bond 0.00392 ( 3498) covalent geometry : angle 0.56246 ( 4680) *********************** 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 96 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 308 ILE cc_start: 0.8817 (mt) cc_final: 0.8546 (mp) REVERT: A 340 LYS cc_start: 0.8570 (ttpt) cc_final: 0.8151 (mttt) REVERT: B 340 LYS cc_start: 0.8516 (ttpt) cc_final: 0.7955 (mttp) REVERT: B 347 LYS cc_start: 0.7755 (mttt) cc_final: 0.7465 (mttm) REVERT: B 348 ASP cc_start: 0.7596 (m-30) cc_final: 0.7343 (m-30) REVERT: C 307 GLN cc_start: 0.7689 (mp10) cc_final: 0.6754 (tp40) REVERT: C 308 ILE cc_start: 0.8852 (mt) cc_final: 0.8403 (mm) REVERT: C 340 LYS cc_start: 0.8537 (ttpt) cc_final: 0.8006 (mttt) REVERT: C 349 ARG cc_start: 0.8222 (mtt180) cc_final: 0.7318 (mmp-170) REVERT: D 340 LYS cc_start: 0.8556 (mtpt) cc_final: 0.7982 (mttp) REVERT: D 349 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7461 (mmm160) REVERT: E 340 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8428 (mttt) REVERT: E 349 ARG cc_start: 0.7899 (mtt180) cc_final: 0.6834 (pmt-80) REVERT: E 370 LYS cc_start: 0.7678 (tttt) cc_final: 0.7067 (ptpt) REVERT: E 372 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7254 (tm-30) REVERT: F 340 LYS cc_start: 0.8872 (ttpt) cc_final: 0.8358 (mtmt) REVERT: F 370 LYS cc_start: 0.8375 (tttt) cc_final: 0.7541 (mttt) outliers start: 9 outliers final: 8 residues processed: 89 average time/residue: 0.5523 time to fit residues: 55.3728 Evaluate side-chains 92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 33 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 = 0.4719 r_free = 0.4719 target = 0.188623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.167146 restraints weight = 13454.637| |-----------------------------------------------------------------------------| r_work (start): 0.4485 rms_B_bonded: 2.15 r_work: 0.4414 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4333 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.002 0.023 3498 Z= 0.094 Angle : 0.486 3.569 4680 Z= 0.256 Chirality : 0.051 0.143 528 Planarity : 0.002 0.021 594 Dihedral : 5.185 14.415 462 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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 (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: -2.08 (0.27), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 330 PHE 0.008 0.001 PHE E 378 TYR 0.006 0.001 TYR C 310 ARG 0.001 0.000 ARG B 379 Details of bonding type rmsd hydrogen bonds : bond 0.01635 ( 66) hydrogen bonds : angle 3.64316 ( 198) covalent geometry : bond 0.00216 ( 3498) covalent geometry : angle 0.48628 ( 4680) *********************** 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 89 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.518 Fit side-chains REVERT: A 308 ILE cc_start: 0.8741 (mt) cc_final: 0.8523 (mp) REVERT: A 340 LYS cc_start: 0.8562 (ttpt) cc_final: 0.8125 (mttt) REVERT: B 340 LYS cc_start: 0.8507 (ttpt) cc_final: 0.7921 (mttp) REVERT: C 307 GLN cc_start: 0.7647 (mp10) cc_final: 0.6913 (tp40) REVERT: C 340 LYS cc_start: 0.8478 (ttpt) cc_final: 0.7991 (mtmt) REVERT: C 349 ARG cc_start: 0.8236 (mtt180) cc_final: 0.7332 (mmp-170) REVERT: D 340 LYS cc_start: 0.8502 (mtpt) cc_final: 0.7950 (mttp) REVERT: D 349 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7467 (mmm160) REVERT: E 340 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8420 (mttt) REVERT: E 349 ARG cc_start: 0.7854 (mtt180) cc_final: 0.6817 (pmt-80) REVERT: E 370 LYS cc_start: 0.7689 (tttt) cc_final: 0.7150 (ptpt) REVERT: E 372 GLU cc_start: 0.7426 (tm-30) cc_final: 0.6987 (tm-30) REVERT: F 340 LYS cc_start: 0.8866 (ttpt) cc_final: 0.8340 (mtmt) outliers start: 9 outliers final: 5 residues processed: 83 average time/residue: 0.5700 time to fit residues: 53.0216 Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 368 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 340 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.4664 r_free = 0.4664 target = 0.183414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.161783 restraints weight = 13738.724| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 2.13 r_work: 0.4342 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4263 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.6747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3498 Z= 0.183 Angle : 0.540 3.737 4680 Z= 0.289 Chirality : 0.052 0.144 528 Planarity : 0.003 0.024 594 Dihedral : 5.622 15.157 462 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.78 % Allowed : 13.38 % 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 (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: -2.24 (0.27), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 362 PHE 0.016 0.002 PHE F 378 TYR 0.009 0.002 TYR C 310 ARG 0.001 0.000 ARG C 349 Details of bonding type rmsd hydrogen bonds : bond 0.01944 ( 66) hydrogen bonds : angle 3.85012 ( 198) covalent geometry : bond 0.00414 ( 3498) covalent geometry : angle 0.53978 ( 4680) *********************** 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 92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 308 ILE cc_start: 0.8825 (mt) cc_final: 0.8560 (mp) REVERT: A 340 LYS cc_start: 0.8601 (ttpt) cc_final: 0.8152 (mttt) REVERT: B 340 LYS cc_start: 0.8530 (mtpt) cc_final: 0.7914 (mttp) REVERT: B 348 ASP cc_start: 0.7565 (m-30) cc_final: 0.7280 (m-30) REVERT: C 307 GLN cc_start: 0.7659 (mp10) cc_final: 0.6831 (tp40) REVERT: C 308 ILE cc_start: 0.8899 (mt) cc_final: 0.8476 (mm) REVERT: C 340 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8015 (mtmt) REVERT: C 349 ARG cc_start: 0.8208 (mtt180) cc_final: 0.7269 (mmp-170) REVERT: D 340 LYS cc_start: 0.8594 (mtpt) cc_final: 0.7979 (mttp) REVERT: D 349 ARG cc_start: 0.8196 (mtt180) cc_final: 0.7479 (mmm160) REVERT: E 340 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8444 (mttt) REVERT: E 349 ARG cc_start: 0.7950 (mtt180) cc_final: 0.6844 (pmt-80) REVERT: E 372 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7257 (tm-30) REVERT: F 340 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8320 (mtmt) REVERT: F 370 LYS cc_start: 0.8351 (tttt) cc_final: 0.7576 (mttt) outliers start: 11 outliers final: 7 residues processed: 84 average time/residue: 0.5718 time to fit residues: 54.0692 Evaluate side-chains 89 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 324 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.184037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.162753 restraints weight = 13595.460| |-----------------------------------------------------------------------------| r_work (start): 0.4431 rms_B_bonded: 2.11 r_work: 0.4355 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4274 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.6983 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= 0.158 Angle : 0.523 3.597 4680 Z= 0.278 Chirality : 0.052 0.144 528 Planarity : 0.003 0.019 594 Dihedral : 5.493 15.058 462 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.27 % Allowed : 13.64 % 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 (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: -2.29 (0.27), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.008 0.001 PHE E 378 TYR 0.007 0.002 TYR A 310 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01825 ( 66) hydrogen bonds : angle 3.82440 ( 198) covalent geometry : bond 0.00361 ( 3498) covalent geometry : angle 0.52298 ( 4680) *********************** 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 93 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.8818 (mt) cc_final: 0.8560 (mp) REVERT: A 340 LYS cc_start: 0.8603 (ttpt) cc_final: 0.8172 (mttt) REVERT: B 340 LYS cc_start: 0.8568 (mtpt) cc_final: 0.7943 (mttp) REVERT: C 307 GLN cc_start: 0.7709 (mp10) cc_final: 0.7000 (tp40) REVERT: C 308 ILE cc_start: 0.8953 (mt) cc_final: 0.8564 (mm) REVERT: C 340 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8023 (mtmt) REVERT: C 349 ARG cc_start: 0.8228 (mtt180) cc_final: 0.7304 (mmp-170) REVERT: D 340 LYS cc_start: 0.8587 (mtpt) cc_final: 0.7948 (mttp) REVERT: D 349 ARG cc_start: 0.8238 (mtt180) cc_final: 0.7508 (mmm160) REVERT: E 340 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8452 (mttt) REVERT: E 349 ARG cc_start: 0.7928 (mtt180) cc_final: 0.6847 (pmt-80) REVERT: E 370 LYS cc_start: 0.8163 (tttm) cc_final: 0.6942 (mttt) REVERT: E 372 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7442 (tm-30) REVERT: F 340 LYS cc_start: 0.8922 (mtpt) cc_final: 0.8314 (mtmt) outliers start: 9 outliers final: 6 residues processed: 86 average time/residue: 0.5812 time to fit residues: 56.2334 Evaluate side-chains 89 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 24 optimal weight: 0.0980 chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.186782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.165073 restraints weight = 13571.980| |-----------------------------------------------------------------------------| r_work (start): 0.4461 rms_B_bonded: 2.16 r_work: 0.4385 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4303 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3498 Z= 0.104 Angle : 0.499 3.975 4680 Z= 0.265 Chirality : 0.051 0.139 528 Planarity : 0.003 0.041 594 Dihedral : 5.105 14.443 462 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.27 % Allowed : 14.39 % Favored : 83.33 % 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: -2.10 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 330 PHE 0.016 0.001 PHE F 378 TYR 0.007 0.002 TYR C 310 ARG 0.007 0.001 ARG F 349 Details of bonding type rmsd hydrogen bonds : bond 0.01552 ( 66) hydrogen bonds : angle 3.61720 ( 198) covalent geometry : bond 0.00243 ( 3498) covalent geometry : angle 0.49877 ( 4680) *********************** 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 95 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.8727 (mt) cc_final: 0.8496 (mp) REVERT: A 340 LYS cc_start: 0.8588 (ttpt) cc_final: 0.8161 (mttt) REVERT: B 340 LYS cc_start: 0.8555 (mtpt) cc_final: 0.7909 (mttp) REVERT: C 307 GLN cc_start: 0.7717 (mp10) cc_final: 0.7028 (tp40) REVERT: C 308 ILE cc_start: 0.8934 (mt) cc_final: 0.8531 (mm) REVERT: C 340 LYS cc_start: 0.8490 (ttpt) cc_final: 0.8010 (mtmt) REVERT: C 349 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7312 (mmp-170) REVERT: D 340 LYS cc_start: 0.8560 (mtpt) cc_final: 0.7929 (mttp) REVERT: D 349 ARG cc_start: 0.8250 (mtt180) cc_final: 0.7523 (mmm160) REVERT: E 340 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8465 (mttt) REVERT: E 349 ARG cc_start: 0.7909 (mtt180) cc_final: 0.6816 (pmt-80) REVERT: E 372 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7453 (tm-30) REVERT: F 340 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8297 (mtmt) outliers start: 9 outliers final: 6 residues processed: 88 average time/residue: 0.5658 time to fit residues: 55.8242 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 : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU 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 368 ASN Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.188375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.166531 restraints weight = 13564.636| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 2.18 r_work: 0.4407 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4325 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.7169 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= 0.097 Angle : 0.492 3.945 4680 Z= 0.260 Chirality : 0.051 0.138 528 Planarity : 0.003 0.036 594 Dihedral : 4.911 13.854 462 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.52 % Allowed : 15.66 % Favored : 82.83 % 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: -1.93 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.014 0.001 PHE A 378 TYR 0.007 0.001 TYR C 310 ARG 0.005 0.000 ARG F 349 Details of bonding type rmsd hydrogen bonds : bond 0.01482 ( 66) hydrogen bonds : angle 3.47235 ( 198) covalent geometry : bond 0.00229 ( 3498) covalent geometry : angle 0.49160 ( 4680) *********************** 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 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8590 (ttpt) cc_final: 0.8161 (mttt) REVERT: B 340 LYS cc_start: 0.8512 (mtpt) cc_final: 0.7880 (mttp) REVERT: C 307 GLN cc_start: 0.7712 (mp10) cc_final: 0.7002 (tp40) REVERT: C 308 ILE cc_start: 0.8911 (mt) cc_final: 0.8503 (mm) REVERT: C 340 LYS cc_start: 0.8477 (ttpt) cc_final: 0.7997 (mtmt) REVERT: C 349 ARG cc_start: 0.8184 (mtt180) cc_final: 0.7329 (mmp-170) REVERT: D 340 LYS cc_start: 0.8520 (mtpt) cc_final: 0.7908 (mttp) REVERT: D 349 ARG cc_start: 0.8262 (mtt180) cc_final: 0.7555 (mmm160) REVERT: E 307 GLN cc_start: 0.7431 (tp-100) cc_final: 0.6680 (pp30) REVERT: E 340 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8459 (mttt) REVERT: E 349 ARG cc_start: 0.7897 (mtt180) cc_final: 0.6809 (pmt-80) REVERT: E 370 LYS cc_start: 0.8141 (tttp) cc_final: 0.6879 (mttt) REVERT: E 372 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7480 (tm-30) REVERT: F 340 LYS cc_start: 0.8900 (mtpt) cc_final: 0.8282 (mtmt) outliers start: 6 outliers final: 5 residues processed: 81 average time/residue: 0.5922 time to fit residues: 53.8589 Evaluate side-chains 84 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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 5 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** ** E 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 = 0.4739 r_free = 0.4739 target = 0.191745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.170126 restraints weight = 13672.297| |-----------------------------------------------------------------------------| r_work (start): 0.4504 rms_B_bonded: 2.35 r_work: 0.4422 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4338 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.7316 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= 0.079 Angle : 0.476 3.707 4680 Z= 0.250 Chirality : 0.051 0.135 528 Planarity : 0.003 0.033 594 Dihedral : 4.719 13.353 462 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.26 % Allowed : 16.16 % Favored : 82.58 % 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 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 330 PHE 0.015 0.001 PHE F 378 TYR 0.006 0.001 TYR C 310 ARG 0.004 0.001 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01379 ( 66) hydrogen bonds : angle 3.33035 ( 198) covalent geometry : bond 0.00190 ( 3498) covalent geometry : angle 0.47638 ( 4680) ********************** 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 82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8059 (mttt) REVERT: B 340 LYS cc_start: 0.8467 (mtpt) cc_final: 0.7773 (mttp) REVERT: C 307 GLN cc_start: 0.7663 (mp10) cc_final: 0.6961 (tp40) REVERT: C 308 ILE cc_start: 0.8848 (mt) cc_final: 0.8409 (mm) REVERT: C 340 LYS cc_start: 0.8469 (ttpt) cc_final: 0.7907 (mtmt) REVERT: C 349 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7238 (mmp-170) REVERT: D 349 ARG cc_start: 0.8329 (mtt180) cc_final: 0.7473 (mmm160) REVERT: E 307 GLN cc_start: 0.7270 (tp-100) cc_final: 0.6616 (pp30) REVERT: E 340 LYS cc_start: 0.8813 (ttpt) cc_final: 0.8394 (mttt) REVERT: E 349 ARG cc_start: 0.7884 (mtt180) cc_final: 0.6727 (pmt-80) REVERT: E 370 LYS cc_start: 0.8132 (tttp) cc_final: 0.6789 (mttt) REVERT: E 372 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7387 (tm-30) REVERT: F 340 LYS cc_start: 0.8880 (mtpt) cc_final: 0.8205 (mtmt) outliers start: 5 outliers final: 5 residues processed: 78 average time/residue: 0.5777 time to fit residues: 50.7644 Evaluate side-chains 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 368 ASN Chi-restraints excluded: chain E residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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** ** E 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 = 0.4698 r_free = 0.4698 target = 0.186134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.164188 restraints weight = 13699.149| |-----------------------------------------------------------------------------| r_work (start): 0.4451 rms_B_bonded: 2.19 r_work: 0.4374 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4291 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.7307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3498 Z= 0.133 Angle : 0.506 3.576 4680 Z= 0.268 Chirality : 0.051 0.141 528 Planarity : 0.003 0.027 594 Dihedral : 5.027 13.641 462 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.26 % Allowed : 16.41 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 330 PHE 0.013 0.002 PHE A 378 TYR 0.008 0.002 TYR C 310 ARG 0.005 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01633 ( 66) hydrogen bonds : angle 3.53829 ( 198) covalent geometry : bond 0.00307 ( 3498) covalent geometry : angle 0.50637 ( 4680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4695.56 seconds wall clock time: 81 minutes 46.59 seconds (4906.59 seconds total)