Starting phenix.real_space_refine on Tue Mar 3 11:36:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qjz_14027/03_2026/7qjz_14027.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qjz_14027/03_2026/7qjz_14027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qjz_14027/03_2026/7qjz_14027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qjz_14027/03_2026/7qjz_14027.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qjz_14027/03_2026/7qjz_14027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qjz_14027/03_2026/7qjz_14027.map" } resolution = 3.4 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2124 2.51 5 N 612 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3378 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "B" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "C" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "D" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "E" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "F" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Time building chain proxies: 0.93, per 1000 atoms: 0.28 Number of scatterers: 3378 At special positions: 0 Unit cell: (122.08, 116.63, 39.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 636 8.00 N 612 7.00 C 2124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 144.6 milliseconds 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 7.040A pdb=" N VAL A 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N VAL C 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.816A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 326 through 330 removed outlier: 7.938A pdb=" N HIS C 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 362 removed outlier: 9.046A pdb=" N ILE A 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N LEU B 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER A 356 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ASN B 359 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP A 358 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N THR B 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 360 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY A 355 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER C 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 370 through 371 removed outlier: 6.479A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 306 through 310 removed outlier: 6.461A pdb=" N GLN D 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYR E 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 313 through 316 removed outlier: 7.341A pdb=" N SER E 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR D 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N CYS E 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS D 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 313 through 316 Processing sheet with id=AB1, first strand: chain 'E' and resid 327 through 330 removed outlier: 6.377A pdb=" N ASN D 327 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N HIS F 330 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N HIS D 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 337 through 340 removed outlier: 6.984A pdb=" N GLU D 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL D 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N LYS F 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL D 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 350 through 362 removed outlier: 8.960A pdb=" N VAL D 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N LYS E 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N SER D 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N GLY E 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N ILE D 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N LEU E 357 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER D 356 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASN E 359 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP D 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR E 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE D 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 350 through 362 removed outlier: 8.960A pdb=" N VAL D 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N LYS E 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N SER D 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N GLY E 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N ILE D 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N LEU E 357 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER D 356 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASN E 359 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP D 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR E 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE D 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE F 354 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY D 355 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER F 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 369 through 371 removed outlier: 6.438A pdb=" N LYS D 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) 51 hydrogen bonds defined for protein. 153 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.41 Time building geometry restraints manager: 0.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 881 1.33 - 1.45: 493 1.45 - 1.57: 2052 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3432 Sorted by residual: bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.03e+00 bond pdb=" CA LYS D 311 " pdb=" CB LYS D 311 " ideal model delta sigma weight residual 1.526 1.553 -0.026 9.30e-03 1.16e+04 8.02e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.69e+00 bond pdb=" CZ ARG B 349 " pdb=" NH2 ARG B 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.45e+00 bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.31e+00 ... (remaining 3427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 3140 2.01 - 4.03: 1170 4.03 - 6.04: 261 6.04 - 8.05: 21 8.05 - 10.06: 4 Bond angle restraints: 4596 Sorted by residual: angle pdb=" CA ASN C 327 " pdb=" CB ASN C 327 " pdb=" CG ASN C 327 " ideal model delta sigma weight residual 112.60 119.73 -7.13 1.00e+00 1.00e+00 5.09e+01 angle pdb=" CA LYS C 331 " pdb=" C LYS C 331 " pdb=" N PRO C 332 " ideal model delta sigma weight residual 118.16 122.99 -4.83 7.00e-01 2.04e+00 4.75e+01 angle pdb=" CA ASN A 327 " pdb=" CB ASN A 327 " pdb=" CG ASN A 327 " ideal model delta sigma weight residual 112.60 119.09 -6.49 1.00e+00 1.00e+00 4.22e+01 angle pdb=" CA LYS B 331 " pdb=" C LYS B 331 " pdb=" N PRO B 332 " ideal model delta sigma weight residual 118.16 122.34 -4.18 7.00e-01 2.04e+00 3.56e+01 angle pdb=" CA ASN B 327 " pdb=" CB ASN B 327 " pdb=" CG ASN B 327 " ideal model delta sigma weight residual 112.60 118.20 -5.60 1.00e+00 1.00e+00 3.13e+01 ... (remaining 4591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 1888 16.24 - 32.48: 156 32.48 - 48.72: 29 48.72 - 64.96: 5 64.96 - 81.19: 10 Dihedral angle restraints: 2088 sinusoidal: 864 harmonic: 1224 Sorted by residual: dihedral pdb=" CA THR A 319 " pdb=" C THR A 319 " pdb=" N SER A 320 " pdb=" CA SER A 320 " ideal model delta harmonic sigma weight residual 180.00 152.94 27.06 0 5.00e+00 4.00e-02 2.93e+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 -153.00 -27.00 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ASP E 314 " pdb=" C ASP E 314 " pdb=" N LEU E 315 " pdb=" CA LEU E 315 " ideal model delta harmonic sigma weight residual 180.00 153.52 26.48 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 2085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 258 0.062 - 0.124: 161 0.124 - 0.185: 73 0.185 - 0.247: 23 0.247 - 0.309: 7 Chirality restraints: 522 Sorted by residual: 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 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA SER A 324 " pdb=" N SER A 324 " pdb=" C SER A 324 " pdb=" CB SER A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ASP D 345 " pdb=" N ASP D 345 " pdb=" C ASP D 345 " pdb=" CB ASP D 345 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 519 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.075 2.00e-02 2.50e+03 5.14e-02 5.29e+01 pdb=" CG TYR E 310 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.044 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " 0.084 2.00e-02 2.50e+03 5.11e-02 5.22e+01 pdb=" CG TYR D 310 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 329 " -0.076 2.00e-02 2.50e+03 5.66e-02 4.81e+01 pdb=" CG HIS F 329 " 0.077 2.00e-02 2.50e+03 pdb=" ND1 HIS F 329 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS F 329 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 HIS F 329 " -0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS F 329 " -0.050 2.00e-02 2.50e+03 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1511 2.97 - 3.45: 2933 3.45 - 3.94: 5105 3.94 - 4.42: 5246 4.42 - 4.90: 10498 Nonbonded interactions: 25293 Sorted by model distance: nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.490 3.040 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.509 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.539 3.040 nonbonded pdb=" N GLY A 366 " pdb=" O GLY A 366 " model vdw 2.640 2.496 nonbonded pdb=" OD2 ASP A 314 " pdb=" NZ LYS A 370 " model vdw 2.643 3.120 ... (remaining 25288 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: 1.380 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.220 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.037 3432 Z= 0.730 Angle : 2.094 10.065 4596 Z= 1.374 Chirality : 0.097 0.309 522 Planarity : 0.013 0.062 582 Dihedral : 13.722 81.195 1308 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.32 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 349 TYR 0.097 0.028 TYR E 310 PHE 0.072 0.018 PHE E 346 HIS 0.013 0.004 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.01133 ( 3432) covalent geometry : angle 2.09381 ( 4596) hydrogen bonds : bond 0.16075 ( 47) hydrogen bonds : angle 7.19338 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 341 SER cc_start: 0.7637 (p) cc_final: 0.7416 (t) REVERT: A 347 LYS cc_start: 0.8093 (mttt) cc_final: 0.7784 (tptm) REVERT: B 341 SER cc_start: 0.7599 (p) cc_final: 0.7307 (t) REVERT: C 341 SER cc_start: 0.8039 (p) cc_final: 0.7824 (t) REVERT: C 345 ASP cc_start: 0.8747 (t0) cc_final: 0.8365 (t0) REVERT: C 347 LYS cc_start: 0.8144 (mttt) cc_final: 0.7858 (tttt) REVERT: C 353 LYS cc_start: 0.8249 (tttm) cc_final: 0.7741 (mtpt) REVERT: E 321 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7754 (tptp) REVERT: E 347 LYS cc_start: 0.7176 (mmtm) cc_final: 0.5850 (mtmm) REVERT: F 343 LYS cc_start: 0.8540 (mtmt) cc_final: 0.6803 (tptt) REVERT: F 348 ASP cc_start: 0.7692 (t0) cc_final: 0.7450 (t0) REVERT: F 349 ARG cc_start: 0.8927 (ttp80) cc_final: 0.7747 (tpm170) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1017 time to fit residues: 10.6546 Evaluate side-chains 57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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: 6.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 ASN D 307 GLN D 336 GLN E 307 GLN E 336 GLN E 362 HIS F 307 GLN F 336 GLN F 362 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.130355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.112716 restraints weight = 5107.418| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.34 r_work: 0.3864 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3432 Z= 0.175 Angle : 0.822 6.518 4596 Z= 0.419 Chirality : 0.055 0.150 522 Planarity : 0.004 0.036 582 Dihedral : 7.804 19.347 450 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.03 % Allowed : 10.00 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.32), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.021 0.004 TYR A 310 PHE 0.007 0.002 PHE A 346 HIS 0.011 0.002 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 3432) covalent geometry : angle 0.82185 ( 4596) hydrogen bonds : bond 0.03502 ( 47) hydrogen bonds : angle 6.20971 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.133 Fit side-chains REVERT: A 345 ASP cc_start: 0.8204 (t0) cc_final: 0.7909 (t0) REVERT: A 347 LYS cc_start: 0.7851 (mttt) cc_final: 0.7554 (tptm) REVERT: A 353 LYS cc_start: 0.8268 (tttm) cc_final: 0.7514 (mtpt) REVERT: A 375 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7938 (tttp) REVERT: C 345 ASP cc_start: 0.8487 (t0) cc_final: 0.7836 (t0) REVERT: C 347 LYS cc_start: 0.7727 (mttt) cc_final: 0.7411 (tttt) REVERT: C 353 LYS cc_start: 0.8276 (tttm) cc_final: 0.7353 (mtpt) REVERT: E 349 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7883 (ttp-170) REVERT: F 349 ARG cc_start: 0.8651 (ttp80) cc_final: 0.7530 (mmp80) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 0.0837 time to fit residues: 6.3439 Evaluate side-chains 52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS D 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.123361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.105316 restraints weight = 5336.901| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.38 r_work: 0.3752 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 3432 Z= 0.363 Angle : 0.912 6.924 4596 Z= 0.479 Chirality : 0.056 0.153 522 Planarity : 0.005 0.036 582 Dihedral : 7.684 19.795 450 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.10 % Allowed : 10.51 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.29), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.22), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.014 0.003 TYR E 310 PHE 0.012 0.003 PHE D 346 HIS 0.010 0.003 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00824 ( 3432) covalent geometry : angle 0.91171 ( 4596) hydrogen bonds : bond 0.03412 ( 47) hydrogen bonds : angle 5.85963 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7215 (tt0) cc_final: 0.6344 (tm-30) REVERT: A 342 GLU cc_start: 0.6172 (tt0) cc_final: 0.5902 (tt0) REVERT: A 347 LYS cc_start: 0.7870 (mttt) cc_final: 0.7545 (tttt) REVERT: A 353 LYS cc_start: 0.8380 (tttm) cc_final: 0.7474 (mtpt) REVERT: A 375 LYS cc_start: 0.8473 (ttpt) cc_final: 0.8077 (tttp) REVERT: B 347 LYS cc_start: 0.8134 (mttt) cc_final: 0.7340 (pttm) REVERT: C 307 GLN cc_start: 0.7537 (tm-30) cc_final: 0.6849 (tm-30) REVERT: C 347 LYS cc_start: 0.7697 (mttt) cc_final: 0.7376 (tttt) REVERT: C 353 LYS cc_start: 0.8275 (tttm) cc_final: 0.7392 (mtpt) REVERT: C 370 LYS cc_start: 0.8357 (tttm) cc_final: 0.7913 (mttt) REVERT: C 375 LYS cc_start: 0.8407 (tttp) cc_final: 0.8198 (tttp) REVERT: E 338 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7779 (tm-30) REVERT: E 348 ASP cc_start: 0.8122 (t70) cc_final: 0.7885 (t0) REVERT: F 349 ARG cc_start: 0.8752 (ttp80) cc_final: 0.7366 (mmp80) outliers start: 16 outliers final: 12 residues processed: 78 average time/residue: 0.0883 time to fit residues: 8.1056 Evaluate side-chains 70 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 = 0.4233 r_free = 0.4233 target = 0.133049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.116077 restraints weight = 4930.484| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.22 r_work: 0.3884 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3432 Z= 0.150 Angle : 0.732 8.289 4596 Z= 0.366 Chirality : 0.051 0.140 522 Planarity : 0.003 0.029 582 Dihedral : 6.657 18.742 450 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.79 % Allowed : 15.13 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.32), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 349 TYR 0.010 0.002 TYR A 310 PHE 0.015 0.002 PHE B 378 HIS 0.007 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 3432) covalent geometry : angle 0.73170 ( 4596) hydrogen bonds : bond 0.02441 ( 47) hydrogen bonds : angle 5.48538 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.101 Fit side-chains REVERT: A 342 GLU cc_start: 0.6047 (tt0) cc_final: 0.5678 (tt0) REVERT: A 347 LYS cc_start: 0.7865 (mttt) cc_final: 0.7434 (tptm) REVERT: A 353 LYS cc_start: 0.8343 (tttm) cc_final: 0.7502 (mtpt) REVERT: A 375 LYS cc_start: 0.8272 (ttpt) cc_final: 0.7828 (tttp) REVERT: B 347 LYS cc_start: 0.8063 (mttt) cc_final: 0.7308 (pttm) REVERT: B 369 LYS cc_start: 0.8749 (tttm) cc_final: 0.7587 (mttt) REVERT: C 307 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7266 (tm-30) REVERT: C 347 LYS cc_start: 0.7743 (mttt) cc_final: 0.7402 (tttt) REVERT: C 353 LYS cc_start: 0.8222 (tttm) cc_final: 0.7353 (mtpt) REVERT: D 338 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7563 (tm-30) REVERT: E 338 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7813 (tm-30) REVERT: E 348 ASP cc_start: 0.7945 (t70) cc_final: 0.7693 (t0) REVERT: F 338 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7955 (tm-30) REVERT: F 349 ARG cc_start: 0.8683 (ttp80) cc_final: 0.7636 (mmp80) outliers start: 7 outliers final: 6 residues processed: 66 average time/residue: 0.0859 time to fit residues: 6.6704 Evaluate side-chains 65 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** 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 = 0.4268 r_free = 0.4268 target = 0.135871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.118693 restraints weight = 4839.224| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.19 r_work: 0.3907 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3432 Z= 0.127 Angle : 0.665 7.017 4596 Z= 0.334 Chirality : 0.051 0.170 522 Planarity : 0.003 0.029 582 Dihedral : 6.011 16.329 450 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.28 % Allowed : 15.64 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 349 TYR 0.007 0.001 TYR A 310 PHE 0.016 0.002 PHE B 378 HIS 0.006 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3432) covalent geometry : angle 0.66477 ( 4596) hydrogen bonds : bond 0.02208 ( 47) hydrogen bonds : angle 5.28108 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.084 Fit side-chains REVERT: A 342 GLU cc_start: 0.5925 (tt0) cc_final: 0.5598 (tt0) REVERT: A 347 LYS cc_start: 0.7893 (mttt) cc_final: 0.7482 (tptm) REVERT: A 353 LYS cc_start: 0.8332 (tttm) cc_final: 0.7498 (mtpt) REVERT: A 363 VAL cc_start: 0.9055 (t) cc_final: 0.8850 (t) REVERT: A 375 LYS cc_start: 0.8190 (ttpt) cc_final: 0.7786 (tttp) REVERT: B 347 LYS cc_start: 0.8062 (mttt) cc_final: 0.7330 (pttm) REVERT: B 369 LYS cc_start: 0.8715 (tttm) cc_final: 0.7588 (mttt) REVERT: C 307 GLN cc_start: 0.7767 (tm-30) cc_final: 0.7103 (tm-30) REVERT: C 347 LYS cc_start: 0.7836 (mttt) cc_final: 0.7528 (tttt) REVERT: C 353 LYS cc_start: 0.8109 (tttm) cc_final: 0.7343 (mtpt) REVERT: C 369 LYS cc_start: 0.8742 (tttp) cc_final: 0.8526 (tttp) REVERT: C 372 GLU cc_start: 0.7568 (mp0) cc_final: 0.7207 (mt-10) REVERT: D 338 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7528 (tm-30) REVERT: E 338 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7818 (tm-30) REVERT: E 348 ASP cc_start: 0.7850 (t70) cc_final: 0.7630 (t0) REVERT: F 338 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7773 (tm-30) REVERT: F 349 ARG cc_start: 0.8564 (ttp80) cc_final: 0.7643 (mmp80) outliers start: 5 outliers final: 5 residues processed: 66 average time/residue: 0.0888 time to fit residues: 6.9090 Evaluate side-chains 65 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- 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 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** 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 = 0.4232 r_free = 0.4232 target = 0.133296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.116187 restraints weight = 4900.857| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.17 r_work: 0.3880 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3432 Z= 0.174 Angle : 0.685 6.566 4596 Z= 0.347 Chirality : 0.051 0.170 522 Planarity : 0.003 0.032 582 Dihedral : 6.028 16.046 450 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.05 % Allowed : 15.90 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.006 0.002 TYR E 310 PHE 0.009 0.002 PHE B 378 HIS 0.005 0.002 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 3432) covalent geometry : angle 0.68454 ( 4596) hydrogen bonds : bond 0.02339 ( 47) hydrogen bonds : angle 5.06819 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.144 Fit side-chains REVERT: A 342 GLU cc_start: 0.6185 (tt0) cc_final: 0.5837 (tt0) REVERT: A 347 LYS cc_start: 0.7888 (mttt) cc_final: 0.7552 (tttt) REVERT: A 353 LYS cc_start: 0.8304 (tttm) cc_final: 0.7478 (mtpt) REVERT: A 363 VAL cc_start: 0.9087 (t) cc_final: 0.8884 (t) REVERT: A 375 LYS cc_start: 0.8291 (ttpt) cc_final: 0.7868 (tttp) REVERT: B 307 GLN cc_start: 0.7044 (mp10) cc_final: 0.6663 (mp10) REVERT: B 347 LYS cc_start: 0.8168 (mttt) cc_final: 0.7381 (pttm) REVERT: B 369 LYS cc_start: 0.8761 (tttm) cc_final: 0.7643 (mttt) REVERT: C 307 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7160 (tm-30) REVERT: C 347 LYS cc_start: 0.7866 (mttt) cc_final: 0.7587 (tttt) REVERT: C 353 LYS cc_start: 0.8154 (tttm) cc_final: 0.7351 (mtpt) REVERT: C 369 LYS cc_start: 0.8732 (tttp) cc_final: 0.8384 (tttp) REVERT: D 338 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7538 (tm-30) REVERT: E 338 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7822 (tm-30) REVERT: F 338 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7752 (tm-30) REVERT: F 349 ARG cc_start: 0.8701 (ttp80) cc_final: 0.7484 (mmp80) outliers start: 8 outliers final: 7 residues processed: 64 average time/residue: 0.0922 time to fit residues: 6.9120 Evaluate side-chains 65 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 9 optimal weight: 0.0020 overall best weight: 2.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** 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 = 0.4212 r_free = 0.4212 target = 0.131819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.113833 restraints weight = 4916.050| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.35 r_work: 0.3888 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3432 Z= 0.147 Angle : 0.661 6.615 4596 Z= 0.334 Chirality : 0.050 0.155 522 Planarity : 0.003 0.034 582 Dihedral : 5.800 15.353 450 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.31 % Allowed : 15.38 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 349 TYR 0.004 0.001 TYR B 310 PHE 0.008 0.002 PHE A 346 HIS 0.005 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 3432) covalent geometry : angle 0.66061 ( 4596) hydrogen bonds : bond 0.02188 ( 47) hydrogen bonds : angle 4.86988 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.146 Fit side-chains REVERT: A 342 GLU cc_start: 0.6095 (tt0) cc_final: 0.5350 (mp0) REVERT: A 347 LYS cc_start: 0.7829 (mttt) cc_final: 0.7532 (tttt) REVERT: A 353 LYS cc_start: 0.8273 (tttm) cc_final: 0.7410 (mtpt) REVERT: A 375 LYS cc_start: 0.8192 (ttpt) cc_final: 0.7865 (tttp) REVERT: B 307 GLN cc_start: 0.7118 (mp10) cc_final: 0.6666 (mp10) REVERT: B 347 LYS cc_start: 0.8203 (mttt) cc_final: 0.7385 (pttm) REVERT: B 369 LYS cc_start: 0.8815 (tttm) cc_final: 0.7658 (mttt) REVERT: C 307 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7268 (tm-30) REVERT: C 347 LYS cc_start: 0.8049 (mttt) cc_final: 0.7776 (tttt) REVERT: C 353 LYS cc_start: 0.8144 (tttm) cc_final: 0.7279 (mtpt) REVERT: C 369 LYS cc_start: 0.8696 (tttp) cc_final: 0.8396 (tttp) REVERT: D 338 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7479 (tm-30) REVERT: E 348 ASP cc_start: 0.8044 (t0) cc_final: 0.7775 (t0) REVERT: F 338 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7123 (tm-30) REVERT: F 349 ARG cc_start: 0.8692 (ttp80) cc_final: 0.7401 (mmp80) outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.0898 time to fit residues: 6.9222 Evaluate side-chains 64 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0670 chunk 41 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** 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 = 0.4204 r_free = 0.4204 target = 0.131462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.114806 restraints weight = 5124.582| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.13 r_work: 0.3851 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3432 Z= 0.205 Angle : 0.696 6.216 4596 Z= 0.356 Chirality : 0.051 0.171 522 Planarity : 0.004 0.034 582 Dihedral : 6.001 15.919 450 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.82 % Allowed : 15.13 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.006 0.002 TYR E 310 PHE 0.009 0.002 PHE D 346 HIS 0.006 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 3432) covalent geometry : angle 0.69580 ( 4596) hydrogen bonds : bond 0.02341 ( 47) hydrogen bonds : angle 4.90386 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.141 Fit side-chains REVERT: A 321 LYS cc_start: 0.8162 (mttp) cc_final: 0.7720 (mptt) REVERT: A 342 GLU cc_start: 0.6192 (tt0) cc_final: 0.5851 (tt0) REVERT: A 347 LYS cc_start: 0.7886 (mttt) cc_final: 0.7638 (tttt) REVERT: A 353 LYS cc_start: 0.8268 (tttm) cc_final: 0.7401 (mtpt) REVERT: A 375 LYS cc_start: 0.8253 (ttpt) cc_final: 0.7995 (tttt) REVERT: B 307 GLN cc_start: 0.7131 (mp10) cc_final: 0.6798 (mp-120) REVERT: B 347 LYS cc_start: 0.8283 (mttt) cc_final: 0.7477 (pttm) REVERT: B 369 LYS cc_start: 0.8867 (tttm) cc_final: 0.7710 (mttt) REVERT: C 307 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7320 (tm-30) REVERT: C 347 LYS cc_start: 0.8043 (mttt) cc_final: 0.7834 (tttt) REVERT: C 353 LYS cc_start: 0.8157 (tttm) cc_final: 0.7296 (mtpt) REVERT: C 369 LYS cc_start: 0.8727 (tttp) cc_final: 0.8294 (tmtt) REVERT: D 338 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7542 (tm-30) REVERT: E 338 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7698 (tm-30) REVERT: E 348 ASP cc_start: 0.8015 (t0) cc_final: 0.7753 (t0) REVERT: F 338 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7231 (tm-30) REVERT: F 349 ARG cc_start: 0.8772 (ttp80) cc_final: 0.7506 (mmp80) outliers start: 11 outliers final: 7 residues processed: 69 average time/residue: 0.0913 time to fit residues: 7.4137 Evaluate side-chains 67 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 6 optimal weight: 0.0470 chunk 40 optimal weight: 0.8980 overall best weight: 2.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** 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 = 0.4250 r_free = 0.4250 target = 0.134709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.117711 restraints weight = 4926.234| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.22 r_work: 0.3893 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3432 Z= 0.130 Angle : 0.646 6.694 4596 Z= 0.326 Chirality : 0.050 0.148 522 Planarity : 0.003 0.036 582 Dihedral : 5.699 15.271 450 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.54 % Allowed : 16.41 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.006 0.001 TYR B 310 PHE 0.007 0.001 PHE A 346 HIS 0.005 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3432) covalent geometry : angle 0.64617 ( 4596) hydrogen bonds : bond 0.02076 ( 47) hydrogen bonds : angle 4.77240 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.110 Fit side-chains REVERT: A 342 GLU cc_start: 0.6152 (tt0) cc_final: 0.5517 (mp0) REVERT: A 347 LYS cc_start: 0.7833 (mttt) cc_final: 0.7571 (tttt) REVERT: A 353 LYS cc_start: 0.8265 (tttm) cc_final: 0.7447 (mtpt) REVERT: A 375 LYS cc_start: 0.8243 (ttpt) cc_final: 0.7909 (tttp) REVERT: B 307 GLN cc_start: 0.7056 (mp10) cc_final: 0.6718 (mp-120) REVERT: B 347 LYS cc_start: 0.8267 (mttt) cc_final: 0.7455 (pttm) REVERT: B 369 LYS cc_start: 0.8784 (tttm) cc_final: 0.7705 (mttt) REVERT: C 307 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7405 (tm-30) REVERT: C 347 LYS cc_start: 0.8056 (mttt) cc_final: 0.7853 (tttt) REVERT: C 353 LYS cc_start: 0.8045 (tttm) cc_final: 0.7307 (mtpt) REVERT: C 369 LYS cc_start: 0.8737 (tttp) cc_final: 0.8311 (tmtt) REVERT: D 338 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7517 (tm-30) REVERT: E 348 ASP cc_start: 0.8123 (t0) cc_final: 0.7880 (t0) REVERT: F 338 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7254 (tm-30) REVERT: F 349 ARG cc_start: 0.8747 (ttp80) cc_final: 0.7444 (mmp80) outliers start: 6 outliers final: 6 residues processed: 64 average time/residue: 0.0915 time to fit residues: 6.8856 Evaluate side-chains 64 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 9 optimal weight: 0.0570 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 16 optimal weight: 0.0270 chunk 10 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 overall best weight: 1.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** 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 = 0.4249 r_free = 0.4249 target = 0.134672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.116814 restraints weight = 4856.470| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.36 r_work: 0.3929 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3432 Z= 0.108 Angle : 0.646 10.219 4596 Z= 0.319 Chirality : 0.050 0.147 522 Planarity : 0.004 0.044 582 Dihedral : 5.387 15.293 450 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.54 % Allowed : 17.44 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 349 TYR 0.007 0.001 TYR B 310 PHE 0.009 0.001 PHE A 346 HIS 0.006 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 3432) covalent geometry : angle 0.64591 ( 4596) hydrogen bonds : bond 0.01925 ( 47) hydrogen bonds : angle 4.58852 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.084 Fit side-chains REVERT: A 342 GLU cc_start: 0.6192 (tt0) cc_final: 0.5542 (mp0) REVERT: A 347 LYS cc_start: 0.7755 (mttt) cc_final: 0.7531 (tttt) REVERT: A 353 LYS cc_start: 0.8251 (tttm) cc_final: 0.7398 (mtpt) REVERT: A 375 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7882 (tttp) REVERT: B 307 GLN cc_start: 0.7097 (mp10) cc_final: 0.6756 (mp-120) REVERT: B 347 LYS cc_start: 0.8216 (mttt) cc_final: 0.7403 (pttm) REVERT: B 369 LYS cc_start: 0.8718 (tttm) cc_final: 0.7673 (mttt) REVERT: C 307 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7417 (tm-30) REVERT: C 353 LYS cc_start: 0.8023 (tttm) cc_final: 0.7276 (mtpt) REVERT: C 369 LYS cc_start: 0.8717 (tttp) cc_final: 0.8346 (tttp) REVERT: D 338 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7510 (tm-30) REVERT: E 348 ASP cc_start: 0.8082 (t0) cc_final: 0.7825 (t0) REVERT: F 338 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7821 (tm-30) REVERT: F 349 ARG cc_start: 0.8700 (ttp80) cc_final: 0.7379 (mmp80) outliers start: 6 outliers final: 6 residues processed: 66 average time/residue: 0.0783 time to fit residues: 6.1328 Evaluate side-chains 65 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 8 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 chunk 39 optimal weight: 0.0770 overall best weight: 6.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** 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 = 0.4177 r_free = 0.4177 target = 0.128845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.112133 restraints weight = 5231.763| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.13 r_work: 0.3822 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3432 Z= 0.274 Angle : 0.760 9.041 4596 Z= 0.390 Chirality : 0.052 0.141 522 Planarity : 0.005 0.042 582 Dihedral : 6.081 15.401 450 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 2.05 % Allowed : 16.67 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.007 0.002 TYR F 310 PHE 0.011 0.002 PHE B 346 HIS 0.005 0.002 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00618 ( 3432) covalent geometry : angle 0.76028 ( 4596) hydrogen bonds : bond 0.02527 ( 47) hydrogen bonds : angle 4.94036 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1019.22 seconds wall clock time: 18 minutes 13.47 seconds (1093.47 seconds total)