Starting phenix.real_space_refine on Fri Aug 22 13:01:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8caq_16532/08_2025/8caq_16532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8caq_16532/08_2025/8caq_16532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8caq_16532/08_2025/8caq_16532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8caq_16532/08_2025/8caq_16532.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8caq_16532/08_2025/8caq_16532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8caq_16532/08_2025/8caq_16532.map" } resolution = 2.3 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= 0.001 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 5 5.16 5 C 1800 2.51 5 N 530 2.21 5 O 535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Restraints were copied for chains: B, C, D, E Time building chain proxies: 0.45, per 1000 atoms: 0.16 Number of scatterers: 2870 At special positions: 0 Unit cell: (139.256, 119.48, 32.136, 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 5 16.00 O 535 8.00 N 530 7.00 C 1800 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: 0.14 Conformation dependent library (CDL) restraints added in 76.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 56.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.367A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.822A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 322 removed outlier: 6.403A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N SER B 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR A 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N CYS B 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS A 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 325 through 330 removed outlier: 8.567A pdb=" N LEU A 325 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N ILE B 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN A 327 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS B 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS A 329 " --> pdb=" O HIS B 330 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY A 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN E 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 346 removed outlier: 6.861A pdb=" N LEU A 344 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP B 345 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE A 346 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU E 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LYS A 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N PHE E 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 357 removed outlier: 6.411A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N SER B 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY A 355 " --> pdb=" O SER B 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.229A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 369 through 378 removed outlier: 6.825A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AB1, first strand: chain 'C' and resid 313 through 314 Processing sheet with id=AB2, first strand: chain 'C' and resid 317 through 322 Processing sheet with id=AB3, first strand: chain 'C' and resid 325 through 330 removed outlier: 6.806A pdb=" N GLY C 326 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN D 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 337 through 346 removed outlier: 6.316A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLU D 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER C 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU D 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LYS C 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N PHE D 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 350 through 357 Processing sheet with id=AB6, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.229A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 369 through 378 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: 0.33 Time building geometry restraints manager: 0.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 681 1.34 - 1.46: 697 1.46 - 1.57: 1532 1.57 - 1.69: 0 1.69 - 1.81: 5 Bond restraints: 2915 Sorted by residual: bond pdb=" CG HIS C 362 " pdb=" CD2 HIS C 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.44e+00 bond pdb=" CG HIS A 362 " pdb=" CD2 HIS A 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.44e+00 bond pdb=" CG HIS B 362 " pdb=" CD2 HIS B 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.43e+00 bond pdb=" CG HIS D 362 " pdb=" CD2 HIS D 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.42e+00 bond pdb=" CG HIS E 362 " pdb=" CD2 HIS E 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.39e+00 ... (remaining 2910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 2935 1.22 - 2.44: 780 2.44 - 3.66: 140 3.66 - 4.89: 40 4.89 - 6.11: 5 Bond angle restraints: 3900 Sorted by residual: angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 110.42 116.53 -6.11 1.49e+00 4.50e-01 1.68e+01 angle pdb=" N GLY B 326 " pdb=" CA GLY B 326 " pdb=" C GLY B 326 " ideal model delta sigma weight residual 110.42 116.52 -6.10 1.49e+00 4.50e-01 1.68e+01 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.42 116.52 -6.10 1.49e+00 4.50e-01 1.67e+01 angle pdb=" N GLY E 326 " pdb=" CA GLY E 326 " pdb=" C GLY E 326 " ideal model delta sigma weight residual 110.42 116.51 -6.09 1.49e+00 4.50e-01 1.67e+01 angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.42 116.51 -6.09 1.49e+00 4.50e-01 1.67e+01 ... (remaining 3895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 1645 15.14 - 30.28: 95 30.28 - 45.42: 25 45.42 - 60.55: 10 60.55 - 75.69: 5 Dihedral angle restraints: 1780 sinusoidal: 745 harmonic: 1035 Sorted by residual: dihedral pdb=" CA GLY B 335 " pdb=" C GLY B 335 " pdb=" N GLN B 336 " pdb=" CA GLN B 336 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLY E 335 " pdb=" C GLY E 335 " pdb=" N GLN E 336 " pdb=" CA GLN E 336 " ideal model delta harmonic sigma weight residual 180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLY A 335 " pdb=" C GLY A 335 " pdb=" N GLN A 336 " pdb=" CA GLN A 336 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 1777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 163 0.043 - 0.085: 173 0.085 - 0.127: 79 0.127 - 0.169: 20 0.169 - 0.212: 5 Chirality restraints: 440 Sorted by residual: chirality pdb=" CA LYS B 369 " pdb=" N LYS B 369 " pdb=" C LYS B 369 " pdb=" CB LYS B 369 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LYS E 369 " pdb=" N LYS E 369 " pdb=" C LYS E 369 " pdb=" CB LYS E 369 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LYS D 369 " pdb=" N LYS D 369 " pdb=" C LYS D 369 " pdb=" CB LYS D 369 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 437 not shown) Planarity restraints: 495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " 0.017 2.00e-02 2.50e+03 1.13e-02 2.56e+00 pdb=" CG TYR D 310 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.017 2.00e-02 2.50e+03 1.13e-02 2.55e+00 pdb=" CG TYR A 310 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.017 2.00e-02 2.50e+03 1.13e-02 2.54e+00 pdb=" CG TYR C 310 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.004 2.00e-02 2.50e+03 ... (remaining 492 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.06: 1590 3.06 - 3.52: 2604 3.52 - 3.98: 4241 3.98 - 4.44: 4342 4.44 - 4.90: 8817 Nonbonded interactions: 21594 Sorted by model distance: nonbonded pdb=" N ASP B 348 " pdb=" O ASP B 348 " model vdw 2.606 2.496 nonbonded pdb=" N ASP A 348 " pdb=" O ASP A 348 " model vdw 2.606 2.496 nonbonded pdb=" N ASP C 348 " pdb=" O ASP C 348 " model vdw 2.607 2.496 nonbonded pdb=" N ASP D 348 " pdb=" O ASP D 348 " model vdw 2.607 2.496 nonbonded pdb=" N ASP E 348 " pdb=" O ASP E 348 " model vdw 2.607 2.496 ... (remaining 21589 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' } 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: 4.110 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.920 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 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 : 0.007 0.042 2915 Z= 0.497 Angle : 1.178 6.107 3900 Z= 0.758 Chirality : 0.071 0.212 440 Planarity : 0.007 0.031 495 Dihedral : 12.141 75.692 1120 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.52 % Allowed : 3.03 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.61 (0.31), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.24), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 349 TYR 0.026 0.007 TYR D 310 PHE 0.008 0.003 PHE B 378 HIS 0.006 0.003 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00744 ( 2915) covalent geometry : angle 1.17762 ( 3900) hydrogen bonds : bond 0.10439 ( 66) hydrogen bonds : angle 6.63460 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.125 Fit side-chains REVERT: B 349 ARG cc_start: 0.9009 (mtt180) cc_final: 0.6996 (pmt-80) REVERT: B 379 ARG cc_start: 0.8324 (mtt180) cc_final: 0.7517 (pmt170) REVERT: C 349 ARG cc_start: 0.9022 (mtt180) cc_final: 0.7029 (pmt170) REVERT: C 379 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7436 (pmt170) REVERT: D 311 LYS cc_start: 0.8725 (mtmt) cc_final: 0.8389 (mmtt) REVERT: D 349 ARG cc_start: 0.8992 (mtt180) cc_final: 0.7199 (mmm160) REVERT: E 307 GLN cc_start: 0.8274 (tt0) cc_final: 0.7991 (mt0) REVERT: E 311 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8461 (mmtt) REVERT: E 349 ARG cc_start: 0.8975 (mtt180) cc_final: 0.7581 (mmp-170) outliers start: 5 outliers final: 0 residues processed: 110 average time/residue: 0.7040 time to fit residues: 78.7571 Evaluate side-chains 71 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 0.0370 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.0370 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 0.0470 overall best weight: 0.8238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 351 GLN C 351 GLN C 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.109797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.099868 restraints weight = 4417.355| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.01 r_work: 0.3733 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2915 Z= 0.095 Angle : 0.564 6.296 3900 Z= 0.272 Chirality : 0.048 0.124 440 Planarity : 0.004 0.025 495 Dihedral : 5.030 15.698 385 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.73 % Allowed : 13.64 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.73 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 379 TYR 0.007 0.002 TYR A 310 PHE 0.003 0.001 PHE A 346 HIS 0.001 0.000 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 2915) covalent geometry : angle 0.56386 ( 3900) hydrogen bonds : bond 0.01899 ( 66) hydrogen bonds : angle 5.16850 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.130 Fit side-chains REVERT: A 338 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: B 338 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8268 (tm-30) REVERT: B 348 ASP cc_start: 0.8977 (t0) cc_final: 0.7470 (p0) REVERT: B 349 ARG cc_start: 0.8788 (mtt180) cc_final: 0.6490 (pmt-80) REVERT: B 379 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7535 (pmt170) REVERT: C 338 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8391 (tm-30) REVERT: C 349 ARG cc_start: 0.8861 (mtt180) cc_final: 0.6549 (pmt-80) REVERT: C 379 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7348 (pmt170) REVERT: D 307 GLN cc_start: 0.8355 (tt0) cc_final: 0.7964 (mt0) REVERT: D 349 ARG cc_start: 0.8794 (mtt180) cc_final: 0.6692 (mmm160) REVERT: D 379 ARG cc_start: 0.5040 (OUTLIER) cc_final: 0.3409 (mmt180) REVERT: E 307 GLN cc_start: 0.8078 (tt0) cc_final: 0.7682 (mt0) REVERT: E 349 ARG cc_start: 0.8765 (mtt180) cc_final: 0.6838 (mmm160) REVERT: E 379 ARG cc_start: 0.5225 (OUTLIER) cc_final: 0.3327 (mmt180) outliers start: 9 outliers final: 0 residues processed: 79 average time/residue: 0.6717 time to fit residues: 54.0743 Evaluate side-chains 69 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 9 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 0.0170 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 overall best weight: 2.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN E 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.105652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.095905 restraints weight = 4477.595| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.98 r_work: 0.3687 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2915 Z= 0.147 Angle : 0.542 5.698 3900 Z= 0.272 Chirality : 0.049 0.128 440 Planarity : 0.003 0.023 495 Dihedral : 4.743 15.690 385 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.03 % Allowed : 14.55 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.014 0.003 TYR A 310 PHE 0.004 0.001 PHE E 346 HIS 0.002 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 2915) covalent geometry : angle 0.54196 ( 3900) hydrogen bonds : bond 0.01857 ( 66) hydrogen bonds : angle 4.83227 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.133 Fit side-chains REVERT: A 338 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: B 314 ASP cc_start: 0.8832 (t70) cc_final: 0.8626 (t0) REVERT: B 338 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8388 (tm-30) REVERT: B 348 ASP cc_start: 0.8945 (t0) cc_final: 0.7422 (p0) REVERT: B 349 ARG cc_start: 0.8806 (mtt180) cc_final: 0.6355 (pmt-80) REVERT: B 379 ARG cc_start: 0.8023 (mtt180) cc_final: 0.7546 (pmt170) REVERT: C 338 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8412 (tm-30) REVERT: C 349 ARG cc_start: 0.8883 (mtt180) cc_final: 0.6552 (pmt-80) REVERT: C 379 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7378 (pmt170) REVERT: D 349 ARG cc_start: 0.8806 (mtt180) cc_final: 0.6701 (mmm160) REVERT: D 379 ARG cc_start: 0.5001 (OUTLIER) cc_final: 0.3207 (mmt180) REVERT: E 349 ARG cc_start: 0.8779 (mtt180) cc_final: 0.6796 (mmm160) outliers start: 10 outliers final: 2 residues processed: 71 average time/residue: 0.6971 time to fit residues: 50.4041 Evaluate side-chains 70 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 305 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN E 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.099702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.090016 restraints weight = 4616.513| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.99 r_work: 0.3604 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9074 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.049 2915 Z= 0.380 Angle : 0.703 6.550 3900 Z= 0.362 Chirality : 0.054 0.138 440 Planarity : 0.004 0.020 495 Dihedral : 5.246 16.423 385 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.73 % Allowed : 16.36 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 379 TYR 0.022 0.006 TYR C 310 PHE 0.007 0.002 PHE E 346 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00878 ( 2915) covalent geometry : angle 0.70295 ( 3900) hydrogen bonds : bond 0.02604 ( 66) hydrogen bonds : angle 5.09634 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.083 Fit side-chains REVERT: A 338 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8355 (tt0) REVERT: B 314 ASP cc_start: 0.8915 (t70) cc_final: 0.8623 (t0) REVERT: B 338 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8372 (tm-30) REVERT: B 348 ASP cc_start: 0.9003 (t0) cc_final: 0.7528 (p0) REVERT: B 349 ARG cc_start: 0.8827 (mtt180) cc_final: 0.6359 (pmt-80) REVERT: B 379 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7563 (pmt170) REVERT: C 314 ASP cc_start: 0.9054 (t0) cc_final: 0.8840 (t0) REVERT: C 338 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8458 (tm-30) REVERT: C 349 ARG cc_start: 0.8908 (mtt180) cc_final: 0.6650 (pmt-80) REVERT: C 379 ARG cc_start: 0.8041 (mtt180) cc_final: 0.7368 (pmt170) REVERT: D 349 ARG cc_start: 0.8777 (mtt180) cc_final: 0.6648 (mmm160) REVERT: D 379 ARG cc_start: 0.5442 (OUTLIER) cc_final: 0.3560 (mmt180) REVERT: E 349 ARG cc_start: 0.8725 (mtt180) cc_final: 0.6948 (mmp-170) outliers start: 9 outliers final: 1 residues processed: 78 average time/residue: 0.6110 time to fit residues: 48.5218 Evaluate side-chains 74 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN E 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.103740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.094242 restraints weight = 4495.684| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.96 r_work: 0.3668 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2915 Z= 0.165 Angle : 0.576 5.521 3900 Z= 0.287 Chirality : 0.049 0.131 440 Planarity : 0.003 0.016 495 Dihedral : 4.930 16.619 385 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.42 % Allowed : 17.27 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 379 TYR 0.012 0.003 TYR A 310 PHE 0.004 0.001 PHE A 346 HIS 0.001 0.000 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 2915) covalent geometry : angle 0.57595 ( 3900) hydrogen bonds : bond 0.01949 ( 66) hydrogen bonds : angle 4.85528 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.135 Fit side-chains REVERT: A 338 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: B 314 ASP cc_start: 0.8926 (t70) cc_final: 0.8683 (t0) REVERT: B 338 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8368 (tm-30) REVERT: B 348 ASP cc_start: 0.8982 (t0) cc_final: 0.7534 (p0) REVERT: B 349 ARG cc_start: 0.8817 (mtt180) cc_final: 0.6493 (pmt-80) REVERT: B 379 ARG cc_start: 0.8065 (mtt180) cc_final: 0.7615 (pmt170) REVERT: C 314 ASP cc_start: 0.8966 (t0) cc_final: 0.8735 (t0) REVERT: C 338 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8402 (tm-30) REVERT: C 349 ARG cc_start: 0.8898 (mtt180) cc_final: 0.6651 (pmt-80) REVERT: C 379 ARG cc_start: 0.7980 (mtt180) cc_final: 0.7456 (pmt170) REVERT: D 349 ARG cc_start: 0.8797 (mtt180) cc_final: 0.6682 (mmm160) REVERT: D 379 ARG cc_start: 0.5393 (OUTLIER) cc_final: 0.3522 (mmt180) REVERT: E 349 ARG cc_start: 0.8770 (mtt180) cc_final: 0.6804 (mmm160) REVERT: E 379 ARG cc_start: 0.4985 (OUTLIER) cc_final: 0.2937 (mmt180) outliers start: 8 outliers final: 1 residues processed: 76 average time/residue: 0.6323 time to fit residues: 48.9345 Evaluate side-chains 75 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 34 optimal weight: 0.0030 chunk 8 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 11 optimal weight: 0.0870 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 362 HIS C 307 GLN C 351 GLN E 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.104108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.094669 restraints weight = 4526.017| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.97 r_work: 0.3675 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2915 Z= 0.153 Angle : 0.554 6.252 3900 Z= 0.273 Chirality : 0.049 0.129 440 Planarity : 0.002 0.015 495 Dihedral : 4.773 15.982 385 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.12 % Allowed : 17.58 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 379 TYR 0.012 0.003 TYR C 310 PHE 0.004 0.001 PHE A 346 HIS 0.001 0.000 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 2915) covalent geometry : angle 0.55408 ( 3900) hydrogen bonds : bond 0.01767 ( 66) hydrogen bonds : angle 4.68114 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.093 Fit side-chains REVERT: A 338 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8305 (tt0) REVERT: B 314 ASP cc_start: 0.8927 (t70) cc_final: 0.8684 (t0) REVERT: B 338 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8275 (tm-30) REVERT: B 348 ASP cc_start: 0.8950 (t0) cc_final: 0.7443 (p0) REVERT: B 349 ARG cc_start: 0.8805 (mtt180) cc_final: 0.6488 (pmt-80) REVERT: B 379 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7660 (pmt170) REVERT: C 314 ASP cc_start: 0.8969 (t0) cc_final: 0.8734 (t0) REVERT: C 338 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8400 (tm-30) REVERT: C 349 ARG cc_start: 0.8904 (mtt180) cc_final: 0.6629 (pmt-80) REVERT: C 379 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7480 (pmt170) REVERT: D 349 ARG cc_start: 0.8771 (mtt180) cc_final: 0.6655 (mmm160) REVERT: D 379 ARG cc_start: 0.5406 (OUTLIER) cc_final: 0.3523 (mmt180) REVERT: E 349 ARG cc_start: 0.8772 (mtt180) cc_final: 0.6773 (mmm160) REVERT: E 379 ARG cc_start: 0.4954 (OUTLIER) cc_final: 0.3001 (mmt180) outliers start: 7 outliers final: 1 residues processed: 74 average time/residue: 0.6075 time to fit residues: 45.7095 Evaluate side-chains 77 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 10 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.099107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.089528 restraints weight = 4666.681| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.96 r_work: 0.3597 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.047 2915 Z= 0.369 Angle : 0.693 6.674 3900 Z= 0.356 Chirality : 0.053 0.141 440 Planarity : 0.003 0.021 495 Dihedral : 5.208 16.726 385 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.12 % Allowed : 17.27 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 379 TYR 0.021 0.005 TYR C 310 PHE 0.009 0.002 PHE D 378 HIS 0.003 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00853 ( 2915) covalent geometry : angle 0.69322 ( 3900) hydrogen bonds : bond 0.02472 ( 66) hydrogen bonds : angle 4.90077 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.099 Fit side-chains REVERT: A 338 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: B 314 ASP cc_start: 0.8925 (t70) cc_final: 0.8675 (t0) REVERT: B 338 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8299 (tm-30) REVERT: B 348 ASP cc_start: 0.9002 (t0) cc_final: 0.7557 (p0) REVERT: B 349 ARG cc_start: 0.8815 (mtt180) cc_final: 0.6397 (pmt-80) REVERT: B 379 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7617 (pmt170) REVERT: C 314 ASP cc_start: 0.9000 (t0) cc_final: 0.8725 (t0) REVERT: C 338 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8429 (tm-30) REVERT: C 349 ARG cc_start: 0.8926 (mtt180) cc_final: 0.6642 (pmt-80) REVERT: C 379 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7482 (pmt170) REVERT: D 349 ARG cc_start: 0.8748 (mtt180) cc_final: 0.6600 (mmm160) REVERT: D 379 ARG cc_start: 0.5307 (OUTLIER) cc_final: 0.3349 (mmt180) REVERT: E 349 ARG cc_start: 0.8737 (mtt180) cc_final: 0.6949 (mmp-170) REVERT: E 379 ARG cc_start: 0.5016 (OUTLIER) cc_final: 0.3056 (mmt180) outliers start: 7 outliers final: 1 residues processed: 77 average time/residue: 0.5667 time to fit residues: 44.4310 Evaluate side-chains 79 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN C 362 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.104972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.095384 restraints weight = 4606.383| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.00 r_work: 0.3693 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2915 Z= 0.118 Angle : 0.538 6.965 3900 Z= 0.262 Chirality : 0.049 0.124 440 Planarity : 0.002 0.014 495 Dihedral : 4.796 16.419 385 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.21 % Allowed : 18.18 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 379 TYR 0.008 0.002 TYR C 310 PHE 0.004 0.001 PHE E 378 HIS 0.001 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 2915) covalent geometry : angle 0.53769 ( 3900) hydrogen bonds : bond 0.01652 ( 66) hydrogen bonds : angle 4.60989 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.117 Fit side-chains REVERT: A 338 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8305 (tt0) REVERT: B 338 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8290 (tm-30) REVERT: B 348 ASP cc_start: 0.8949 (t0) cc_final: 0.7447 (p0) REVERT: B 349 ARG cc_start: 0.8796 (mtt180) cc_final: 0.6468 (pmt-80) REVERT: B 379 ARG cc_start: 0.8124 (mtt180) cc_final: 0.7671 (pmt170) REVERT: C 314 ASP cc_start: 0.8964 (t0) cc_final: 0.8736 (t0) REVERT: C 338 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8472 (tm-30) REVERT: C 349 ARG cc_start: 0.8893 (mtt180) cc_final: 0.6573 (pmt170) REVERT: C 379 ARG cc_start: 0.8064 (mtt180) cc_final: 0.7468 (pmt170) REVERT: D 349 ARG cc_start: 0.8753 (mtt180) cc_final: 0.6636 (mmm160) REVERT: E 349 ARG cc_start: 0.8778 (mtt180) cc_final: 0.6777 (mmm160) outliers start: 4 outliers final: 0 residues processed: 69 average time/residue: 0.6657 time to fit residues: 46.7201 Evaluate side-chains 71 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.098577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.088951 restraints weight = 4768.887| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.00 r_work: 0.3585 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.059 2915 Z= 0.470 Angle : 0.749 6.562 3900 Z= 0.390 Chirality : 0.056 0.145 440 Planarity : 0.004 0.024 495 Dihedral : 5.320 17.142 385 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.52 % Allowed : 18.18 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 379 TYR 0.026 0.006 TYR C 310 PHE 0.012 0.002 PHE D 378 HIS 0.004 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.01092 ( 2915) covalent geometry : angle 0.74919 ( 3900) hydrogen bonds : bond 0.02708 ( 66) hydrogen bonds : angle 4.94763 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.100 Fit side-chains REVERT: A 338 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: B 338 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8327 (tm-30) REVERT: B 348 ASP cc_start: 0.9021 (t0) cc_final: 0.7574 (p0) REVERT: B 349 ARG cc_start: 0.8831 (mtt180) cc_final: 0.6414 (pmt-80) REVERT: B 379 ARG cc_start: 0.8187 (mtt180) cc_final: 0.7652 (pmt170) REVERT: C 314 ASP cc_start: 0.9031 (t0) cc_final: 0.8776 (t0) REVERT: C 338 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8458 (tm-30) REVERT: C 349 ARG cc_start: 0.8936 (mtt180) cc_final: 0.6617 (pmt170) REVERT: C 379 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7507 (pmt170) REVERT: D 349 ARG cc_start: 0.8745 (mtt180) cc_final: 0.6596 (mmm160) REVERT: E 349 ARG cc_start: 0.8735 (mtt180) cc_final: 0.6935 (mmp-170) REVERT: E 379 ARG cc_start: 0.4796 (OUTLIER) cc_final: 0.2876 (mmt180) outliers start: 5 outliers final: 1 residues processed: 78 average time/residue: 0.5817 time to fit residues: 46.2352 Evaluate side-chains 80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 0.8980 chunk 19 optimal weight: 0.0170 chunk 7 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 0.8980 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN E 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.105309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.095829 restraints weight = 4505.367| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.96 r_work: 0.3690 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2915 Z= 0.120 Angle : 0.582 8.715 3900 Z= 0.279 Chirality : 0.049 0.125 440 Planarity : 0.002 0.014 495 Dihedral : 4.894 16.687 385 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.91 % Allowed : 18.79 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 379 TYR 0.007 0.001 TYR A 310 PHE 0.003 0.001 PHE E 378 HIS 0.001 0.000 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 2915) covalent geometry : angle 0.58176 ( 3900) hydrogen bonds : bond 0.01709 ( 66) hydrogen bonds : angle 4.62974 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.186 Fit side-chains REVERT: A 338 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: B 338 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8292 (tm-30) REVERT: B 348 ASP cc_start: 0.8944 (t0) cc_final: 0.7440 (p0) REVERT: B 349 ARG cc_start: 0.8798 (mtt180) cc_final: 0.6428 (pmt-80) REVERT: B 379 ARG cc_start: 0.8170 (mtt180) cc_final: 0.7781 (pmt170) REVERT: C 314 ASP cc_start: 0.8957 (t0) cc_final: 0.8729 (t0) REVERT: C 338 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8471 (tm-30) REVERT: C 349 ARG cc_start: 0.8891 (mtt180) cc_final: 0.6578 (pmt170) REVERT: C 379 ARG cc_start: 0.8077 (mtt180) cc_final: 0.7532 (pmt170) REVERT: D 349 ARG cc_start: 0.8752 (mtt180) cc_final: 0.6643 (mmm160) REVERT: E 349 ARG cc_start: 0.8785 (mtt180) cc_final: 0.6798 (mmm160) outliers start: 3 outliers final: 0 residues processed: 70 average time/residue: 0.7177 time to fit residues: 51.1231 Evaluate side-chains 72 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 27 optimal weight: 0.0980 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.102786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.093275 restraints weight = 4550.173| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.94 r_work: 0.3654 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2915 Z= 0.206 Angle : 0.632 9.243 3900 Z= 0.311 Chirality : 0.050 0.132 440 Planarity : 0.002 0.014 495 Dihedral : 4.903 16.139 385 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.91 % Allowed : 19.09 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 379 TYR 0.014 0.003 TYR E 310 PHE 0.006 0.001 PHE D 378 HIS 0.002 0.000 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 2915) covalent geometry : angle 0.63178 ( 3900) hydrogen bonds : bond 0.01934 ( 66) hydrogen bonds : angle 4.62422 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1604.74 seconds wall clock time: 27 minutes 58.86 seconds (1678.86 seconds total)