Starting phenix.real_space_refine on Fri Aug 22 14:27:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bgv_16039/08_2025/8bgv_16039.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bgv_16039/08_2025/8bgv_16039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bgv_16039/08_2025/8bgv_16039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bgv_16039/08_2025/8bgv_16039.map" model { file = "/net/cci-nas-00/data/ceres_data/8bgv_16039/08_2025/8bgv_16039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bgv_16039/08_2025/8bgv_16039.cif" } resolution = 3.27 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 7 5.16 5 C 2569 2.51 5 N 756 2.21 5 O 777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 4109 Number of models: 1 Model: "" Number of chains: 1 Chain: "n" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Restraints were copied for chains: A, B, C, D, E, F Time building chain proxies: 0.76, per 1000 atoms: 0.18 Number of scatterers: 4109 At special positions: 0 Unit cell: (145.95, 100.08, 40.032, 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 7 16.00 O 777 8.00 N 756 7.00 C 2569 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: 0.37 Conformation dependent library (CDL) restraints added in 184.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 938 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 310 removed outlier: 6.670A pdb=" N SER n 305 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ILE B 308 " --> pdb=" O SER n 305 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLN n 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N TYR B 310 " --> pdb=" O GLN n 307 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL n 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.784A pdb=" N VAL n 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 318 removed outlier: 6.351A pdb=" N LYS n 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.405A pdb=" N HIS n 329 " --> pdb=" O HIS B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 348 removed outlier: 5.716A pdb=" N LYS A 347 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS B 347 " --> pdb=" O PHE n 346 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS n 347 " --> pdb=" O ASP E 348 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 352 removed outlier: 6.700A pdb=" N GLN n 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 369 through 373 removed outlier: 6.121A pdb=" N LYS A 370 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR B 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU A 372 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS n 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N THR E 373 " --> pdb=" O LYS n 370 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU n 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 376 through 379 removed outlier: 6.586A pdb=" N LEU A 376 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ARG B 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE A 378 " --> pdb=" O ARG B 379 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU n 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ARG E 379 " --> pdb=" O LEU n 376 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE n 378 " --> pdb=" O ARG E 379 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 305 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 318 Processing sheet with id=AB3, first strand: chain 'C' and resid 328 through 330 Processing sheet with id=AB4, first strand: chain 'C' and resid 346 through 348 removed outlier: 5.716A pdb=" N LYS C 347 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS D 347 " --> pdb=" O ASP F 348 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 351 through 352 Processing sheet with id=AB6, first strand: chain 'C' and resid 369 through 373 removed outlier: 6.121A pdb=" N LYS C 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR D 373 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU C 372 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LYS D 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N THR F 373 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU D 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.587A pdb=" N LEU C 376 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ARG D 379 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE C 378 " --> pdb=" O ARG D 379 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU D 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ARG F 379 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE D 378 " --> pdb=" O ARG F 379 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 48 hydrogen bonds defined for protein. 144 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: 0.52 Time building geometry restraints manager: 0.44 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: 1003 1.33 - 1.45: 864 1.45 - 1.57: 2298 1.57 - 1.69: 0 1.69 - 1.81: 7 Bond restraints: 4172 Sorted by residual: bond pdb=" CG HIS C 330 " pdb=" CD2 HIS C 330 " ideal model delta sigma weight residual 1.354 1.314 0.040 1.10e-02 8.26e+03 1.35e+01 bond pdb=" CG HIS D 330 " pdb=" CD2 HIS D 330 " ideal model delta sigma weight residual 1.354 1.314 0.040 1.10e-02 8.26e+03 1.34e+01 bond pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 1.354 1.314 0.040 1.10e-02 8.26e+03 1.33e+01 bond pdb=" CG HIS n 330 " pdb=" CD2 HIS n 330 " ideal model delta sigma weight residual 1.354 1.314 0.040 1.10e-02 8.26e+03 1.32e+01 bond pdb=" CG HIS F 330 " pdb=" CD2 HIS F 330 " ideal model delta sigma weight residual 1.354 1.314 0.040 1.10e-02 8.26e+03 1.32e+01 ... (remaining 4167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 4276 1.91 - 3.81: 1083 3.81 - 5.72: 190 5.72 - 7.63: 23 7.63 - 9.53: 7 Bond angle restraints: 5579 Sorted by residual: angle pdb=" N PRO E 332 " pdb=" CA PRO E 332 " pdb=" C PRO E 332 " ideal model delta sigma weight residual 110.55 120.08 -9.53 1.63e+00 3.76e-01 3.42e+01 angle pdb=" N PRO C 332 " pdb=" CA PRO C 332 " pdb=" C PRO C 332 " ideal model delta sigma weight residual 110.55 120.06 -9.51 1.63e+00 3.76e-01 3.41e+01 angle pdb=" N PRO n 332 " pdb=" CA PRO n 332 " pdb=" C PRO n 332 " ideal model delta sigma weight residual 110.55 120.06 -9.51 1.63e+00 3.76e-01 3.40e+01 angle pdb=" N PRO D 332 " pdb=" CA PRO D 332 " pdb=" C PRO D 332 " ideal model delta sigma weight residual 110.55 120.06 -9.51 1.63e+00 3.76e-01 3.40e+01 angle pdb=" N PRO A 332 " pdb=" CA PRO A 332 " pdb=" C PRO A 332 " ideal model delta sigma weight residual 110.55 120.05 -9.50 1.63e+00 3.76e-01 3.40e+01 ... (remaining 5574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.86: 2072 10.86 - 21.72: 329 21.72 - 32.58: 112 32.58 - 43.43: 14 43.43 - 54.29: 14 Dihedral angle restraints: 2541 sinusoidal: 1064 harmonic: 1477 Sorted by residual: dihedral pdb=" CA GLY C 326 " pdb=" C GLY C 326 " pdb=" N ASN C 327 " pdb=" CA ASN C 327 " ideal model delta harmonic sigma weight residual 180.00 -150.69 -29.31 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA GLY F 326 " pdb=" C GLY F 326 " pdb=" N ASN F 327 " pdb=" CA ASN F 327 " ideal model delta harmonic sigma weight residual 180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA GLY n 326 " pdb=" C GLY n 326 " pdb=" N ASN n 327 " pdb=" CA ASN n 327 " ideal model delta harmonic sigma weight residual -180.00 -150.72 -29.28 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 2538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 217 0.048 - 0.097: 194 0.097 - 0.145: 121 0.145 - 0.194: 70 0.194 - 0.242: 21 Chirality restraints: 623 Sorted by residual: chirality pdb=" CA LYS C 347 " pdb=" N LYS C 347 " pdb=" C LYS C 347 " pdb=" CB LYS C 347 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA LYS A 347 " pdb=" N LYS A 347 " pdb=" C LYS A 347 " pdb=" CB LYS A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA LYS D 347 " pdb=" N LYS D 347 " pdb=" C LYS D 347 " pdb=" CB LYS D 347 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 620 not shown) Planarity restraints: 714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 349 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C ARG F 349 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG F 349 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL F 350 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 349 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C ARG B 349 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG B 349 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL B 350 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG n 349 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C ARG n 349 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG n 349 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL n 350 " 0.014 2.00e-02 2.50e+03 ... (remaining 711 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 1651 2.94 - 3.43: 3616 3.43 - 3.92: 5966 3.92 - 4.41: 6465 4.41 - 4.90: 13471 Nonbonded interactions: 31169 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.452 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.453 3.040 nonbonded pdb=" OD1 ASP n 314 " pdb=" OG SER n 316 " model vdw 2.453 3.040 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.453 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.453 3.040 ... (remaining 31164 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 'n' selection = 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: 2.020 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.730 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 : 0.009 0.050 4172 Z= 0.633 Angle : 1.720 9.532 5579 Z= 1.106 Chirality : 0.095 0.242 623 Planarity : 0.010 0.052 714 Dihedral : 12.413 54.292 1603 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.49 % Allowed : 1.49 % Favored : 97.01 % 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: -3.78 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG C 349 TYR 0.018 0.006 TYR B 310 PHE 0.008 0.003 PHE A 378 HIS 0.007 0.004 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00881 ( 4172) covalent geometry : angle 1.72040 ( 5579) hydrogen bonds : bond 0.23307 ( 48) hydrogen bonds : angle 7.49002 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: n 321 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8320 (mttp) REVERT: n 340 LYS cc_start: 0.9019 (mttt) cc_final: 0.8726 (mtpt) REVERT: n 377 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8218 (p) REVERT: A 321 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8501 (mttm) REVERT: A 340 LYS cc_start: 0.9140 (mttt) cc_final: 0.8846 (mtpp) REVERT: B 311 LYS cc_start: 0.8875 (mttt) cc_final: 0.8509 (pttt) REVERT: B 321 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8370 (mttp) REVERT: B 340 LYS cc_start: 0.9006 (mttt) cc_final: 0.8771 (mtpt) REVERT: B 377 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8147 (p) REVERT: C 321 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8490 (mttp) REVERT: C 340 LYS cc_start: 0.9053 (mttt) cc_final: 0.8822 (mtpt) REVERT: C 377 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8522 (p) REVERT: D 321 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8445 (mttp) REVERT: D 340 LYS cc_start: 0.9093 (mttt) cc_final: 0.8775 (mtpt) REVERT: D 349 ARG cc_start: 0.7655 (mtt-85) cc_final: 0.7433 (mtp180) REVERT: E 321 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8269 (mttp) REVERT: E 340 LYS cc_start: 0.9062 (mttt) cc_final: 0.8721 (mtpt) REVERT: E 349 ARG cc_start: 0.7717 (mtt-85) cc_final: 0.7458 (mtp180) REVERT: E 371 ILE cc_start: 0.8732 (mm) cc_final: 0.8491 (mt) REVERT: F 311 LYS cc_start: 0.8848 (mttt) cc_final: 0.8515 (pttt) REVERT: F 321 LYS cc_start: 0.8773 (mtpt) cc_final: 0.8430 (mttm) REVERT: F 331 LYS cc_start: 0.9074 (tttt) cc_final: 0.8826 (ttpt) REVERT: F 340 LYS cc_start: 0.9064 (mttt) cc_final: 0.8714 (mtpt) REVERT: F 349 ARG cc_start: 0.7744 (mtt-85) cc_final: 0.7500 (mtp180) REVERT: F 377 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8460 (m) outliers start: 7 outliers final: 0 residues processed: 75 average time/residue: 0.1442 time to fit residues: 12.3686 Evaluate side-chains 60 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 377 THR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 351 GLN n 362 HIS A 330 HIS A 351 GLN A 362 HIS B 351 GLN B 362 HIS C 330 HIS C 351 GLN C 362 HIS D 351 GLN D 362 HIS E 351 GLN E 362 HIS F 351 GLN F 362 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.131843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.106442 restraints weight = 5058.598| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.39 r_work: 0.3648 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 4172 Z= 0.119 Angle : 0.638 6.161 5579 Z= 0.334 Chirality : 0.051 0.134 623 Planarity : 0.003 0.023 714 Dihedral : 7.107 23.232 557 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.85 % Allowed : 5.76 % Favored : 93.39 % 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: -3.03 (0.27), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.21), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG n 349 TYR 0.007 0.002 TYR F 310 PHE 0.005 0.001 PHE E 346 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 4172) covalent geometry : angle 0.63760 ( 5579) hydrogen bonds : bond 0.02210 ( 48) hydrogen bonds : angle 5.51417 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: n 317 LYS cc_start: 0.7993 (ptmt) cc_final: 0.7513 (ptmm) REVERT: n 340 LYS cc_start: 0.8708 (mttt) cc_final: 0.8318 (mtpt) REVERT: A 331 LYS cc_start: 0.8754 (ttmt) cc_final: 0.6937 (tptt) REVERT: A 340 LYS cc_start: 0.8896 (mttt) cc_final: 0.8478 (mtpt) REVERT: B 311 LYS cc_start: 0.8352 (mttt) cc_final: 0.7936 (pttt) REVERT: B 315 LEU cc_start: 0.8656 (mt) cc_final: 0.8197 (tt) REVERT: B 340 LYS cc_start: 0.8807 (mttt) cc_final: 0.8483 (mtpt) REVERT: C 340 LYS cc_start: 0.8698 (mttt) cc_final: 0.8343 (mtpt) REVERT: D 340 LYS cc_start: 0.8793 (mttt) cc_final: 0.8316 (mtpt) REVERT: D 369 LYS cc_start: 0.8704 (ptpt) cc_final: 0.8406 (ptpp) REVERT: E 340 LYS cc_start: 0.8756 (mttt) cc_final: 0.8308 (mtpt) REVERT: E 369 LYS cc_start: 0.8695 (ptpt) cc_final: 0.8420 (ptpp) REVERT: F 311 LYS cc_start: 0.8431 (mttt) cc_final: 0.8043 (pttt) REVERT: F 331 LYS cc_start: 0.8478 (tttt) cc_final: 0.6841 (tptt) REVERT: F 340 LYS cc_start: 0.8792 (mttt) cc_final: 0.8301 (mtpt) REVERT: F 369 LYS cc_start: 0.8694 (ptpt) cc_final: 0.8342 (ptpp) outliers start: 4 outliers final: 0 residues processed: 63 average time/residue: 0.1556 time to fit residues: 11.1093 Evaluate side-chains 52 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 43 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 9 optimal weight: 0.1980 chunk 11 optimal weight: 0.0570 chunk 31 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 overall best weight: 2.8504 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.128070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.101230 restraints weight = 5057.754| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.42 r_work: 0.3588 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4172 Z= 0.150 Angle : 0.605 6.139 5579 Z= 0.320 Chirality : 0.051 0.133 623 Planarity : 0.003 0.030 714 Dihedral : 6.340 16.833 553 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.64 % Allowed : 7.46 % Favored : 91.90 % 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: -2.70 (0.28), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.21), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 349 TYR 0.014 0.003 TYR C 310 PHE 0.005 0.002 PHE E 378 HIS 0.003 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 4172) covalent geometry : angle 0.60459 ( 5579) hydrogen bonds : bond 0.02236 ( 48) hydrogen bonds : angle 5.13388 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.173 Fit side-chains REVERT: n 315 LEU cc_start: 0.8458 (mt) cc_final: 0.8185 (tt) REVERT: n 317 LYS cc_start: 0.8024 (ptmt) cc_final: 0.7539 (ptmm) REVERT: n 340 LYS cc_start: 0.8689 (mttt) cc_final: 0.8207 (mtpt) REVERT: A 331 LYS cc_start: 0.8773 (ttmt) cc_final: 0.7002 (tptt) REVERT: A 340 LYS cc_start: 0.8968 (mttt) cc_final: 0.8530 (mtpt) REVERT: A 344 LEU cc_start: 0.8836 (mp) cc_final: 0.8636 (mp) REVERT: B 311 LYS cc_start: 0.8313 (mttt) cc_final: 0.7885 (pttt) REVERT: B 315 LEU cc_start: 0.8615 (mt) cc_final: 0.8260 (tt) REVERT: B 340 LYS cc_start: 0.8800 (mttt) cc_final: 0.8368 (mtpt) REVERT: C 340 LYS cc_start: 0.8789 (mttt) cc_final: 0.8399 (mtpt) REVERT: D 340 LYS cc_start: 0.8866 (mttt) cc_final: 0.8383 (mtpt) REVERT: E 315 LEU cc_start: 0.8318 (mt) cc_final: 0.7997 (tt) REVERT: E 340 LYS cc_start: 0.8736 (mttt) cc_final: 0.8284 (mtpt) REVERT: E 369 LYS cc_start: 0.8744 (ptpt) cc_final: 0.8384 (ptpp) REVERT: F 311 LYS cc_start: 0.8395 (mttt) cc_final: 0.7974 (pttt) REVERT: F 315 LEU cc_start: 0.8262 (mt) cc_final: 0.7912 (tt) REVERT: F 331 LYS cc_start: 0.8565 (tttt) cc_final: 0.6894 (tptt) REVERT: F 340 LYS cc_start: 0.8709 (mttt) cc_final: 0.8176 (mtpt) REVERT: F 369 LYS cc_start: 0.8691 (ptpt) cc_final: 0.8359 (ptpp) outliers start: 3 outliers final: 2 residues processed: 56 average time/residue: 0.1370 time to fit residues: 8.7872 Evaluate side-chains 54 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 32 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.126874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.099848 restraints weight = 5043.377| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.43 r_work: 0.3518 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 4172 Z= 0.324 Angle : 0.735 5.818 5579 Z= 0.402 Chirality : 0.055 0.139 623 Planarity : 0.004 0.035 714 Dihedral : 7.018 18.981 553 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.85 % Allowed : 9.17 % Favored : 89.98 % 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: -2.72 (0.28), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.21), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG n 349 TYR 0.024 0.006 TYR C 310 PHE 0.008 0.003 PHE C 378 HIS 0.005 0.002 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00746 ( 4172) covalent geometry : angle 0.73469 ( 5579) hydrogen bonds : bond 0.03046 ( 48) hydrogen bonds : angle 5.11095 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.168 Fit side-chains REVERT: n 315 LEU cc_start: 0.8522 (mt) cc_final: 0.8208 (tt) REVERT: n 340 LYS cc_start: 0.8849 (mttt) cc_final: 0.8351 (mtpt) REVERT: B 311 LYS cc_start: 0.8360 (mttt) cc_final: 0.7892 (pttt) REVERT: B 340 LYS cc_start: 0.8842 (mttt) cc_final: 0.8418 (mtpt) REVERT: C 340 LYS cc_start: 0.8885 (mttt) cc_final: 0.8483 (mtpt) REVERT: D 321 LYS cc_start: 0.8516 (mtpt) cc_final: 0.7920 (mttt) REVERT: D 340 LYS cc_start: 0.8913 (mttt) cc_final: 0.8389 (mtpt) REVERT: E 315 LEU cc_start: 0.8424 (mt) cc_final: 0.8059 (tt) REVERT: E 321 LYS cc_start: 0.8594 (mtpt) cc_final: 0.7956 (mttp) REVERT: E 340 LYS cc_start: 0.8812 (mttt) cc_final: 0.8315 (mtpt) REVERT: E 344 LEU cc_start: 0.9072 (mp) cc_final: 0.8748 (mp) REVERT: F 311 LYS cc_start: 0.8450 (mttt) cc_final: 0.7967 (pttt) REVERT: F 315 LEU cc_start: 0.8504 (mt) cc_final: 0.8040 (tt) REVERT: F 340 LYS cc_start: 0.8754 (mttt) cc_final: 0.8260 (mtpt) outliers start: 4 outliers final: 2 residues processed: 45 average time/residue: 0.1278 time to fit residues: 6.7987 Evaluate side-chains 43 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.129738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.102979 restraints weight = 4987.646| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.33 r_work: 0.3561 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 4172 Z= 0.198 Angle : 0.619 5.626 5579 Z= 0.334 Chirality : 0.051 0.127 623 Planarity : 0.004 0.033 714 Dihedral : 6.410 17.097 553 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.85 % Allowed : 11.30 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.61 (0.28), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG n 349 TYR 0.016 0.004 TYR C 310 PHE 0.005 0.002 PHE B 378 HIS 0.003 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 4172) covalent geometry : angle 0.61942 ( 5579) hydrogen bonds : bond 0.02132 ( 48) hydrogen bonds : angle 5.01642 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.167 Fit side-chains REVERT: n 340 LYS cc_start: 0.8815 (mttt) cc_final: 0.8358 (mtpt) REVERT: B 311 LYS cc_start: 0.8338 (mttt) cc_final: 0.7968 (pttt) REVERT: B 340 LYS cc_start: 0.8857 (mttt) cc_final: 0.8474 (mtpt) REVERT: C 340 LYS cc_start: 0.8839 (mttt) cc_final: 0.8477 (mtpt) REVERT: E 315 LEU cc_start: 0.8428 (mt) cc_final: 0.8025 (tt) REVERT: E 321 LYS cc_start: 0.8644 (mtpt) cc_final: 0.8031 (mttm) REVERT: E 340 LYS cc_start: 0.8797 (mttt) cc_final: 0.8299 (mtpt) REVERT: E 344 LEU cc_start: 0.9079 (mp) cc_final: 0.8758 (mp) REVERT: F 311 LYS cc_start: 0.8410 (mttt) cc_final: 0.7980 (pttt) REVERT: F 340 LYS cc_start: 0.8630 (mttt) cc_final: 0.8185 (mtpt) outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 0.1066 time to fit residues: 5.6841 Evaluate side-chains 42 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 10 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.126288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.099564 restraints weight = 5094.974| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.33 r_work: 0.3504 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 4172 Z= 0.303 Angle : 0.718 6.191 5579 Z= 0.390 Chirality : 0.054 0.143 623 Planarity : 0.004 0.031 714 Dihedral : 6.857 21.787 553 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.49 % Allowed : 14.07 % Favored : 84.43 % 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: -2.87 (0.28), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.21), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.022 0.005 TYR C 310 PHE 0.008 0.002 PHE C 378 HIS 0.005 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00704 ( 4172) covalent geometry : angle 0.71775 ( 5579) hydrogen bonds : bond 0.02804 ( 48) hydrogen bonds : angle 4.96473 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.178 Fit side-chains REVERT: n 340 LYS cc_start: 0.8866 (mttt) cc_final: 0.8391 (mtpt) REVERT: B 311 LYS cc_start: 0.8410 (mttt) cc_final: 0.8004 (pttt) REVERT: B 340 LYS cc_start: 0.8866 (mttt) cc_final: 0.8465 (mtpt) REVERT: C 340 LYS cc_start: 0.8886 (mttt) cc_final: 0.8525 (mtpt) REVERT: D 321 LYS cc_start: 0.8635 (mtpt) cc_final: 0.8119 (mttt) REVERT: E 315 LEU cc_start: 0.8585 (mt) cc_final: 0.8092 (tt) REVERT: E 321 LYS cc_start: 0.8676 (mtpt) cc_final: 0.8062 (mttm) REVERT: E 340 LYS cc_start: 0.8831 (mttt) cc_final: 0.8342 (mtpt) REVERT: E 344 LEU cc_start: 0.9088 (mp) cc_final: 0.8805 (mp) REVERT: F 311 LYS cc_start: 0.8476 (mttt) cc_final: 0.8046 (pttt) REVERT: F 340 LYS cc_start: 0.8730 (mttt) cc_final: 0.8265 (mtpt) outliers start: 7 outliers final: 3 residues processed: 42 average time/residue: 0.1135 time to fit residues: 5.7334 Evaluate side-chains 39 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain E residue 357 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.132443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.105823 restraints weight = 4964.838| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.35 r_work: 0.3624 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 4172 Z= 0.118 Angle : 0.545 5.036 5579 Z= 0.288 Chirality : 0.049 0.123 623 Planarity : 0.003 0.030 714 Dihedral : 5.808 15.574 553 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.07 % Allowed : 14.71 % Favored : 84.22 % 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: -2.54 (0.28), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG n 349 TYR 0.010 0.002 TYR C 310 PHE 0.004 0.001 PHE n 346 HIS 0.003 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4172) covalent geometry : angle 0.54496 ( 5579) hydrogen bonds : bond 0.01464 ( 48) hydrogen bonds : angle 4.80220 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.173 Fit side-chains REVERT: n 340 LYS cc_start: 0.8762 (mttt) cc_final: 0.8292 (mtpt) REVERT: n 344 LEU cc_start: 0.8941 (mp) cc_final: 0.8716 (mp) REVERT: B 311 LYS cc_start: 0.8261 (mttt) cc_final: 0.7823 (pttt) REVERT: B 340 LYS cc_start: 0.8815 (mttt) cc_final: 0.8439 (mtpt) REVERT: C 344 LEU cc_start: 0.8829 (mp) cc_final: 0.8594 (mp) REVERT: D 344 LEU cc_start: 0.8960 (mp) cc_final: 0.8446 (mp) REVERT: E 315 LEU cc_start: 0.8478 (mt) cc_final: 0.8085 (tt) REVERT: E 321 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8042 (mttm) REVERT: E 340 LYS cc_start: 0.8630 (mttt) cc_final: 0.8182 (mtpt) REVERT: E 344 LEU cc_start: 0.9093 (mp) cc_final: 0.8794 (mp) REVERT: F 311 LYS cc_start: 0.8351 (mttt) cc_final: 0.7938 (pttt) REVERT: F 340 LYS cc_start: 0.8604 (mttt) cc_final: 0.8161 (mtpt) outliers start: 5 outliers final: 1 residues processed: 49 average time/residue: 0.0916 time to fit residues: 5.5640 Evaluate side-chains 47 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 373 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 17 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.129341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.102420 restraints weight = 4943.558| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.38 r_work: 0.3557 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 4172 Z= 0.199 Angle : 0.634 5.869 5579 Z= 0.333 Chirality : 0.051 0.125 623 Planarity : 0.003 0.026 714 Dihedral : 6.124 18.833 553 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.21 % Allowed : 15.57 % Favored : 84.22 % 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: -2.64 (0.28), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.016 0.004 TYR C 310 PHE 0.005 0.002 PHE n 378 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 4172) covalent geometry : angle 0.63447 ( 5579) hydrogen bonds : bond 0.02165 ( 48) hydrogen bonds : angle 4.75274 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.140 Fit side-chains REVERT: n 340 LYS cc_start: 0.8746 (mttt) cc_final: 0.8264 (mtpt) REVERT: B 311 LYS cc_start: 0.8285 (mttt) cc_final: 0.7831 (pttt) REVERT: B 340 LYS cc_start: 0.8788 (mttt) cc_final: 0.8371 (mtpt) REVERT: D 321 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8046 (mttt) REVERT: D 340 LYS cc_start: 0.8810 (mttt) cc_final: 0.8372 (mtpt) REVERT: D 344 LEU cc_start: 0.8888 (mp) cc_final: 0.8596 (mp) REVERT: E 321 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8012 (mttp) REVERT: E 340 LYS cc_start: 0.8684 (mttt) cc_final: 0.8217 (mtpt) REVERT: E 344 LEU cc_start: 0.9075 (mp) cc_final: 0.8781 (mp) REVERT: F 311 LYS cc_start: 0.8381 (mttt) cc_final: 0.7928 (pttt) REVERT: F 340 LYS cc_start: 0.8649 (mttt) cc_final: 0.8214 (mtpt) outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.1169 time to fit residues: 5.9387 Evaluate side-chains 43 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 373 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 48 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 9 optimal weight: 0.0050 chunk 8 optimal weight: 9.9990 chunk 25 optimal weight: 0.0670 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 0.0010 overall best weight: 1.8142 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.133596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.106717 restraints weight = 4948.600| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.39 r_work: 0.3638 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 4172 Z= 0.106 Angle : 0.568 9.204 5579 Z= 0.286 Chirality : 0.048 0.120 623 Planarity : 0.003 0.027 714 Dihedral : 5.492 15.152 553 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.64 % Allowed : 16.42 % Favored : 82.94 % 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: -2.46 (0.29), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.009 0.002 TYR A 310 PHE 0.003 0.001 PHE D 346 HIS 0.003 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 4172) covalent geometry : angle 0.56771 ( 5579) hydrogen bonds : bond 0.01433 ( 48) hydrogen bonds : angle 4.67357 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.182 Fit side-chains REVERT: n 340 LYS cc_start: 0.8643 (mttt) cc_final: 0.8228 (mtpt) REVERT: B 311 LYS cc_start: 0.8218 (mttt) cc_final: 0.7762 (pttt) REVERT: B 340 LYS cc_start: 0.8777 (mttt) cc_final: 0.8386 (mtpt) REVERT: B 369 LYS cc_start: 0.8765 (ptpt) cc_final: 0.8549 (ptpp) REVERT: D 344 LEU cc_start: 0.8966 (mp) cc_final: 0.8440 (mp) REVERT: E 340 LYS cc_start: 0.8609 (mttt) cc_final: 0.8198 (mtpt) REVERT: E 344 LEU cc_start: 0.9079 (mp) cc_final: 0.8790 (mp) REVERT: F 311 LYS cc_start: 0.8315 (mttt) cc_final: 0.7874 (pttt) REVERT: F 340 LYS cc_start: 0.8632 (mttt) cc_final: 0.8104 (mtpp) outliers start: 3 outliers final: 3 residues processed: 46 average time/residue: 0.1010 time to fit residues: 5.7081 Evaluate side-chains 48 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain E residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.132271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.105450 restraints weight = 4889.879| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.38 r_work: 0.3612 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4172 Z= 0.135 Angle : 0.609 9.768 5579 Z= 0.302 Chirality : 0.049 0.123 623 Planarity : 0.003 0.025 714 Dihedral : 5.554 16.276 553 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.64 % Allowed : 16.63 % Favored : 82.73 % 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: -2.46 (0.29), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.012 0.003 TYR C 310 PHE 0.005 0.001 PHE D 346 HIS 0.002 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4172) covalent geometry : angle 0.60928 ( 5579) hydrogen bonds : bond 0.01723 ( 48) hydrogen bonds : angle 4.61972 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.181 Fit side-chains REVERT: n 340 LYS cc_start: 0.8611 (mttt) cc_final: 0.8181 (mtpt) REVERT: B 311 LYS cc_start: 0.8212 (mttt) cc_final: 0.7733 (pttt) REVERT: B 340 LYS cc_start: 0.8675 (mttt) cc_final: 0.8253 (mtpt) REVERT: B 369 LYS cc_start: 0.8749 (ptpt) cc_final: 0.8521 (ptpp) REVERT: D 344 LEU cc_start: 0.8944 (mp) cc_final: 0.8692 (mp) REVERT: E 340 LYS cc_start: 0.8633 (mttt) cc_final: 0.8164 (mtpt) REVERT: E 344 LEU cc_start: 0.9086 (mp) cc_final: 0.8777 (mp) REVERT: F 311 LYS cc_start: 0.8313 (mttt) cc_final: 0.7863 (pttt) REVERT: F 340 LYS cc_start: 0.8653 (mttt) cc_final: 0.8111 (mtpp) outliers start: 3 outliers final: 3 residues processed: 45 average time/residue: 0.0982 time to fit residues: 5.3856 Evaluate side-chains 47 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain E residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 20 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 6 optimal weight: 0.0670 chunk 47 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.129590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.102903 restraints weight = 4972.858| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.34 r_work: 0.3559 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4172 Z= 0.210 Angle : 0.660 11.567 5579 Z= 0.337 Chirality : 0.051 0.127 623 Planarity : 0.003 0.024 714 Dihedral : 5.996 19.181 553 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.07 % Allowed : 16.20 % Favored : 82.73 % 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: -2.56 (0.29), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.016 0.004 TYR C 310 PHE 0.006 0.002 PHE n 378 HIS 0.003 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 4172) covalent geometry : angle 0.66037 ( 5579) hydrogen bonds : bond 0.02198 ( 48) hydrogen bonds : angle 4.60586 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1153.17 seconds wall clock time: 20 minutes 31.92 seconds (1231.92 seconds total)