Starting phenix.real_space_refine on Fri May 9 22:51:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bgv_16039/05_2025/8bgv_16039.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bgv_16039/05_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_16039/05_2025/8bgv_16039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bgv_16039/05_2025/8bgv_16039.map" model { file = "/net/cci-nas-00/data/ceres_data/8bgv_16039/05_2025/8bgv_16039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bgv_16039/05_2025/8bgv_16039.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4109 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B, E, D, F, n Time building chain proxies: 1.97, per 1000 atoms: 0.48 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: 0.88 Conformation dependent library (CDL) restraints added in 480.1 milliseconds 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: 0.60 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: 0.82 Time building geometry restraints manager: 1.04 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.260 Find NCS groups from input model: 0.080 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.500 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.007 0.004 HIS B 330 PHE 0.008 0.003 PHE A 378 TYR 0.018 0.006 TYR B 310 ARG 0.005 0.002 ARG C 349 Details of bonding type rmsd hydrogen bonds : bond 0.23307 ( 48) hydrogen bonds : angle 7.49002 ( 144) covalent geometry : bond 0.00881 ( 4172) covalent geometry : angle 1.72040 ( 5579) *********************** 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 : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: n 321 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8321 (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: 0.8219 (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: 0.8510 (pttt) REVERT: B 321 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8369 (mttp) REVERT: B 340 LYS cc_start: 0.9006 (mttt) cc_final: 0.8772 (mtpt) REVERT: B 377 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8146 (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: 0.8824 (mtpt) REVERT: C 377 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8523 (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: 0.8777 (mtpt) REVERT: D 349 ARG cc_start: 0.7655 (mtt-85) cc_final: 0.7432 (mtp180) REVERT: E 321 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8268 (mttp) REVERT: E 340 LYS cc_start: 0.9062 (mttt) cc_final: 0.8720 (mtpt) REVERT: E 349 ARG cc_start: 0.7717 (mtt-85) cc_final: 0.7461 (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: 0.8431 (mttm) REVERT: F 331 LYS cc_start: 0.9074 (tttt) cc_final: 0.8823 (ttpt) REVERT: F 340 LYS cc_start: 0.9064 (mttt) cc_final: 0.8712 (mtpt) REVERT: F 349 ARG cc_start: 0.7744 (mtt-85) cc_final: 0.7502 (mtp180) REVERT: F 377 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8461 (m) outliers start: 7 outliers final: 0 residues processed: 75 average time/residue: 0.3133 time to fit residues: 26.8383 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 : 0.512 ------------------------------------------------------------------------------- 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 41 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4038 r_free = 0.4038 target = 0.126524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.101117 restraints weight = 5105.986| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.32 r_work: 0.3556 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4172 Z= 0.187 Angle : 0.706 5.044 5579 Z= 0.377 Chirality : 0.053 0.140 623 Planarity : 0.003 0.025 714 Dihedral : 7.710 29.418 557 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.27), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.21), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 362 PHE 0.006 0.002 PHE n 378 TYR 0.015 0.004 TYR B 310 ARG 0.003 0.000 ARG n 349 Details of bonding type rmsd hydrogen bonds : bond 0.03069 ( 48) hydrogen bonds : angle 5.64626 ( 144) covalent geometry : bond 0.00422 ( 4172) covalent geometry : angle 0.70588 ( 5579) *********************** 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 59 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.451 Fit side-chains REVERT: n 317 LYS cc_start: 0.8013 (ptmt) cc_final: 0.7674 (ptmm) REVERT: n 340 LYS cc_start: 0.8794 (mttt) cc_final: 0.8350 (mtpt) REVERT: A 340 LYS cc_start: 0.8953 (mttt) cc_final: 0.8500 (mtpt) REVERT: B 311 LYS cc_start: 0.8409 (mttt) cc_final: 0.7972 (pttt) REVERT: B 340 LYS cc_start: 0.8857 (mttt) cc_final: 0.8478 (mtpt) REVERT: B 377 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.8011 (p) REVERT: C 340 LYS cc_start: 0.8761 (mttt) cc_final: 0.8398 (mtpt) REVERT: D 340 LYS cc_start: 0.8896 (mttt) cc_final: 0.8410 (mtpt) REVERT: D 369 LYS cc_start: 0.8735 (ptpt) cc_final: 0.8443 (ptpp) REVERT: E 340 LYS cc_start: 0.8804 (mttt) cc_final: 0.8373 (mtpt) REVERT: E 369 LYS cc_start: 0.8764 (ptpt) cc_final: 0.8405 (ptpp) REVERT: F 311 LYS cc_start: 0.8497 (mttt) cc_final: 0.8101 (pttt) REVERT: F 315 LEU cc_start: 0.8639 (mt) cc_final: 0.8180 (tt) REVERT: F 331 LYS cc_start: 0.8674 (tttt) cc_final: 0.6943 (tptt) REVERT: F 340 LYS cc_start: 0.8870 (mttt) cc_final: 0.8373 (mtpt) REVERT: F 369 LYS cc_start: 0.8748 (ptpt) cc_final: 0.8413 (ptpp) REVERT: F 377 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8106 (p) outliers start: 4 outliers final: 0 residues processed: 59 average time/residue: 0.3463 time to fit residues: 23.1982 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 : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.126455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.099675 restraints weight = 4992.040| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.32 r_work: 0.3519 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 4172 Z= 0.292 Angle : 0.748 5.893 5579 Z= 0.406 Chirality : 0.055 0.143 623 Planarity : 0.004 0.032 714 Dihedral : 7.676 43.138 555 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.85 % Allowed : 8.10 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.27), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.21), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 362 PHE 0.011 0.002 PHE B 378 TYR 0.022 0.005 TYR C 310 ARG 0.003 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 48) hydrogen bonds : angle 5.26963 ( 144) covalent geometry : bond 0.00669 ( 4172) covalent geometry : angle 0.74790 ( 5579) *********************** 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 45 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.464 Fit side-chains REVERT: n 315 LEU cc_start: 0.8535 (mt) cc_final: 0.8149 (tt) REVERT: n 340 LYS cc_start: 0.8860 (mttt) cc_final: 0.8359 (mtpt) REVERT: A 340 LYS cc_start: 0.9024 (mttt) cc_final: 0.8572 (mtpp) REVERT: B 311 LYS cc_start: 0.8378 (mttt) cc_final: 0.7926 (pttt) REVERT: B 340 LYS cc_start: 0.8840 (mttt) cc_final: 0.8412 (mtpt) REVERT: C 340 LYS cc_start: 0.8838 (mttt) cc_final: 0.8440 (mtpt) REVERT: D 315 LEU cc_start: 0.8501 (mt) cc_final: 0.8239 (tt) REVERT: D 321 LYS cc_start: 0.8559 (mtpt) cc_final: 0.7981 (mttt) REVERT: D 340 LYS cc_start: 0.8955 (mttt) cc_final: 0.8438 (mtpt) REVERT: E 315 LEU cc_start: 0.8476 (mt) cc_final: 0.8036 (tt) REVERT: E 321 LYS cc_start: 0.8632 (mtpt) cc_final: 0.8013 (mttm) REVERT: E 340 LYS cc_start: 0.8928 (mttt) cc_final: 0.8449 (mtpt) REVERT: F 311 LYS cc_start: 0.8473 (mttt) cc_final: 0.8050 (pttt) REVERT: F 315 LEU cc_start: 0.8575 (mt) cc_final: 0.8125 (tt) REVERT: F 340 LYS cc_start: 0.8897 (mttt) cc_final: 0.8409 (mtpt) outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 0.2527 time to fit residues: 13.2866 Evaluate side-chains 40 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.128733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.101859 restraints weight = 4985.036| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.33 r_work: 0.3544 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4172 Z= 0.223 Angle : 0.665 5.881 5579 Z= 0.358 Chirality : 0.052 0.132 623 Planarity : 0.004 0.032 714 Dihedral : 7.382 54.493 555 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.49 % Allowed : 10.87 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.28), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.21), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.008 0.002 PHE F 378 TYR 0.017 0.004 TYR A 310 ARG 0.002 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.02332 ( 48) hydrogen bonds : angle 5.09451 ( 144) covalent geometry : bond 0.00514 ( 4172) covalent geometry : angle 0.66502 ( 5579) *********************** 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 47 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.543 Fit side-chains REVERT: n 315 LEU cc_start: 0.8540 (mt) cc_final: 0.8141 (tt) REVERT: n 340 LYS cc_start: 0.8825 (mttt) cc_final: 0.8395 (mtpt) REVERT: B 311 LYS cc_start: 0.8393 (mttt) cc_final: 0.7975 (pttt) REVERT: B 340 LYS cc_start: 0.8839 (mttt) cc_final: 0.8479 (mtpt) REVERT: C 340 LYS cc_start: 0.8862 (mttt) cc_final: 0.8481 (mtpt) REVERT: D 315 LEU cc_start: 0.8467 (mt) cc_final: 0.8198 (tt) REVERT: D 340 LYS cc_start: 0.8937 (mttt) cc_final: 0.8433 (mtpt) REVERT: E 315 LEU cc_start: 0.8432 (mt) cc_final: 0.7965 (tt) REVERT: E 321 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8047 (mttm) REVERT: E 340 LYS cc_start: 0.8854 (mttt) cc_final: 0.8410 (mtpt) REVERT: F 311 LYS cc_start: 0.8448 (mttt) cc_final: 0.8014 (pttt) REVERT: F 315 LEU cc_start: 0.8556 (mt) cc_final: 0.8118 (tt) REVERT: F 340 LYS cc_start: 0.8788 (mttt) cc_final: 0.8337 (mtpt) outliers start: 7 outliers final: 3 residues processed: 45 average time/residue: 0.2345 time to fit residues: 12.9282 Evaluate side-chains 43 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 0 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.130849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.103550 restraints weight = 5027.153| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.38 r_work: 0.3593 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 4172 Z= 0.155 Angle : 0.584 5.724 5579 Z= 0.313 Chirality : 0.050 0.125 623 Planarity : 0.003 0.029 714 Dihedral : 7.013 59.139 555 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.92 % Allowed : 12.58 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (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 HIS 0.003 0.001 HIS D 330 PHE 0.006 0.001 PHE B 378 TYR 0.013 0.003 TYR C 310 ARG 0.001 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01834 ( 48) hydrogen bonds : angle 4.95451 ( 144) covalent geometry : bond 0.00356 ( 4172) covalent geometry : angle 0.58413 ( 5579) *********************** 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 51 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.463 Fit side-chains REVERT: n 340 LYS cc_start: 0.8781 (mttt) cc_final: 0.8326 (mtpt) REVERT: B 311 LYS cc_start: 0.8293 (mttt) cc_final: 0.7858 (pttt) REVERT: B 340 LYS cc_start: 0.8817 (mttt) cc_final: 0.8447 (mtpt) REVERT: C 340 LYS cc_start: 0.8833 (mttt) cc_final: 0.8465 (mtpt) REVERT: C 344 LEU cc_start: 0.8829 (mp) cc_final: 0.8586 (mp) REVERT: D 315 LEU cc_start: 0.8445 (mt) cc_final: 0.8192 (tt) REVERT: D 340 LYS cc_start: 0.8908 (mttt) cc_final: 0.8407 (mtpt) REVERT: E 315 LEU cc_start: 0.8442 (mt) cc_final: 0.8016 (tt) REVERT: E 321 LYS cc_start: 0.8637 (mtpt) cc_final: 0.8024 (mttm) REVERT: E 340 LYS cc_start: 0.8735 (mttt) cc_final: 0.8273 (mtpt) REVERT: E 344 LEU cc_start: 0.9096 (mp) cc_final: 0.8830 (mp) REVERT: F 311 LYS cc_start: 0.8387 (mttt) cc_final: 0.7929 (pttt) REVERT: F 315 LEU cc_start: 0.8509 (mt) cc_final: 0.8101 (tt) REVERT: F 340 LYS cc_start: 0.8707 (mttt) cc_final: 0.8244 (mtpt) outliers start: 9 outliers final: 4 residues processed: 49 average time/residue: 0.2197 time to fit residues: 13.0952 Evaluate side-chains 48 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 12 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.132242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.105326 restraints weight = 4894.218| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.33 r_work: 0.3605 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4172 Z= 0.143 Angle : 0.583 6.888 5579 Z= 0.305 Chirality : 0.049 0.124 623 Planarity : 0.003 0.030 714 Dihedral : 6.814 57.713 555 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.71 % Allowed : 14.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.28), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 330 PHE 0.005 0.001 PHE B 378 TYR 0.012 0.003 TYR C 310 ARG 0.001 0.000 ARG n 349 Details of bonding type rmsd hydrogen bonds : bond 0.01779 ( 48) hydrogen bonds : angle 4.86844 ( 144) covalent geometry : bond 0.00331 ( 4172) covalent geometry : angle 0.58290 ( 5579) *********************** 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 54 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.482 Fit side-chains REVERT: n 340 LYS cc_start: 0.8739 (mttt) cc_final: 0.8307 (mtpt) REVERT: B 311 LYS cc_start: 0.8293 (mttt) cc_final: 0.7854 (pttt) REVERT: B 340 LYS cc_start: 0.8775 (mttt) cc_final: 0.8452 (mtpt) REVERT: C 344 LEU cc_start: 0.8884 (mp) cc_final: 0.8599 (mp) REVERT: D 315 LEU cc_start: 0.8428 (mt) cc_final: 0.8120 (tt) REVERT: D 340 LYS cc_start: 0.8908 (mttt) cc_final: 0.8424 (mtpt) REVERT: E 321 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8021 (mttm) REVERT: E 340 LYS cc_start: 0.8741 (mttt) cc_final: 0.8268 (mtpt) REVERT: F 311 LYS cc_start: 0.8357 (mttt) cc_final: 0.7873 (pttt) REVERT: F 315 LEU cc_start: 0.8496 (mt) cc_final: 0.8100 (tt) REVERT: F 340 LYS cc_start: 0.8652 (mttt) cc_final: 0.8239 (mtpt) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.2138 time to fit residues: 13.4366 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 : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 10 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- 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 = 0.4095 r_free = 0.4095 target = 0.131779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.104816 restraints weight = 4953.486| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.36 r_work: 0.3604 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4172 Z= 0.147 Angle : 0.586 6.076 5579 Z= 0.303 Chirality : 0.049 0.122 623 Planarity : 0.003 0.028 714 Dihedral : 6.669 57.096 555 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.92 % Allowed : 15.57 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.28), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 330 PHE 0.005 0.001 PHE F 378 TYR 0.012 0.003 TYR C 310 ARG 0.001 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01784 ( 48) hydrogen bonds : angle 4.79433 ( 144) covalent geometry : bond 0.00339 ( 4172) covalent geometry : angle 0.58607 ( 5579) *********************** 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 52 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.474 Fit side-chains REVERT: n 340 LYS cc_start: 0.8708 (mttt) cc_final: 0.8250 (mtpt) REVERT: B 311 LYS cc_start: 0.8281 (mttt) cc_final: 0.7841 (pttt) REVERT: B 340 LYS cc_start: 0.8759 (mttt) cc_final: 0.8356 (mtpt) REVERT: C 344 LEU cc_start: 0.8905 (mp) cc_final: 0.8608 (mp) REVERT: D 315 LEU cc_start: 0.8422 (mt) cc_final: 0.8103 (tt) REVERT: D 340 LYS cc_start: 0.8922 (mttt) cc_final: 0.8433 (mtpt) REVERT: E 321 LYS cc_start: 0.8632 (mtpt) cc_final: 0.8022 (mttm) REVERT: E 340 LYS cc_start: 0.8687 (mttt) cc_final: 0.8243 (mtpt) REVERT: F 311 LYS cc_start: 0.8351 (mttt) cc_final: 0.7868 (pttt) REVERT: F 315 LEU cc_start: 0.8485 (mt) cc_final: 0.8089 (tt) REVERT: F 340 LYS cc_start: 0.8765 (mttt) cc_final: 0.8223 (mtpt) outliers start: 9 outliers final: 7 residues processed: 49 average time/residue: 0.2014 time to fit residues: 12.2123 Evaluate side-chains 50 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 43 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 39 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 = 0.4004 r_free = 0.4004 target = 0.126587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.099767 restraints weight = 5002.785| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.32 r_work: 0.3504 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 4172 Z= 0.296 Angle : 0.718 7.333 5579 Z= 0.383 Chirality : 0.053 0.137 623 Planarity : 0.003 0.025 714 Dihedral : 7.191 50.982 555 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 2.56 % Allowed : 16.20 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (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 HIS 0.004 0.001 HIS F 362 PHE 0.009 0.003 PHE A 346 TYR 0.022 0.005 TYR A 310 ARG 0.001 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.02811 ( 48) hydrogen bonds : angle 4.79558 ( 144) covalent geometry : bond 0.00684 ( 4172) covalent geometry : angle 0.71833 ( 5579) *********************** 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 51 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.518 Fit side-chains REVERT: n 340 LYS cc_start: 0.8703 (mttt) cc_final: 0.8222 (mtpt) REVERT: B 311 LYS cc_start: 0.8415 (mttt) cc_final: 0.7999 (pttt) REVERT: B 340 LYS cc_start: 0.8721 (mttt) cc_final: 0.8326 (mtpt) REVERT: C 340 LYS cc_start: 0.8885 (mttt) cc_final: 0.8519 (mtpt) REVERT: D 321 LYS cc_start: 0.8620 (mtpt) cc_final: 0.8107 (mttt) REVERT: D 340 LYS cc_start: 0.8911 (mttt) cc_final: 0.8422 (mtpt) REVERT: E 321 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8052 (mttm) REVERT: E 340 LYS cc_start: 0.8768 (mttt) cc_final: 0.8300 (mtpt) REVERT: F 311 LYS cc_start: 0.8438 (mttt) cc_final: 0.8023 (pttt) REVERT: F 315 LEU cc_start: 0.8585 (mt) cc_final: 0.8122 (tt) REVERT: F 340 LYS cc_start: 0.8766 (mttt) cc_final: 0.8302 (mtpt) outliers start: 12 outliers final: 11 residues processed: 48 average time/residue: 0.2303 time to fit residues: 13.4362 Evaluate side-chains 47 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 25 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.128191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.101451 restraints weight = 4974.252| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.33 r_work: 0.3532 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4172 Z= 0.214 Angle : 0.659 7.652 5579 Z= 0.347 Chirality : 0.051 0.127 623 Planarity : 0.003 0.023 714 Dihedral : 6.767 45.309 555 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.56 % Allowed : 16.63 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.28), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.21), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.006 0.002 PHE B 378 TYR 0.016 0.004 TYR C 310 ARG 0.001 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.02252 ( 48) hydrogen bonds : angle 4.78728 ( 144) covalent geometry : bond 0.00496 ( 4172) covalent geometry : angle 0.65926 ( 5579) *********************** 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 55 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.487 Fit side-chains REVERT: n 340 LYS cc_start: 0.8627 (mttt) cc_final: 0.8177 (mtpt) REVERT: B 311 LYS cc_start: 0.8393 (mttt) cc_final: 0.7977 (pttt) REVERT: B 340 LYS cc_start: 0.8731 (mttt) cc_final: 0.8336 (mtpt) REVERT: C 340 LYS cc_start: 0.8871 (mttt) cc_final: 0.8510 (mtpt) REVERT: C 344 LEU cc_start: 0.8939 (mp) cc_final: 0.8602 (mp) REVERT: D 321 LYS cc_start: 0.8626 (mtpt) cc_final: 0.8100 (mttt) REVERT: D 340 LYS cc_start: 0.8870 (mttt) cc_final: 0.8418 (mtpt) REVERT: E 321 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8066 (mttm) REVERT: E 340 LYS cc_start: 0.8716 (mttt) cc_final: 0.8258 (mtpt) REVERT: F 311 LYS cc_start: 0.8433 (mttt) cc_final: 0.8008 (pttt) REVERT: F 340 LYS cc_start: 0.8679 (mttt) cc_final: 0.8252 (mtpt) outliers start: 12 outliers final: 10 residues processed: 50 average time/residue: 0.2235 time to fit residues: 13.5864 Evaluate side-chains 54 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.129260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.102365 restraints weight = 4923.056| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.35 r_work: 0.3545 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4172 Z= 0.187 Angle : 0.632 7.272 5579 Z= 0.331 Chirality : 0.051 0.147 623 Planarity : 0.003 0.023 714 Dihedral : 6.458 40.821 555 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.13 % Allowed : 17.27 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.28), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.21), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.005 0.002 PHE B 378 TYR 0.015 0.004 TYR C 310 ARG 0.001 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.02056 ( 48) hydrogen bonds : angle 4.70408 ( 144) covalent geometry : bond 0.00436 ( 4172) covalent geometry : angle 0.63151 ( 5579) ********************** 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 54 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.534 Fit side-chains REVERT: n 340 LYS cc_start: 0.8616 (mttt) cc_final: 0.8184 (mtpt) REVERT: B 311 LYS cc_start: 0.8329 (mttt) cc_final: 0.7874 (pttt) REVERT: B 340 LYS cc_start: 0.8639 (mttt) cc_final: 0.8267 (mtpt) REVERT: C 340 LYS cc_start: 0.8862 (mttt) cc_final: 0.8486 (mtpt) REVERT: C 344 LEU cc_start: 0.8955 (mp) cc_final: 0.8616 (mp) REVERT: D 321 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8066 (mttt) REVERT: D 340 LYS cc_start: 0.8856 (mttt) cc_final: 0.8399 (mtpt) REVERT: E 321 LYS cc_start: 0.8644 (mtpt) cc_final: 0.8030 (mttm) REVERT: E 340 LYS cc_start: 0.8691 (mttt) cc_final: 0.8232 (mtpt) REVERT: F 311 LYS cc_start: 0.8383 (mttt) cc_final: 0.7951 (pttt) REVERT: F 340 LYS cc_start: 0.8655 (mttt) cc_final: 0.8116 (mtpp) outliers start: 10 outliers final: 9 residues processed: 49 average time/residue: 0.2359 time to fit residues: 14.1522 Evaluate side-chains 53 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.128878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.102083 restraints weight = 4917.765| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.34 r_work: 0.3539 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4172 Z= 0.207 Angle : 0.648 8.766 5579 Z= 0.340 Chirality : 0.051 0.125 623 Planarity : 0.003 0.023 714 Dihedral : 6.450 38.100 555 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.92 % Allowed : 17.06 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.28), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.21), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.006 0.002 PHE B 378 TYR 0.016 0.004 TYR A 310 ARG 0.001 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.02223 ( 48) hydrogen bonds : angle 4.65371 ( 144) covalent geometry : bond 0.00484 ( 4172) covalent geometry : angle 0.64797 ( 5579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2360.13 seconds wall clock time: 41 minutes 41.16 seconds (2501.16 seconds total)