Starting phenix.real_space_refine on Thu Nov 14 05:10:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgv_16039/11_2024/8bgv_16039.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgv_16039/11_2024/8bgv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgv_16039/11_2024/8bgv_16039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgv_16039/11_2024/8bgv_16039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgv_16039/11_2024/8bgv_16039.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgv_16039/11_2024/8bgv_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-5513/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: 2.19, per 1000 atoms: 0.53 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: 0.90 Conformation dependent library (CDL) restraints added in 483.8 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: 0.63 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: 0.93 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 1.890 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.750 Find NCS groups from input model: 0.150 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.900 ------------------------------------------------------------------------------- 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= 0.608 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 *********************** 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 : 0.492 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: 0.3132 time to fit residues: 26.7638 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 : 0.487 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 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= 0.296 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 *********************** 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 : 0.490 Fit side-chains REVERT: n 340 LYS cc_start: 0.8918 (mttt) cc_final: 0.8655 (mtpt) REVERT: A 340 LYS cc_start: 0.9030 (mttt) cc_final: 0.8745 (mtpt) REVERT: B 311 LYS cc_start: 0.8626 (mttt) cc_final: 0.8267 (pttt) REVERT: B 340 LYS cc_start: 0.8970 (mttt) cc_final: 0.8757 (mtpt) REVERT: B 377 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8304 (p) REVERT: C 340 LYS cc_start: 0.8909 (mttt) cc_final: 0.8690 (mtpt) REVERT: D 340 LYS cc_start: 0.9028 (mttt) cc_final: 0.8713 (mtpt) REVERT: E 340 LYS cc_start: 0.8947 (mttt) cc_final: 0.8672 (mtpt) REVERT: E 369 LYS cc_start: 0.8767 (ptpt) cc_final: 0.8517 (ptpp) REVERT: F 311 LYS cc_start: 0.8648 (mttt) cc_final: 0.8289 (pttt) REVERT: F 315 LEU cc_start: 0.8737 (mt) cc_final: 0.8327 (tt) REVERT: F 331 LYS cc_start: 0.8758 (tttt) cc_final: 0.7380 (tptt) REVERT: F 340 LYS cc_start: 0.9014 (mttt) cc_final: 0.8683 (mtpt) REVERT: F 369 LYS cc_start: 0.8788 (ptpt) cc_final: 0.8571 (ptpp) REVERT: F 377 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8385 (p) outliers start: 4 outliers final: 0 residues processed: 59 average time/residue: 0.3561 time to fit residues: 23.9401 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 : 0.488 ------------------------------------------------------------------------------- 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 24 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 4172 Z= 0.460 Angle : 0.740 5.957 5579 Z= 0.401 Chirality : 0.055 0.143 623 Planarity : 0.004 0.032 714 Dihedral : 7.615 42.139 555 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.07 % Allowed : 7.89 % 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: -3.04 (0.27), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.21), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 362 PHE 0.010 0.002 PHE B 378 TYR 0.021 0.005 TYR C 310 ARG 0.004 0.001 ARG B 349 *********************** 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 46 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.489 Fit side-chains REVERT: n 315 LEU cc_start: 0.8640 (mt) cc_final: 0.8323 (tt) REVERT: n 340 LYS cc_start: 0.9008 (mttt) cc_final: 0.8703 (mtpt) REVERT: A 340 LYS cc_start: 0.9099 (mttt) cc_final: 0.8799 (mtpp) REVERT: B 311 LYS cc_start: 0.8619 (mttt) cc_final: 0.8254 (pttt) REVERT: B 340 LYS cc_start: 0.8970 (mttt) cc_final: 0.8706 (mtpt) REVERT: C 340 LYS cc_start: 0.8943 (mttt) cc_final: 0.8704 (mtpt) REVERT: D 315 LEU cc_start: 0.8609 (mt) cc_final: 0.8381 (tt) REVERT: D 321 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8452 (mttt) REVERT: D 340 LYS cc_start: 0.9084 (mttt) cc_final: 0.8755 (mtpt) REVERT: E 315 LEU cc_start: 0.8585 (mt) cc_final: 0.8225 (tt) REVERT: E 321 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8474 (mttm) REVERT: E 340 LYS cc_start: 0.9059 (mttt) cc_final: 0.8742 (mtpt) REVERT: F 311 LYS cc_start: 0.8649 (mttt) cc_final: 0.8276 (pttt) REVERT: F 315 LEU cc_start: 0.8693 (mt) cc_final: 0.8301 (tt) REVERT: F 340 LYS cc_start: 0.9069 (mttt) cc_final: 0.8753 (mtpt) outliers start: 5 outliers final: 2 residues processed: 45 average time/residue: 0.2498 time to fit residues: 13.4932 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 : 0.492 ------------------------------------------------------------------------------- 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 23 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 42 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4172 Z= 0.252 Angle : 0.606 6.253 5579 Z= 0.322 Chirality : 0.051 0.127 623 Planarity : 0.003 0.031 714 Dihedral : 6.855 45.246 555 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.28 % Allowed : 9.81 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 A 330 PHE 0.006 0.001 PHE B 378 TYR 0.013 0.003 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** 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 44 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.487 Fit side-chains REVERT: n 315 LEU cc_start: 0.8625 (mt) cc_final: 0.8351 (tt) REVERT: n 340 LYS cc_start: 0.8858 (mttt) cc_final: 0.8603 (mtpt) REVERT: B 311 LYS cc_start: 0.8514 (mttt) cc_final: 0.8138 (pttt) REVERT: B 340 LYS cc_start: 0.8929 (mttt) cc_final: 0.8706 (mtpt) REVERT: C 340 LYS cc_start: 0.8939 (mttt) cc_final: 0.8716 (mtpt) REVERT: C 358 ASP cc_start: 0.8624 (p0) cc_final: 0.8259 (p0) REVERT: E 315 LEU cc_start: 0.8539 (mt) cc_final: 0.8228 (tt) REVERT: E 340 LYS cc_start: 0.8903 (mttt) cc_final: 0.8612 (mtpt) REVERT: F 311 LYS cc_start: 0.8567 (mttt) cc_final: 0.8143 (pttt) REVERT: F 315 LEU cc_start: 0.8631 (mt) cc_final: 0.8281 (tt) REVERT: F 340 LYS cc_start: 0.8891 (mttt) cc_final: 0.8586 (mtpt) outliers start: 6 outliers final: 3 residues processed: 43 average time/residue: 0.2103 time to fit residues: 11.1557 Evaluate side-chains 42 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 35 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 9 optimal weight: 0.0470 chunk 27 optimal weight: 6.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4172 Z= 0.296 Angle : 0.608 4.967 5579 Z= 0.325 Chirality : 0.051 0.127 623 Planarity : 0.003 0.031 714 Dihedral : 6.857 51.273 555 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.71 % Allowed : 12.37 % Favored : 85.93 % 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: -2.68 (0.28), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.21), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.007 0.002 PHE B 378 TYR 0.015 0.003 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** 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 48 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.487 Fit side-chains REVERT: n 315 LEU cc_start: 0.8578 (mt) cc_final: 0.8283 (tt) REVERT: n 340 LYS cc_start: 0.8944 (mttt) cc_final: 0.8648 (mtpt) REVERT: B 311 LYS cc_start: 0.8548 (mttt) cc_final: 0.8193 (pttt) REVERT: B 340 LYS cc_start: 0.8949 (mttt) cc_final: 0.8716 (mtpt) REVERT: C 340 LYS cc_start: 0.8956 (mttt) cc_final: 0.8741 (mtpt) REVERT: D 315 LEU cc_start: 0.8607 (mt) cc_final: 0.8258 (tt) REVERT: E 315 LEU cc_start: 0.8511 (mt) cc_final: 0.8168 (tt) REVERT: E 321 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8451 (mttm) REVERT: E 340 LYS cc_start: 0.8943 (mttt) cc_final: 0.8629 (mtpt) REVERT: E 344 LEU cc_start: 0.9145 (mp) cc_final: 0.8866 (mp) REVERT: F 311 LYS cc_start: 0.8575 (mttt) cc_final: 0.8143 (pttt) REVERT: F 315 LEU cc_start: 0.8656 (mt) cc_final: 0.8274 (tt) REVERT: F 340 LYS cc_start: 0.8900 (mttt) cc_final: 0.8613 (mtpt) outliers start: 8 outliers final: 3 residues processed: 47 average time/residue: 0.2121 time to fit residues: 12.3495 Evaluate side-chains 45 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3266 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= 0.278 Angle : 0.599 7.348 5579 Z= 0.316 Chirality : 0.050 0.124 623 Planarity : 0.003 0.030 714 Dihedral : 6.785 55.799 555 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.49 % Allowed : 13.86 % Favored : 84.65 % 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: -2.58 (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 0.006 0.002 PHE B 378 TYR 0.014 0.003 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** 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 51 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.439 Fit side-chains REVERT: n 315 LEU cc_start: 0.8556 (mt) cc_final: 0.8351 (tt) REVERT: n 340 LYS cc_start: 0.8854 (mttt) cc_final: 0.8592 (mtpt) REVERT: A 344 LEU cc_start: 0.8689 (mp) cc_final: 0.8452 (mp) REVERT: B 311 LYS cc_start: 0.8516 (mttt) cc_final: 0.8155 (pttt) REVERT: C 340 LYS cc_start: 0.8975 (mttt) cc_final: 0.8760 (mtpt) REVERT: E 315 LEU cc_start: 0.8551 (mt) cc_final: 0.8201 (tt) REVERT: E 321 LYS cc_start: 0.8866 (mtpt) cc_final: 0.8453 (mttm) REVERT: E 340 LYS cc_start: 0.8919 (mttt) cc_final: 0.8608 (mtpt) REVERT: E 344 LEU cc_start: 0.9156 (mp) cc_final: 0.8870 (mp) REVERT: F 311 LYS cc_start: 0.8572 (mttt) cc_final: 0.8141 (pttt) REVERT: F 315 LEU cc_start: 0.8648 (mt) cc_final: 0.8275 (tt) REVERT: F 340 LYS cc_start: 0.8811 (mttt) cc_final: 0.8524 (mtpt) outliers start: 7 outliers final: 5 residues processed: 48 average time/residue: 0.2098 time to fit residues: 12.4130 Evaluate side-chains 45 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 373 THR Chi-restraints excluded: chain B residue 377 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 26 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 4172 Z= 0.401 Angle : 0.668 7.747 5579 Z= 0.355 Chirality : 0.052 0.131 623 Planarity : 0.003 0.028 714 Dihedral : 7.218 56.074 555 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 1.71 % Allowed : 15.99 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.68 (0.28), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.008 0.002 PHE B 378 TYR 0.018 0.004 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** 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 45 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.504 Fit side-chains REVERT: n 340 LYS cc_start: 0.8893 (mttt) cc_final: 0.8602 (mtpt) REVERT: B 311 LYS cc_start: 0.8597 (mttt) cc_final: 0.8253 (pttt) REVERT: C 340 LYS cc_start: 0.9007 (mttt) cc_final: 0.8789 (mtpt) REVERT: D 321 LYS cc_start: 0.8862 (mtpt) cc_final: 0.8537 (mttt) REVERT: E 321 LYS cc_start: 0.8882 (mtpt) cc_final: 0.8474 (mttm) REVERT: E 340 LYS cc_start: 0.8958 (mttt) cc_final: 0.8642 (mtpt) REVERT: E 344 LEU cc_start: 0.9141 (mp) cc_final: 0.8882 (mp) REVERT: F 311 LYS cc_start: 0.8605 (mttt) cc_final: 0.8198 (pttt) REVERT: F 340 LYS cc_start: 0.8895 (mttt) cc_final: 0.8520 (mtpt) outliers start: 8 outliers final: 7 residues processed: 43 average time/residue: 0.2364 time to fit residues: 12.3712 Evaluate side-chains 45 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 373 THR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 357 LEU 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 23 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 41 optimal weight: 0.0870 chunk 44 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 4172 Z= 0.185 Angle : 0.557 8.093 5579 Z= 0.287 Chirality : 0.049 0.121 623 Planarity : 0.003 0.027 714 Dihedral : 6.504 54.242 555 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.49 % Allowed : 16.63 % Favored : 81.88 % 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 0.004 0.001 PHE D 346 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** 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 49 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.522 Fit side-chains REVERT: n 340 LYS cc_start: 0.8792 (mttt) cc_final: 0.8537 (mtpt) REVERT: n 344 LEU cc_start: 0.9178 (mp) cc_final: 0.8964 (mp) REVERT: B 311 LYS cc_start: 0.8501 (mttt) cc_final: 0.8138 (pttt) REVERT: D 344 LEU cc_start: 0.9186 (mp) cc_final: 0.8877 (mp) REVERT: E 340 LYS cc_start: 0.8806 (mttt) cc_final: 0.8509 (mtpt) REVERT: E 344 LEU cc_start: 0.9151 (mp) cc_final: 0.8889 (mp) REVERT: F 311 LYS cc_start: 0.8544 (mttt) cc_final: 0.8143 (pttt) REVERT: F 340 LYS cc_start: 0.8840 (mttt) cc_final: 0.8493 (mtpp) outliers start: 7 outliers final: 5 residues processed: 47 average time/residue: 0.2113 time to fit residues: 12.3562 Evaluate side-chains 47 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU 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 F residue 377 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.4980 chunk 41 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3541 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= 0.306 Angle : 0.614 7.438 5579 Z= 0.320 Chirality : 0.050 0.123 623 Planarity : 0.003 0.024 714 Dihedral : 6.713 57.747 555 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.13 % Allowed : 16.63 % 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: -2.57 (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 B 362 PHE 0.006 0.002 PHE F 378 TYR 0.015 0.003 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** 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 52 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.514 Fit side-chains REVERT: n 340 LYS cc_start: 0.8839 (mttt) cc_final: 0.8554 (mtpt) REVERT: B 311 LYS cc_start: 0.8518 (mttt) cc_final: 0.8145 (pttt) REVERT: C 340 LYS cc_start: 0.9015 (mttt) cc_final: 0.8789 (mtpt) REVERT: D 321 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8510 (mttt) REVERT: D 344 LEU cc_start: 0.9158 (mp) cc_final: 0.8848 (mp) REVERT: E 321 LYS cc_start: 0.8884 (mtpt) cc_final: 0.8473 (mttm) REVERT: E 340 LYS cc_start: 0.8912 (mttt) cc_final: 0.8602 (mtpt) REVERT: E 344 LEU cc_start: 0.9140 (mp) cc_final: 0.8875 (mp) REVERT: F 311 LYS cc_start: 0.8572 (mttt) cc_final: 0.8207 (pttt) REVERT: F 340 LYS cc_start: 0.8890 (mttt) cc_final: 0.8519 (mtpp) outliers start: 10 outliers final: 9 residues processed: 48 average time/residue: 0.2355 time to fit residues: 13.7570 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 : 0.464 ------------------------------------------------------------------------------- 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 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3654 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= 0.232 Angle : 0.582 7.293 5579 Z= 0.298 Chirality : 0.049 0.122 623 Planarity : 0.003 0.025 714 Dihedral : 6.410 57.999 555 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.92 % Allowed : 16.63 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.47 (0.29), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 330 PHE 0.004 0.001 PHE F 378 TYR 0.012 0.003 TYR C 310 ARG 0.001 0.000 ARG B 349 ********************** 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 52 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.435 Fit side-chains REVERT: n 340 LYS cc_start: 0.8749 (mttt) cc_final: 0.8483 (mtpt) REVERT: n 344 LEU cc_start: 0.9177 (mp) cc_final: 0.8948 (mp) REVERT: B 311 LYS cc_start: 0.8500 (mttt) cc_final: 0.8139 (pttt) REVERT: D 344 LEU cc_start: 0.9177 (mp) cc_final: 0.8637 (mp) REVERT: E 321 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8464 (mttm) REVERT: E 340 LYS cc_start: 0.8868 (mttt) cc_final: 0.8572 (mtpt) REVERT: E 344 LEU cc_start: 0.9133 (mp) cc_final: 0.8879 (mp) REVERT: F 311 LYS cc_start: 0.8554 (mttt) cc_final: 0.8195 (pttt) REVERT: F 340 LYS cc_start: 0.8873 (mttt) cc_final: 0.8504 (mtpp) outliers start: 9 outliers final: 9 residues processed: 47 average time/residue: 0.2171 time to fit residues: 12.5640 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 : 0.530 ------------------------------------------------------------------------------- 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 34 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.127946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.101117 restraints weight = 4950.048| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.32 r_work: 0.3527 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 4172 Z= 0.409 Angle : 0.680 7.956 5579 Z= 0.355 Chirality : 0.052 0.128 623 Planarity : 0.003 0.022 714 Dihedral : 6.830 55.149 555 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 1.92 % Allowed : 16.84 % 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: -2.66 (0.28), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.007 0.002 PHE F 378 TYR 0.019 0.005 TYR C 310 ARG 0.001 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1273.54 seconds wall clock time: 23 minutes 58.34 seconds (1438.34 seconds total)