Starting phenix.real_space_refine on Wed Mar 5 16:49:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8caq_16532/03_2025/8caq_16532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8caq_16532/03_2025/8caq_16532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8caq_16532/03_2025/8caq_16532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8caq_16532/03_2025/8caq_16532.map" model { file = "/net/cci-nas-00/data/ceres_data/8caq_16532/03_2025/8caq_16532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8caq_16532/03_2025/8caq_16532.cif" } resolution = 2.3 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 1800 2.51 5 N 530 2.21 5 O 535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Restraints were copied for chains: C, B, E, D Time building chain proxies: 2.16, per 1000 atoms: 0.75 Number of scatterers: 2870 At special positions: 0 Unit cell: (139.256, 119.48, 32.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 535 8.00 N 530 7.00 C 1800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 347.3 milliseconds 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 56.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.367A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.822A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 322 removed outlier: 6.403A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N SER B 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR A 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N CYS B 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS A 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 325 through 330 removed outlier: 8.567A pdb=" N LEU A 325 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N ILE B 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN A 327 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS B 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS A 329 " --> pdb=" O HIS B 330 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY A 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN E 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 346 removed outlier: 6.861A pdb=" N LEU A 344 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP B 345 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE A 346 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU E 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LYS A 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N PHE E 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 357 removed outlier: 6.411A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N SER B 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY A 355 " --> pdb=" O SER B 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.229A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 369 through 378 removed outlier: 6.825A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AB1, first strand: chain 'C' and resid 313 through 314 Processing sheet with id=AB2, first strand: chain 'C' and resid 317 through 322 Processing sheet with id=AB3, first strand: chain 'C' and resid 325 through 330 removed outlier: 6.806A pdb=" N GLY C 326 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN D 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 337 through 346 removed outlier: 6.316A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLU D 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER C 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU D 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LYS C 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N PHE D 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 350 through 357 Processing sheet with id=AB6, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.229A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 369 through 378 66 hydrogen bonds defined for protein. 198 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.58 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 681 1.34 - 1.46: 697 1.46 - 1.57: 1532 1.57 - 1.69: 0 1.69 - 1.81: 5 Bond restraints: 2915 Sorted by residual: bond pdb=" CG HIS C 362 " pdb=" CD2 HIS C 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.44e+00 bond pdb=" CG HIS A 362 " pdb=" CD2 HIS A 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.44e+00 bond pdb=" CG HIS B 362 " pdb=" CD2 HIS B 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.43e+00 bond pdb=" CG HIS D 362 " pdb=" CD2 HIS D 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.42e+00 bond pdb=" CG HIS E 362 " pdb=" CD2 HIS E 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.39e+00 ... (remaining 2910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 2935 1.22 - 2.44: 780 2.44 - 3.66: 140 3.66 - 4.89: 40 4.89 - 6.11: 5 Bond angle restraints: 3900 Sorted by residual: angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 110.42 116.53 -6.11 1.49e+00 4.50e-01 1.68e+01 angle pdb=" N GLY B 326 " pdb=" CA GLY B 326 " pdb=" C GLY B 326 " ideal model delta sigma weight residual 110.42 116.52 -6.10 1.49e+00 4.50e-01 1.68e+01 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.42 116.52 -6.10 1.49e+00 4.50e-01 1.67e+01 angle pdb=" N GLY E 326 " pdb=" CA GLY E 326 " pdb=" C GLY E 326 " ideal model delta sigma weight residual 110.42 116.51 -6.09 1.49e+00 4.50e-01 1.67e+01 angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.42 116.51 -6.09 1.49e+00 4.50e-01 1.67e+01 ... (remaining 3895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 1645 15.14 - 30.28: 95 30.28 - 45.42: 25 45.42 - 60.55: 10 60.55 - 75.69: 5 Dihedral angle restraints: 1780 sinusoidal: 745 harmonic: 1035 Sorted by residual: dihedral pdb=" CA GLY B 335 " pdb=" C GLY B 335 " pdb=" N GLN B 336 " pdb=" CA GLN B 336 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLY E 335 " pdb=" C GLY E 335 " pdb=" N GLN E 336 " pdb=" CA GLN E 336 " ideal model delta harmonic sigma weight residual 180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLY A 335 " pdb=" C GLY A 335 " pdb=" N GLN A 336 " pdb=" CA GLN A 336 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 1777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 163 0.043 - 0.085: 173 0.085 - 0.127: 79 0.127 - 0.169: 20 0.169 - 0.212: 5 Chirality restraints: 440 Sorted by residual: chirality pdb=" CA LYS B 369 " pdb=" N LYS B 369 " pdb=" C LYS B 369 " pdb=" CB LYS B 369 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LYS E 369 " pdb=" N LYS E 369 " pdb=" C LYS E 369 " pdb=" CB LYS E 369 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LYS D 369 " pdb=" N LYS D 369 " pdb=" C LYS D 369 " pdb=" CB LYS D 369 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 437 not shown) Planarity restraints: 495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " 0.017 2.00e-02 2.50e+03 1.13e-02 2.56e+00 pdb=" CG TYR D 310 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.017 2.00e-02 2.50e+03 1.13e-02 2.55e+00 pdb=" CG TYR A 310 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.017 2.00e-02 2.50e+03 1.13e-02 2.54e+00 pdb=" CG TYR C 310 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.004 2.00e-02 2.50e+03 ... (remaining 492 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.06: 1590 3.06 - 3.52: 2604 3.52 - 3.98: 4241 3.98 - 4.44: 4342 4.44 - 4.90: 8817 Nonbonded interactions: 21594 Sorted by model distance: nonbonded pdb=" N ASP B 348 " pdb=" O ASP B 348 " model vdw 2.606 2.496 nonbonded pdb=" N ASP A 348 " pdb=" O ASP A 348 " model vdw 2.606 2.496 nonbonded pdb=" N ASP C 348 " pdb=" O ASP C 348 " model vdw 2.607 2.496 nonbonded pdb=" N ASP D 348 " pdb=" O ASP D 348 " model vdw 2.607 2.496 nonbonded pdb=" N ASP E 348 " pdb=" O ASP E 348 " model vdw 2.607 2.496 ... (remaining 21589 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.240 Find NCS groups from input model: 0.050 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:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 2915 Z= 0.497 Angle : 1.178 6.107 3900 Z= 0.758 Chirality : 0.071 0.212 440 Planarity : 0.007 0.031 495 Dihedral : 12.141 75.692 1120 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.52 % Allowed : 3.03 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.61 (0.31), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.24), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS E 362 PHE 0.008 0.003 PHE B 378 TYR 0.026 0.007 TYR D 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.323 Fit side-chains REVERT: B 349 ARG cc_start: 0.9009 (mtt180) cc_final: 0.6996 (pmt-80) REVERT: B 379 ARG cc_start: 0.8324 (mtt180) cc_final: 0.7517 (pmt170) REVERT: C 349 ARG cc_start: 0.9022 (mtt180) cc_final: 0.7029 (pmt170) REVERT: C 379 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7436 (pmt170) REVERT: D 311 LYS cc_start: 0.8725 (mtmt) cc_final: 0.8389 (mmtt) REVERT: D 349 ARG cc_start: 0.8992 (mtt180) cc_final: 0.7199 (mmm160) REVERT: E 307 GLN cc_start: 0.8274 (tt0) cc_final: 0.7991 (mt0) REVERT: E 311 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8461 (mmtt) REVERT: E 349 ARG cc_start: 0.8975 (mtt180) cc_final: 0.7581 (mmp-170) outliers start: 5 outliers final: 0 residues processed: 110 average time/residue: 1.5039 time to fit residues: 168.3826 Evaluate side-chains 71 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 0.0970 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 351 GLN C 351 GLN C 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.106448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.096528 restraints weight = 4424.400| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.99 r_work: 0.3692 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2915 Z= 0.222 Angle : 0.585 6.314 3900 Z= 0.289 Chirality : 0.048 0.127 440 Planarity : 0.004 0.025 495 Dihedral : 5.100 15.670 385 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.94 % Allowed : 12.42 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.69 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.26), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.004 0.001 PHE A 346 TYR 0.012 0.003 TYR C 310 ARG 0.003 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.343 Fit side-chains REVERT: A 338 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: B 338 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8320 (tm-30) REVERT: B 348 ASP cc_start: 0.8960 (t0) cc_final: 0.7482 (p0) REVERT: B 349 ARG cc_start: 0.8792 (mtt180) cc_final: 0.6504 (pmt-80) REVERT: B 379 ARG cc_start: 0.7909 (mtt180) cc_final: 0.7528 (pmt170) REVERT: C 338 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8423 (tm-30) REVERT: C 349 ARG cc_start: 0.8880 (mtt180) cc_final: 0.6536 (pmt-80) REVERT: C 379 ARG cc_start: 0.7829 (mtt180) cc_final: 0.7367 (pmt170) REVERT: D 349 ARG cc_start: 0.8800 (mtt180) cc_final: 0.6694 (mmm160) REVERT: D 379 ARG cc_start: 0.4961 (OUTLIER) cc_final: 0.3335 (mmt180) REVERT: E 349 ARG cc_start: 0.8770 (mtt180) cc_final: 0.6826 (mmm160) outliers start: 13 outliers final: 1 residues processed: 79 average time/residue: 1.4717 time to fit residues: 118.6119 Evaluate side-chains 72 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 25 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.100416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.090651 restraints weight = 4510.362| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.97 r_work: 0.3615 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 2915 Z= 0.506 Angle : 0.675 6.120 3900 Z= 0.349 Chirality : 0.052 0.138 440 Planarity : 0.004 0.022 495 Dihedral : 5.234 16.205 385 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.42 % Allowed : 15.15 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.29 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.006 0.002 PHE E 346 TYR 0.021 0.005 TYR C 310 ARG 0.004 0.001 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.331 Fit side-chains REVERT: A 338 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: B 314 ASP cc_start: 0.8876 (t70) cc_final: 0.8574 (t0) REVERT: B 338 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8369 (tm-30) REVERT: B 348 ASP cc_start: 0.9000 (t0) cc_final: 0.7540 (p0) REVERT: B 349 ARG cc_start: 0.8829 (mtt180) cc_final: 0.6368 (pmt-80) REVERT: B 379 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7540 (pmt170) REVERT: C 338 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8465 (tm-30) REVERT: C 349 ARG cc_start: 0.8904 (mtt180) cc_final: 0.6578 (pmt170) REVERT: C 379 ARG cc_start: 0.7966 (mtt180) cc_final: 0.7372 (pmt170) REVERT: D 349 ARG cc_start: 0.8772 (mtt180) cc_final: 0.6657 (mmm160) REVERT: D 379 ARG cc_start: 0.5354 (OUTLIER) cc_final: 0.3508 (mmt180) REVERT: E 349 ARG cc_start: 0.8765 (mtt180) cc_final: 0.6770 (mmm160) outliers start: 8 outliers final: 0 residues processed: 77 average time/residue: 1.5089 time to fit residues: 118.4830 Evaluate side-chains 71 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 362 HIS C 307 GLN C 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.101623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.091921 restraints weight = 4630.884| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.99 r_work: 0.3635 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 2915 Z= 0.429 Angle : 0.643 5.463 3900 Z= 0.327 Chirality : 0.051 0.137 440 Planarity : 0.003 0.016 495 Dihedral : 5.159 16.917 385 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.42 % Allowed : 15.76 % Favored : 81.82 % 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: -2.16 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.005 0.001 PHE D 378 TYR 0.016 0.004 TYR E 310 ARG 0.004 0.001 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.359 Fit side-chains REVERT: A 338 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8366 (tt0) REVERT: B 314 ASP cc_start: 0.8939 (t70) cc_final: 0.8615 (t0) REVERT: B 338 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8348 (tm-30) REVERT: B 348 ASP cc_start: 0.9009 (t0) cc_final: 0.7544 (p0) REVERT: B 349 ARG cc_start: 0.8831 (mtt180) cc_final: 0.6396 (pmt-80) REVERT: B 379 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7588 (pmt170) REVERT: C 338 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8428 (tm-30) REVERT: C 349 ARG cc_start: 0.8928 (mtt180) cc_final: 0.6643 (pmt-80) REVERT: C 379 ARG cc_start: 0.8030 (mtt180) cc_final: 0.7411 (pmt170) REVERT: D 349 ARG cc_start: 0.8759 (mtt180) cc_final: 0.6621 (mmm160) REVERT: D 379 ARG cc_start: 0.5410 (OUTLIER) cc_final: 0.3505 (mmt180) REVERT: E 349 ARG cc_start: 0.8762 (mtt180) cc_final: 0.6904 (mmp-170) REVERT: E 379 ARG cc_start: 0.5047 (OUTLIER) cc_final: 0.3018 (mmt180) outliers start: 8 outliers final: 0 residues processed: 76 average time/residue: 1.5721 time to fit residues: 121.7992 Evaluate side-chains 76 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 28 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.100682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.091063 restraints weight = 4596.962| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.97 r_work: 0.3619 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 2915 Z= 0.490 Angle : 0.663 5.601 3900 Z= 0.340 Chirality : 0.052 0.138 440 Planarity : 0.003 0.016 495 Dihedral : 5.232 17.205 385 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.73 % Allowed : 15.15 % Favored : 82.12 % 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: -2.10 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.007 0.002 PHE D 378 TYR 0.018 0.004 TYR C 310 ARG 0.005 0.001 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.379 Fit side-chains REVERT: A 338 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: B 314 ASP cc_start: 0.8898 (t70) cc_final: 0.8591 (t0) REVERT: B 338 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8269 (tm-30) REVERT: B 348 ASP cc_start: 0.9003 (t0) cc_final: 0.7520 (p0) REVERT: B 349 ARG cc_start: 0.8821 (mtt180) cc_final: 0.6378 (pmt-80) REVERT: B 379 ARG cc_start: 0.8097 (mtt180) cc_final: 0.7610 (pmt170) REVERT: C 338 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8426 (tm-30) REVERT: C 349 ARG cc_start: 0.8932 (mtt180) cc_final: 0.6633 (pmt-80) REVERT: C 379 ARG cc_start: 0.8044 (mtt180) cc_final: 0.7466 (pmt170) REVERT: D 349 ARG cc_start: 0.8736 (mtt180) cc_final: 0.6590 (mmm160) REVERT: D 379 ARG cc_start: 0.5283 (OUTLIER) cc_final: 0.3333 (mmt180) REVERT: E 349 ARG cc_start: 0.8760 (mtt180) cc_final: 0.6767 (mmm160) REVERT: E 379 ARG cc_start: 0.5061 (OUTLIER) cc_final: 0.3119 (mmt180) outliers start: 9 outliers final: 1 residues processed: 76 average time/residue: 1.5251 time to fit residues: 118.2757 Evaluate side-chains 78 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 2 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN C 362 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.102163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.092540 restraints weight = 4592.631| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.98 r_work: 0.3641 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2915 Z= 0.364 Angle : 0.622 5.900 3900 Z= 0.314 Chirality : 0.050 0.134 440 Planarity : 0.003 0.015 495 Dihedral : 5.129 17.092 385 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.82 % Allowed : 16.67 % Favored : 81.52 % 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: -2.10 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 362 PHE 0.005 0.001 PHE D 378 TYR 0.014 0.003 TYR C 310 ARG 0.004 0.001 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.372 Fit side-chains REVERT: A 338 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8365 (tt0) REVERT: B 314 ASP cc_start: 0.8889 (t70) cc_final: 0.8575 (t0) REVERT: B 338 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: B 348 ASP cc_start: 0.8995 (t0) cc_final: 0.7542 (p0) REVERT: B 349 ARG cc_start: 0.8816 (mtt180) cc_final: 0.6449 (pmt-80) REVERT: B 379 ARG cc_start: 0.8085 (mtt180) cc_final: 0.7624 (pmt170) REVERT: C 338 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8419 (tm-30) REVERT: C 349 ARG cc_start: 0.8920 (mtt180) cc_final: 0.6644 (pmt-80) REVERT: C 379 ARG cc_start: 0.8034 (mtt180) cc_final: 0.7498 (pmt170) REVERT: D 349 ARG cc_start: 0.8736 (mtt180) cc_final: 0.6614 (mmm160) REVERT: D 379 ARG cc_start: 0.5281 (OUTLIER) cc_final: 0.3347 (mmt180) REVERT: E 349 ARG cc_start: 0.8772 (mtt180) cc_final: 0.6797 (mmm160) REVERT: E 379 ARG cc_start: 0.5045 (OUTLIER) cc_final: 0.3173 (mmt180) outliers start: 6 outliers final: 0 residues processed: 75 average time/residue: 1.5689 time to fit residues: 119.9703 Evaluate side-chains 78 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 0 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.103616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 19)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.094048 restraints weight = 4622.961| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.99 r_work: 0.3666 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2915 Z= 0.268 Angle : 0.588 6.507 3900 Z= 0.294 Chirality : 0.049 0.130 440 Planarity : 0.002 0.015 495 Dihedral : 4.971 16.520 385 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.12 % Allowed : 16.36 % Favored : 81.52 % 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: -2.07 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 362 PHE 0.005 0.001 PHE D 378 TYR 0.011 0.003 TYR C 310 ARG 0.003 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.366 Fit side-chains REVERT: A 338 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: B 314 ASP cc_start: 0.8897 (t70) cc_final: 0.8664 (t0) REVERT: B 338 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: B 348 ASP cc_start: 0.8993 (t0) cc_final: 0.7527 (p0) REVERT: B 349 ARG cc_start: 0.8818 (mtt180) cc_final: 0.6472 (pmt-80) REVERT: B 379 ARG cc_start: 0.8087 (mtt180) cc_final: 0.7671 (pmt170) REVERT: C 338 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8416 (tm-30) REVERT: C 349 ARG cc_start: 0.8913 (mtt180) cc_final: 0.6606 (pmt-80) REVERT: C 379 ARG cc_start: 0.8033 (mtt180) cc_final: 0.7507 (pmt170) REVERT: D 349 ARG cc_start: 0.8744 (mtt180) cc_final: 0.6633 (mmm160) REVERT: E 349 ARG cc_start: 0.8765 (mtt180) cc_final: 0.6753 (mmm160) outliers start: 7 outliers final: 0 residues processed: 74 average time/residue: 1.4761 time to fit residues: 111.4251 Evaluate side-chains 75 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN E 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.102159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.092537 restraints weight = 4630.685| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.96 r_work: 0.3642 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2915 Z= 0.379 Angle : 0.626 6.385 3900 Z= 0.316 Chirality : 0.050 0.133 440 Planarity : 0.003 0.016 495 Dihedral : 5.075 16.548 385 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.82 % Allowed : 16.67 % Favored : 81.52 % 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: -2.06 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 362 PHE 0.007 0.001 PHE D 378 TYR 0.015 0.004 TYR E 310 ARG 0.004 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.374 Fit side-chains REVERT: A 338 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: B 314 ASP cc_start: 0.8891 (t70) cc_final: 0.8633 (t0) REVERT: B 338 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8271 (tm-30) REVERT: B 348 ASP cc_start: 0.8982 (t0) cc_final: 0.7533 (p0) REVERT: B 349 ARG cc_start: 0.8814 (mtt180) cc_final: 0.6448 (pmt-80) REVERT: B 379 ARG cc_start: 0.8190 (mtt180) cc_final: 0.7694 (pmt170) REVERT: C 338 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8407 (tm-30) REVERT: C 349 ARG cc_start: 0.8908 (mtt180) cc_final: 0.6603 (pmt-80) REVERT: C 379 ARG cc_start: 0.8085 (mtt180) cc_final: 0.7495 (pmt170) REVERT: D 349 ARG cc_start: 0.8732 (mtt180) cc_final: 0.6602 (mmm160) REVERT: E 349 ARG cc_start: 0.8780 (mtt180) cc_final: 0.6793 (mmm160) outliers start: 6 outliers final: 0 residues processed: 73 average time/residue: 1.5281 time to fit residues: 113.7328 Evaluate side-chains 75 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 0.0270 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 362 HIS C 307 GLN C 351 GLN E 307 GLN E 362 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.106434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.096929 restraints weight = 4507.660| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.98 r_work: 0.3712 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2915 Z= 0.154 Angle : 0.554 6.345 3900 Z= 0.271 Chirality : 0.049 0.123 440 Planarity : 0.002 0.020 495 Dihedral : 4.722 15.870 385 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.52 % Allowed : 16.67 % Favored : 81.82 % 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: -1.94 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 330 PHE 0.004 0.001 PHE A 346 TYR 0.006 0.001 TYR A 310 ARG 0.001 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.348 Fit side-chains REVERT: A 338 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: B 314 ASP cc_start: 0.8874 (t70) cc_final: 0.8628 (t0) REVERT: B 338 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8259 (tm-30) REVERT: B 348 ASP cc_start: 0.8921 (t0) cc_final: 0.7395 (p0) REVERT: B 349 ARG cc_start: 0.8819 (mtt180) cc_final: 0.6483 (pmt-80) REVERT: B 379 ARG cc_start: 0.8120 (mtt180) cc_final: 0.7782 (pmt170) REVERT: C 338 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8480 (tm-30) REVERT: C 348 ASP cc_start: 0.8905 (t0) cc_final: 0.7246 (p0) REVERT: C 349 ARG cc_start: 0.8883 (mtt180) cc_final: 0.6494 (pmt-80) REVERT: C 379 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7491 (pmt170) REVERT: D 349 ARG cc_start: 0.8731 (mtt180) cc_final: 0.6664 (mmm160) REVERT: E 349 ARG cc_start: 0.8770 (mtt180) cc_final: 0.6756 (mmm160) outliers start: 5 outliers final: 0 residues processed: 73 average time/residue: 1.5562 time to fit residues: 115.7771 Evaluate side-chains 74 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 23 optimal weight: 0.3980 chunk 10 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 368 ASN C 307 GLN E 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.106612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.097092 restraints weight = 4555.281| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.98 r_work: 0.3716 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 2915 Z= 0.172 Angle : 0.554 6.110 3900 Z= 0.271 Chirality : 0.049 0.126 440 Planarity : 0.002 0.022 495 Dihedral : 4.579 14.889 385 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.91 % Allowed : 17.58 % Favored : 81.52 % 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: -1.86 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 362 PHE 0.004 0.001 PHE E 378 TYR 0.008 0.002 TYR D 310 ARG 0.002 0.000 ARG E 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.329 Fit side-chains REVERT: A 338 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: B 338 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8277 (tm-30) REVERT: B 348 ASP cc_start: 0.8916 (t0) cc_final: 0.7415 (p0) REVERT: B 349 ARG cc_start: 0.8797 (mtt180) cc_final: 0.6482 (pmt-80) REVERT: B 379 ARG cc_start: 0.8135 (mtt180) cc_final: 0.7794 (pmt170) REVERT: C 338 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8406 (tm-30) REVERT: C 348 ASP cc_start: 0.8901 (t0) cc_final: 0.7266 (p0) REVERT: C 349 ARG cc_start: 0.8883 (mtt180) cc_final: 0.6497 (pmt-80) REVERT: C 379 ARG cc_start: 0.8014 (mtt180) cc_final: 0.7532 (pmt170) REVERT: D 307 GLN cc_start: 0.8400 (tt0) cc_final: 0.8034 (mt0) REVERT: D 349 ARG cc_start: 0.8722 (mtt180) cc_final: 0.6652 (mmm160) REVERT: E 349 ARG cc_start: 0.8746 (mtt180) cc_final: 0.6748 (mmm160) outliers start: 3 outliers final: 0 residues processed: 72 average time/residue: 1.4843 time to fit residues: 108.9500 Evaluate side-chains 73 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 27 optimal weight: 0.0170 chunk 13 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN E 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.102904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.093241 restraints weight = 4513.208| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.95 r_work: 0.3655 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2915 Z= 0.345 Angle : 0.625 6.437 3900 Z= 0.313 Chirality : 0.050 0.133 440 Planarity : 0.003 0.018 495 Dihedral : 4.881 15.491 385 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.91 % Allowed : 18.18 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.90 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.006 0.001 PHE D 378 TYR 0.015 0.004 TYR E 310 ARG 0.004 0.000 ARG E 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3582.23 seconds wall clock time: 61 minutes 52.20 seconds (3712.20 seconds total)