Starting phenix.real_space_refine on Wed Jun 3 10:03:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r8a_53809/06_2026/9r8a_53809.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r8a_53809/06_2026/9r8a_53809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r8a_53809/06_2026/9r8a_53809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r8a_53809/06_2026/9r8a_53809.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r8a_53809/06_2026/9r8a_53809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r8a_53809/06_2026/9r8a_53809.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 1835 2.51 5 N 540 2.21 5 O 555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2935 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: B, C, D, E Time building chain proxies: 0.63, per 1000 atoms: 0.21 Number of scatterers: 2935 At special positions: 0 Unit cell: (145.024, 81.576, 33.784, 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 555 8.00 N 540 7.00 C 1835 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: 0.22 Conformation dependent library (CDL) restraints added in 123.9 milliseconds 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 670 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 51.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.368A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.687A 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: 6.703A 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: 6.523A pdb=" N VAL A 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N LYS E 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER A 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 329 through 330 removed outlier: 6.575A pdb=" N HIS A 329 " --> pdb=" O HIS B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.491A pdb=" N GLN A 336 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N VAL B 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLU A 338 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 343 through 346 removed outlier: 6.540A pdb=" N LEU A 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 350 through 362 removed outlier: 6.951A pdb=" N GLN B 351 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER A 352 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS B 353 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE A 354 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY B 355 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 10.346A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N SER E 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLY A 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASP E 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ILE E 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN A 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N HIS E 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.464A 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 379 removed outlier: 6.683A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.216A 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 removed outlier: 6.524A pdb=" N VAL C 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N LYS D 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER C 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 329 through 330 Processing sheet with id=AB4, first strand: chain 'C' and resid 336 through 340 Processing sheet with id=AB5, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.541A pdb=" N LEU C 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 350 through 362 removed outlier: 8.889A pdb=" N GLN C 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N ILE D 354 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N LYS C 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N SER D 356 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLY C 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ASP D 358 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU C 357 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ILE D 360 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASN C 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N HIS D 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.464A 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 379 55 hydrogen bonds defined for protein. 165 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: 0.34 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 600 1.33 - 1.45: 620 1.45 - 1.57: 1755 1.57 - 1.69: 0 1.69 - 1.81: 5 Bond restraints: 2980 Sorted by residual: bond pdb=" CG HIS E 330 " pdb=" CD2 HIS E 330 " ideal model delta sigma weight residual 1.354 1.319 0.035 1.10e-02 8.26e+03 9.87e+00 bond pdb=" CG HIS D 330 " pdb=" CD2 HIS D 330 " ideal model delta sigma weight residual 1.354 1.320 0.034 1.10e-02 8.26e+03 9.83e+00 bond pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 1.354 1.320 0.034 1.10e-02 8.26e+03 9.73e+00 bond pdb=" CG HIS C 330 " pdb=" CD2 HIS C 330 " ideal model delta sigma weight residual 1.354 1.320 0.034 1.10e-02 8.26e+03 9.55e+00 bond pdb=" CG HIS B 330 " pdb=" CD2 HIS B 330 " ideal model delta sigma weight residual 1.354 1.320 0.034 1.10e-02 8.26e+03 9.31e+00 ... (remaining 2975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 3139 1.90 - 3.81: 639 3.81 - 5.71: 167 5.71 - 7.61: 30 7.61 - 9.51: 10 Bond angle restraints: 3985 Sorted by residual: angle pdb=" N LEU C 325 " pdb=" CA LEU C 325 " pdb=" CB LEU C 325 " ideal model delta sigma weight residual 110.07 119.58 -9.51 1.45e+00 4.76e-01 4.31e+01 angle pdb=" N LEU E 325 " pdb=" CA LEU E 325 " pdb=" CB LEU E 325 " ideal model delta sigma weight residual 110.07 119.58 -9.51 1.45e+00 4.76e-01 4.31e+01 angle pdb=" N LEU D 325 " pdb=" CA LEU D 325 " pdb=" CB LEU D 325 " ideal model delta sigma weight residual 110.07 119.58 -9.51 1.45e+00 4.76e-01 4.30e+01 angle pdb=" N LEU A 325 " pdb=" CA LEU A 325 " pdb=" CB LEU A 325 " ideal model delta sigma weight residual 110.07 119.58 -9.51 1.45e+00 4.76e-01 4.30e+01 angle pdb=" N LEU B 325 " pdb=" CA LEU B 325 " pdb=" CB LEU B 325 " ideal model delta sigma weight residual 110.07 119.57 -9.50 1.45e+00 4.76e-01 4.29e+01 ... (remaining 3980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.63: 1605 12.63 - 25.25: 135 25.25 - 37.88: 40 37.88 - 50.51: 25 50.51 - 63.14: 10 Dihedral angle restraints: 1815 sinusoidal: 760 harmonic: 1055 Sorted by residual: dihedral pdb=" CA GLY E 326 " pdb=" C GLY E 326 " pdb=" N ASN E 327 " pdb=" CA ASN E 327 " ideal model delta harmonic sigma weight residual -180.00 -151.94 -28.06 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA GLY D 326 " pdb=" C GLY D 326 " pdb=" N ASN D 327 " pdb=" CA ASN D 327 " ideal model delta harmonic sigma weight residual 180.00 -151.96 -28.04 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA GLY A 326 " pdb=" C GLY A 326 " pdb=" N ASN A 327 " pdb=" CA ASN A 327 " ideal model delta harmonic sigma weight residual -180.00 -151.98 -28.02 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 1812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 277 0.084 - 0.167: 136 0.167 - 0.250: 22 0.250 - 0.334: 0 0.334 - 0.417: 10 Chirality restraints: 445 Sorted by residual: chirality pdb=" CA ASP D 348 " pdb=" N ASP D 348 " pdb=" C ASP D 348 " pdb=" CB ASP D 348 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA ASP C 348 " pdb=" N ASP C 348 " pdb=" C ASP C 348 " pdb=" CB ASP C 348 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA ASP B 348 " pdb=" N ASP B 348 " pdb=" C ASP B 348 " pdb=" CB ASP B 348 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 442 not shown) Planarity restraints: 510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 367 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.26e+00 pdb=" C GLY B 367 " 0.050 2.00e-02 2.50e+03 pdb=" O GLY B 367 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN B 368 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 367 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.21e+00 pdb=" C GLY D 367 " -0.050 2.00e-02 2.50e+03 pdb=" O GLY D 367 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN D 368 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 367 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C GLY E 367 " 0.049 2.00e-02 2.50e+03 pdb=" O GLY E 367 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN E 368 " -0.016 2.00e-02 2.50e+03 ... (remaining 507 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 781 2.86 - 3.37: 2280 3.37 - 3.88: 4659 3.88 - 4.39: 4822 4.39 - 4.90: 9406 Nonbonded interactions: 21948 Sorted by model distance: nonbonded pdb=" OD2 ASP C 314 " pdb=" OG SER D 316 " model vdw 2.354 3.040 nonbonded pdb=" OG SER A 316 " pdb=" OD2 ASP B 314 " model vdw 2.354 3.040 nonbonded pdb=" OD2 ASP A 314 " pdb=" OG SER E 316 " model vdw 2.354 3.040 nonbonded pdb=" OE1 GLN A 336 " pdb=" NZ LYS D 331 " model vdw 2.594 3.120 nonbonded pdb=" NZ LYS A 331 " pdb=" OE1 GLN C 336 " model vdw 2.594 3.120 ... (remaining 21943 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.160 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 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 : 0.011 0.048 2980 Z= 0.696 Angle : 1.790 9.515 3985 Z= 1.128 Chirality : 0.110 0.417 445 Planarity : 0.010 0.029 510 Dihedral : 12.776 63.136 1145 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 2.99 % Allowed : 4.48 % Favored : 92.54 % Cbeta Deviations : 4.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.32), residues: 375 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.24), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG E 349 TYR 0.021 0.008 TYR B 310 PHE 0.012 0.006 PHE E 346 HIS 0.013 0.005 HIS D 330 Details of bonding type rmsd/Z covalent geometry : bond 0.01110 / 0.70 ( 2980) covalent geometry : angle 1.79023 / 1.13 ( 3985) hydrogen bonds : bond 0.14163 / 10.04 ( 55) hydrogen bonds : angle 6.96035 / 4.70 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.093 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8676 (mtpt) cc_final: 0.8459 (mtmm) REVERT: A 340 LYS cc_start: 0.8738 (mtpt) cc_final: 0.8268 (mmtm) REVERT: A 343 LYS cc_start: 0.8797 (mttt) cc_final: 0.8317 (ttpp) REVERT: A 349 ARG cc_start: 0.8384 (mtt180) cc_final: 0.8003 (mtm180) REVERT: B 340 LYS cc_start: 0.8992 (mtpt) cc_final: 0.8558 (mmtm) REVERT: B 343 LYS cc_start: 0.9002 (mttt) cc_final: 0.8566 (ttpp) REVERT: B 349 ARG cc_start: 0.8514 (mtt180) cc_final: 0.8160 (mtm180) REVERT: C 314 ASP cc_start: 0.9034 (t70) cc_final: 0.8788 (t0) REVERT: C 340 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8531 (mmtm) REVERT: C 343 LYS cc_start: 0.8954 (mttt) cc_final: 0.8605 (mtpp) REVERT: C 349 ARG cc_start: 0.8563 (mtt180) cc_final: 0.8222 (mtm180) REVERT: D 311 LYS cc_start: 0.8712 (mtpt) cc_final: 0.8477 (mttm) REVERT: D 319 THR cc_start: 0.9118 (m) cc_final: 0.8854 (p) REVERT: D 338 GLU cc_start: 0.9131 (tt0) cc_final: 0.8799 (tm-30) REVERT: D 343 LYS cc_start: 0.8803 (mttt) cc_final: 0.8265 (ttpp) REVERT: D 349 ARG cc_start: 0.8381 (mtt180) cc_final: 0.8043 (mtm180) REVERT: E 340 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8242 (mmtm) REVERT: E 347 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8220 (mtmm) REVERT: E 349 ARG cc_start: 0.8451 (mtt180) cc_final: 0.8120 (mtm180) outliers start: 10 outliers final: 0 residues processed: 142 average time/residue: 0.7077 time to fit residues: 102.1771 Evaluate side-chains 123 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS A 374 HIS B 330 HIS B 336 GLN B 374 HIS C 330 HIS C 374 HIS D 330 HIS D 374 HIS E 330 HIS E 351 GLN E 374 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.141014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.115242 restraints weight = 3260.918| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.98 r_work: 0.3516 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2980 Z= 0.109 Angle : 0.638 6.884 3985 Z= 0.312 Chirality : 0.049 0.131 445 Planarity : 0.003 0.019 510 Dihedral : 5.108 13.562 395 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.99 % Allowed : 15.22 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.34), residues: 375 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.26), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 379 TYR 0.008 0.002 TYR C 310 PHE 0.020 0.002 PHE D 378 HIS 0.001 0.000 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 2980) covalent geometry : angle 0.63776 / 0.31 ( 3985) hydrogen bonds : bond 0.02224 / 1.51 ( 55) hydrogen bonds : angle 5.76528 / 3.71 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8311 (mtpt) cc_final: 0.7978 (mttt) REVERT: A 338 GLU cc_start: 0.8794 (tt0) cc_final: 0.8480 (tm-30) REVERT: A 343 LYS cc_start: 0.8655 (mttt) cc_final: 0.8170 (ttpp) REVERT: B 343 LYS cc_start: 0.8861 (mttt) cc_final: 0.8466 (ttpp) REVERT: B 347 LYS cc_start: 0.8831 (mtpm) cc_final: 0.8492 (mtmm) REVERT: C 314 ASP cc_start: 0.8805 (t70) cc_final: 0.8457 (t0) REVERT: C 340 LYS cc_start: 0.8644 (mtpt) cc_final: 0.8196 (mmtm) REVERT: C 343 LYS cc_start: 0.8826 (mttt) cc_final: 0.8495 (mtpp) REVERT: C 375 LYS cc_start: 0.8860 (ttmm) cc_final: 0.8584 (ttmm) REVERT: D 311 LYS cc_start: 0.8457 (mtpt) cc_final: 0.8194 (mttt) REVERT: D 314 ASP cc_start: 0.8920 (t0) cc_final: 0.8673 (t0) REVERT: D 319 THR cc_start: 0.8951 (m) cc_final: 0.8720 (p) REVERT: D 338 GLU cc_start: 0.8778 (tt0) cc_final: 0.8375 (tm-30) REVERT: D 343 LYS cc_start: 0.8702 (mttt) cc_final: 0.8254 (ttpp) REVERT: E 311 LYS cc_start: 0.8406 (mttt) cc_final: 0.7557 (mttm) REVERT: E 343 LYS cc_start: 0.8826 (mtpm) cc_final: 0.8377 (mtpp) REVERT: E 347 LYS cc_start: 0.8411 (mtpt) cc_final: 0.7967 (mtmm) outliers start: 10 outliers final: 2 residues processed: 119 average time/residue: 0.7741 time to fit residues: 93.5262 Evaluate side-chains 106 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain C residue 380 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.138782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.112694 restraints weight = 3210.591| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.96 r_work: 0.3497 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2980 Z= 0.116 Angle : 0.610 5.820 3985 Z= 0.296 Chirality : 0.048 0.129 445 Planarity : 0.003 0.018 510 Dihedral : 4.894 14.546 395 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.90 % Allowed : 19.40 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.36), residues: 375 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.28), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.008 0.002 TYR A 310 PHE 0.005 0.001 PHE A 346 HIS 0.002 0.000 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 2980) covalent geometry : angle 0.61023 / 0.30 ( 3985) hydrogen bonds : bond 0.02158 / 1.50 ( 55) hydrogen bonds : angle 5.11362 / 3.34 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.123 Fit side-chains REVERT: A 311 LYS cc_start: 0.8318 (mtpt) cc_final: 0.8110 (mttt) REVERT: A 343 LYS cc_start: 0.8643 (mttt) cc_final: 0.8165 (ttpp) REVERT: B 343 LYS cc_start: 0.8817 (mttt) cc_final: 0.8426 (ttpp) REVERT: B 347 LYS cc_start: 0.8835 (mtpm) cc_final: 0.8494 (mtmm) REVERT: C 314 ASP cc_start: 0.8825 (t70) cc_final: 0.8523 (t0) REVERT: C 340 LYS cc_start: 0.8653 (mtpt) cc_final: 0.8205 (mmtm) REVERT: C 347 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8526 (mtmm) REVERT: D 311 LYS cc_start: 0.8466 (mtpt) cc_final: 0.8185 (mttt) REVERT: D 338 GLU cc_start: 0.8793 (tt0) cc_final: 0.8359 (tm-30) REVERT: D 343 LYS cc_start: 0.8698 (mttt) cc_final: 0.8251 (ttpp) REVERT: E 343 LYS cc_start: 0.8780 (mtpm) cc_final: 0.8321 (mtpp) outliers start: 3 outliers final: 1 residues processed: 100 average time/residue: 0.7288 time to fit residues: 74.0562 Evaluate side-chains 98 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 369 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 17 optimal weight: 0.0050 chunk 22 optimal weight: 5.9990 overall best weight: 4.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.134819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.108366 restraints weight = 3210.002| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.93 r_work: 0.3434 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 2980 Z= 0.266 Angle : 0.735 6.455 3985 Z= 0.365 Chirality : 0.052 0.137 445 Planarity : 0.004 0.025 510 Dihedral : 5.664 17.876 395 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.39 % Allowed : 20.60 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.38), residues: 375 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.014 0.003 TYR A 310 PHE 0.008 0.002 PHE A 346 HIS 0.002 0.001 HIS D 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.27 ( 2980) covalent geometry : angle 0.73531 / 0.36 ( 3985) hydrogen bonds : bond 0.03023 / 2.12 ( 55) hydrogen bonds : angle 5.19747 / 3.38 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.089 Fit side-chains REVERT: A 311 LYS cc_start: 0.8420 (mtpt) cc_final: 0.8062 (mttt) REVERT: A 343 LYS cc_start: 0.8613 (mttt) cc_final: 0.8121 (ttpp) REVERT: B 347 LYS cc_start: 0.8882 (mtpm) cc_final: 0.8497 (mtmm) REVERT: C 314 ASP cc_start: 0.8820 (t70) cc_final: 0.8528 (t0) REVERT: C 347 LYS cc_start: 0.8840 (mtpp) cc_final: 0.8576 (mtmm) REVERT: D 311 LYS cc_start: 0.8510 (mtpt) cc_final: 0.8299 (mttt) REVERT: D 314 ASP cc_start: 0.8927 (t0) cc_final: 0.8669 (t0) REVERT: D 338 GLU cc_start: 0.8812 (tt0) cc_final: 0.8415 (tm-30) REVERT: D 343 LYS cc_start: 0.8637 (mttt) cc_final: 0.8431 (mtpp) REVERT: E 343 LYS cc_start: 0.8691 (mtpm) cc_final: 0.8420 (mtpt) outliers start: 8 outliers final: 2 residues processed: 102 average time/residue: 0.7096 time to fit residues: 73.6219 Evaluate side-chains 81 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain E residue 369 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.137020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.111009 restraints weight = 3172.567| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.92 r_work: 0.3476 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2980 Z= 0.135 Angle : 0.635 6.905 3985 Z= 0.306 Chirality : 0.048 0.129 445 Planarity : 0.003 0.022 510 Dihedral : 5.018 14.950 395 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.49 % Allowed : 21.79 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.39), residues: 375 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.009 0.002 TYR A 310 PHE 0.004 0.001 PHE A 346 HIS 0.001 0.000 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 2980) covalent geometry : angle 0.63536 / 0.31 ( 3985) hydrogen bonds : bond 0.02141 / 1.48 ( 55) hydrogen bonds : angle 4.85176 / 3.16 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.134 Fit side-chains REVERT: A 311 LYS cc_start: 0.8336 (mtpt) cc_final: 0.8001 (mttt) REVERT: A 343 LYS cc_start: 0.8619 (mttt) cc_final: 0.8167 (ttpp) REVERT: C 314 ASP cc_start: 0.8823 (t70) cc_final: 0.8563 (t0) REVERT: D 311 LYS cc_start: 0.8466 (mtpt) cc_final: 0.8247 (mttt) REVERT: D 314 ASP cc_start: 0.8916 (t0) cc_final: 0.8677 (t0) REVERT: D 338 GLU cc_start: 0.8758 (tt0) cc_final: 0.8353 (tm-30) REVERT: D 343 LYS cc_start: 0.8668 (mttt) cc_final: 0.8450 (mtpp) REVERT: E 343 LYS cc_start: 0.8735 (mtpm) cc_final: 0.8465 (mtpt) outliers start: 5 outliers final: 1 residues processed: 85 average time/residue: 0.6661 time to fit residues: 57.7535 Evaluate side-chains 81 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.139118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.113526 restraints weight = 3194.143| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.93 r_work: 0.3515 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2980 Z= 0.092 Angle : 0.589 7.511 3985 Z= 0.274 Chirality : 0.048 0.125 445 Planarity : 0.002 0.018 510 Dihedral : 4.553 14.626 395 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.49 % Allowed : 22.09 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.40), residues: 375 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.007 0.001 TYR A 310 PHE 0.004 0.001 PHE A 346 HIS 0.001 0.000 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.09 ( 2980) covalent geometry : angle 0.58869 / 0.27 ( 3985) hydrogen bonds : bond 0.01706 / 1.18 ( 55) hydrogen bonds : angle 4.56767 / 2.99 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.090 Fit side-chains REVERT: A 311 LYS cc_start: 0.8304 (mtpt) cc_final: 0.8093 (mttt) REVERT: A 343 LYS cc_start: 0.8627 (mttt) cc_final: 0.8200 (ttpp) REVERT: C 314 ASP cc_start: 0.8821 (t70) cc_final: 0.8560 (t0) REVERT: D 311 LYS cc_start: 0.8426 (mtpt) cc_final: 0.8223 (mttt) REVERT: D 328 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8864 (mp) REVERT: D 338 GLU cc_start: 0.8747 (tt0) cc_final: 0.8344 (tm-30) REVERT: D 347 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8471 (mtmm) REVERT: E 343 LYS cc_start: 0.8762 (mtpm) cc_final: 0.8493 (mtpt) outliers start: 5 outliers final: 1 residues processed: 82 average time/residue: 0.6280 time to fit residues: 52.5296 Evaluate side-chains 74 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 347 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 33 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.136417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.110463 restraints weight = 3226.314| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.92 r_work: 0.3473 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2980 Z= 0.142 Angle : 0.649 7.963 3985 Z= 0.303 Chirality : 0.049 0.127 445 Planarity : 0.003 0.020 510 Dihedral : 4.889 14.908 395 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.19 % Allowed : 22.69 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.40), residues: 375 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.010 0.002 TYR A 310 PHE 0.005 0.001 PHE A 346 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 ( 2980) covalent geometry : angle 0.64878 / 0.30 ( 3985) hydrogen bonds : bond 0.02109 / 1.49 ( 55) hydrogen bonds : angle 4.63985 / 3.04 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.088 Fit side-chains REVERT: A 311 LYS cc_start: 0.8318 (mtpt) cc_final: 0.7981 (mttt) REVERT: A 343 LYS cc_start: 0.8613 (mttt) cc_final: 0.8165 (ttpp) REVERT: C 314 ASP cc_start: 0.8822 (t70) cc_final: 0.8575 (t0) REVERT: D 311 LYS cc_start: 0.8447 (mtpt) cc_final: 0.7725 (mttm) REVERT: D 314 ASP cc_start: 0.8931 (t70) cc_final: 0.8700 (t0) REVERT: D 328 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.8954 (mt) REVERT: D 338 GLU cc_start: 0.8752 (tt0) cc_final: 0.8344 (tm-30) REVERT: D 347 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8399 (mtmm) REVERT: E 343 LYS cc_start: 0.8715 (mtpm) cc_final: 0.8459 (mtpt) outliers start: 4 outliers final: 2 residues processed: 77 average time/residue: 0.6538 time to fit residues: 51.3989 Evaluate side-chains 76 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 347 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 0.0030 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.136948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.111125 restraints weight = 3242.067| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.92 r_work: 0.3477 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2980 Z= 0.132 Angle : 0.636 7.667 3985 Z= 0.297 Chirality : 0.048 0.126 445 Planarity : 0.003 0.020 510 Dihedral : 4.813 15.033 395 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.09 % Allowed : 22.09 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.40), residues: 375 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 379 TYR 0.009 0.002 TYR A 310 PHE 0.004 0.001 PHE A 346 HIS 0.002 0.000 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 ( 2980) covalent geometry : angle 0.63640 / 0.30 ( 3985) hydrogen bonds : bond 0.01979 / 1.39 ( 55) hydrogen bonds : angle 4.60059 / 3.01 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.125 Fit side-chains REVERT: A 311 LYS cc_start: 0.8328 (mtpt) cc_final: 0.7995 (mttt) REVERT: A 343 LYS cc_start: 0.8624 (mttt) cc_final: 0.8158 (ttpp) REVERT: D 311 LYS cc_start: 0.8458 (mtpt) cc_final: 0.7738 (mttm) REVERT: D 314 ASP cc_start: 0.8913 (t70) cc_final: 0.8700 (t0) REVERT: D 328 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.8956 (mt) REVERT: D 338 GLU cc_start: 0.8759 (tt0) cc_final: 0.8350 (tm-30) REVERT: D 347 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8454 (mtmm) REVERT: E 343 LYS cc_start: 0.8718 (mtpm) cc_final: 0.8466 (mtpt) outliers start: 7 outliers final: 3 residues processed: 77 average time/residue: 0.6577 time to fit residues: 51.7283 Evaluate side-chains 77 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 347 LYS 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 26 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 25 optimal weight: 0.0970 chunk 12 optimal weight: 0.0770 chunk 5 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 overall best weight: 1.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.138191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.112471 restraints weight = 3277.376| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.95 r_work: 0.3499 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2980 Z= 0.100 Angle : 0.606 8.075 3985 Z= 0.278 Chirality : 0.048 0.126 445 Planarity : 0.002 0.018 510 Dihedral : 4.586 14.825 395 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.49 % Allowed : 22.39 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.40), residues: 375 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 379 TYR 0.008 0.002 TYR A 310 PHE 0.004 0.001 PHE A 346 HIS 0.001 0.000 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 ( 2980) covalent geometry : angle 0.60591 / 0.28 ( 3985) hydrogen bonds : bond 0.01710 / 1.20 ( 55) hydrogen bonds : angle 4.46743 / 2.93 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.194 Fit side-chains REVERT: A 311 LYS cc_start: 0.8289 (mtpt) cc_final: 0.8077 (mttt) REVERT: A 343 LYS cc_start: 0.8622 (mttt) cc_final: 0.8158 (ttpp) REVERT: C 314 ASP cc_start: 0.8824 (t70) cc_final: 0.8581 (t0) REVERT: D 311 LYS cc_start: 0.8448 (mtpt) cc_final: 0.7724 (mttm) REVERT: D 314 ASP cc_start: 0.8905 (t70) cc_final: 0.8701 (t0) REVERT: D 328 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.8899 (mt) REVERT: D 338 GLU cc_start: 0.8754 (tt0) cc_final: 0.8342 (tm-30) REVERT: D 347 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8475 (mtmm) REVERT: E 343 LYS cc_start: 0.8735 (mtpm) cc_final: 0.8485 (mtpt) outliers start: 5 outliers final: 2 residues processed: 78 average time/residue: 0.6566 time to fit residues: 52.2340 Evaluate side-chains 77 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 347 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 27 optimal weight: 0.0030 chunk 31 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.135035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.108929 restraints weight = 3270.516| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.93 r_work: 0.3443 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2980 Z= 0.193 Angle : 0.693 8.424 3985 Z= 0.326 Chirality : 0.050 0.128 445 Planarity : 0.003 0.022 510 Dihedral : 5.150 15.441 395 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.49 % Allowed : 22.99 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.40), residues: 375 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.012 0.003 TYR A 310 PHE 0.006 0.002 PHE A 346 HIS 0.002 0.001 HIS D 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.19 ( 2980) covalent geometry : angle 0.69320 / 0.33 ( 3985) hydrogen bonds : bond 0.02387 / 1.71 ( 55) hydrogen bonds : angle 4.71154 / 3.09 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.090 Fit side-chains REVERT: A 311 LYS cc_start: 0.8370 (mtpt) cc_final: 0.8019 (mttt) REVERT: A 343 LYS cc_start: 0.8600 (mttt) cc_final: 0.8093 (ttpp) REVERT: D 311 LYS cc_start: 0.8484 (mtpt) cc_final: 0.7749 (mttm) REVERT: D 314 ASP cc_start: 0.8933 (t70) cc_final: 0.8694 (t0) REVERT: D 328 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.8926 (mp) REVERT: D 338 GLU cc_start: 0.8773 (tt0) cc_final: 0.8348 (tm-30) REVERT: D 347 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8451 (mtmm) REVERT: E 343 LYS cc_start: 0.8677 (mtpm) cc_final: 0.8424 (mtpt) outliers start: 5 outliers final: 2 residues processed: 78 average time/residue: 0.6776 time to fit residues: 53.9512 Evaluate side-chains 76 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 347 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.135084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.109007 restraints weight = 3263.830| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.93 r_work: 0.3451 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2980 Z= 0.179 Angle : 0.687 8.302 3985 Z= 0.322 Chirality : 0.049 0.129 445 Planarity : 0.003 0.024 510 Dihedral : 5.088 15.413 395 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.49 % Allowed : 22.99 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.40), residues: 375 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.011 0.002 TYR A 310 PHE 0.005 0.002 PHE A 346 HIS 0.002 0.001 HIS E 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 ( 2980) covalent geometry : angle 0.68710 / 0.32 ( 3985) hydrogen bonds : bond 0.02286 / 1.62 ( 55) hydrogen bonds : angle 4.71456 / 3.09 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1784.39 seconds wall clock time: 31 minutes 13.01 seconds (1873.01 seconds total)