Starting phenix.real_space_refine on Fri Aug 22 13:44:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ot9_17173/08_2025/8ot9_17173.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ot9_17173/08_2025/8ot9_17173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ot9_17173/08_2025/8ot9_17173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ot9_17173/08_2025/8ot9_17173.map" model { file = "/net/cci-nas-00/data/ceres_data/8ot9_17173/08_2025/8ot9_17173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ot9_17173/08_2025/8ot9_17173.cif" } resolution = 3.4 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 6 5.16 5 C 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3444 Number of models: 1 Model: "" Number of chains: 6 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} Chain: "B" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 0.87, per 1000 atoms: 0.25 Number of scatterers: 3444 At special positions: 0 Unit cell: (98.056, 127.72, 37.08, 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 6 16.00 O 642 8.00 N 636 7.00 C 2160 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: 0.16 Conformation dependent library (CDL) restraints added in 92.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 308 through 310 removed outlier: 6.829A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.799A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 324 through 330 removed outlier: 6.357A pdb=" N LEU A 325 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE C 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASN A 327 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N HIS C 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A 328 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N HIS E 329 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS A 330 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.023A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 342 through 346 removed outlier: 6.900A pdb=" N LYS C 343 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS A 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N PHE E 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 357 removed outlier: 6.358A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LYS C 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N SER A 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLY C 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE A 354 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU C 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER A 356 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.186A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 371 through 374 removed outlier: 6.841A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 377 through 378 removed outlier: 6.549A pdb=" N THR A 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 308 through 310 removed outlier: 6.880A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.742A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 324 through 325 removed outlier: 6.159A pdb=" N SER B 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 337 through 339 removed outlier: 6.034A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 342 through 346 removed outlier: 8.685A pdb=" N GLU B 342 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ASP D 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU F 344 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASP B 345 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE F 346 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.457A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LYS F 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N SER B 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N GLY F 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE B 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU F 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER B 356 " --> pdb=" O LEU F 357 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.223A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 371 through 374 removed outlier: 6.730A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 377 through 378 removed outlier: 6.659A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 44 hydrogen bonds defined for protein. 132 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: 0.32 Time building geometry restraints manager: 0.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 918 1.33 - 1.45: 767 1.45 - 1.57: 1807 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3498 Sorted by residual: bond pdb=" CG HIS F 362 " pdb=" CD2 HIS F 362 " ideal model delta sigma weight residual 1.354 1.292 0.062 1.10e-02 8.26e+03 3.16e+01 bond pdb=" CG HIS B 362 " pdb=" CD2 HIS B 362 " ideal model delta sigma weight residual 1.354 1.292 0.062 1.10e-02 8.26e+03 3.15e+01 bond pdb=" CG HIS D 362 " pdb=" CD2 HIS D 362 " ideal model delta sigma weight residual 1.354 1.292 0.062 1.10e-02 8.26e+03 3.13e+01 bond pdb=" CG HIS D 330 " pdb=" CD2 HIS D 330 " ideal model delta sigma weight residual 1.354 1.296 0.058 1.10e-02 8.26e+03 2.82e+01 bond pdb=" CG HIS F 330 " pdb=" CD2 HIS F 330 " ideal model delta sigma weight residual 1.354 1.296 0.058 1.10e-02 8.26e+03 2.77e+01 ... (remaining 3493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 3412 1.62 - 3.24: 917 3.24 - 4.86: 254 4.86 - 6.48: 79 6.48 - 8.10: 18 Bond angle restraints: 4680 Sorted by residual: angle pdb=" CB HIS B 362 " pdb=" CG HIS B 362 " pdb=" CD2 HIS B 362 " ideal model delta sigma weight residual 131.20 124.11 7.09 1.30e+00 5.92e-01 2.98e+01 angle pdb=" CB HIS F 362 " pdb=" CG HIS F 362 " pdb=" CD2 HIS F 362 " ideal model delta sigma weight residual 131.20 124.11 7.09 1.30e+00 5.92e-01 2.98e+01 angle pdb=" CB HIS D 362 " pdb=" CG HIS D 362 " pdb=" CD2 HIS D 362 " ideal model delta sigma weight residual 131.20 124.12 7.08 1.30e+00 5.92e-01 2.96e+01 angle pdb=" CB HIS D 362 " pdb=" CG HIS D 362 " pdb=" ND1 HIS D 362 " ideal model delta sigma weight residual 122.70 129.58 -6.88 1.50e+00 4.44e-01 2.10e+01 angle pdb=" C PRO C 332 " pdb=" CA PRO C 332 " pdb=" CB PRO C 332 " ideal model delta sigma weight residual 110.85 117.32 -6.47 1.41e+00 5.03e-01 2.10e+01 ... (remaining 4675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.83: 1743 14.83 - 29.67: 312 29.67 - 44.50: 60 44.50 - 59.34: 18 59.34 - 74.17: 3 Dihedral angle restraints: 2136 sinusoidal: 894 harmonic: 1242 Sorted by residual: dihedral pdb=" CA VAL A 306 " pdb=" C VAL A 306 " pdb=" N GLN A 307 " pdb=" CA GLN A 307 " ideal model delta harmonic sigma weight residual 180.00 146.02 33.98 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA VAL C 306 " pdb=" C VAL C 306 " pdb=" N GLN C 307 " pdb=" CA GLN C 307 " ideal model delta harmonic sigma weight residual 180.00 146.02 33.98 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA VAL E 306 " pdb=" C VAL E 306 " pdb=" N GLN E 307 " pdb=" CA GLN E 307 " ideal model delta harmonic sigma weight residual 180.00 146.05 33.95 0 5.00e+00 4.00e-02 4.61e+01 ... (remaining 2133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 286 0.073 - 0.146: 188 0.146 - 0.219: 36 0.219 - 0.291: 9 0.291 - 0.364: 9 Chirality restraints: 528 Sorted by residual: chirality pdb=" CB ILE C 328 " pdb=" CA ILE C 328 " pdb=" CG1 ILE C 328 " pdb=" CG2 ILE C 328 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB ILE A 328 " pdb=" CA ILE A 328 " pdb=" CG1 ILE A 328 " pdb=" CG2 ILE A 328 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CB ILE E 328 " pdb=" CA ILE E 328 " pdb=" CG1 ILE E 328 " pdb=" CG2 ILE E 328 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 525 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 349 " 0.234 9.50e-02 1.11e+02 1.05e-01 7.44e+00 pdb=" NE ARG F 349 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG F 349 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG F 349 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG F 349 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 349 " 0.234 9.50e-02 1.11e+02 1.05e-01 7.39e+00 pdb=" NE ARG B 349 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 349 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 349 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 349 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 349 " 0.234 9.50e-02 1.11e+02 1.05e-01 7.38e+00 pdb=" NE ARG D 349 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG D 349 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 349 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG D 349 " 0.004 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1305 2.91 - 3.41: 3126 3.41 - 3.91: 5461 3.91 - 4.40: 5760 4.40 - 4.90: 11555 Nonbonded interactions: 27207 Sorted by model distance: nonbonded pdb=" OG1 THR B 361 " pdb=" ND1 HIS F 330 " model vdw 2.415 3.120 nonbonded pdb=" ND1 HIS B 330 " pdb=" OG1 THR D 361 " model vdw 2.415 3.120 nonbonded pdb=" N GLY A 366 " pdb=" O GLY C 366 " model vdw 2.555 3.120 nonbonded pdb=" O GLY A 366 " pdb=" N GLY E 366 " model vdw 2.555 3.120 nonbonded pdb=" O PRO B 332 " pdb=" OG SER D 356 " model vdw 2.570 3.040 ... (remaining 27202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 5.080 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: 0.010 Process input model: 3.980 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 3498 Z= 0.623 Angle : 1.750 8.101 4680 Z= 1.116 Chirality : 0.099 0.364 528 Planarity : 0.013 0.105 594 Dihedral : 15.346 74.171 1344 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 6.82 % Allowed : 5.30 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.00 (0.21), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.16), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.004 ARG C 349 TYR 0.025 0.006 TYR F 310 PHE 0.017 0.004 PHE F 346 HIS 0.014 0.006 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00884 ( 3498) covalent geometry : angle 1.75004 ( 4680) hydrogen bonds : bond 0.18408 ( 44) hydrogen bonds : angle 8.12046 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.084 Fit side-chains REVERT: A 331 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8891 (ttpt) REVERT: A 348 ASP cc_start: 0.9022 (t0) cc_final: 0.8526 (t0) REVERT: B 311 LYS cc_start: 0.9019 (mtmt) cc_final: 0.8342 (tttt) REVERT: C 349 ARG cc_start: 0.9057 (mtt180) cc_final: 0.7482 (mmp-170) REVERT: C 375 LYS cc_start: 0.8746 (tttt) cc_final: 0.8507 (ttmm) REVERT: D 311 LYS cc_start: 0.9035 (mtmt) cc_final: 0.8410 (tttt) REVERT: D 343 LYS cc_start: 0.8789 (mtpp) cc_final: 0.7163 (pptt) REVERT: D 349 ARG cc_start: 0.8988 (ptt-90) cc_final: 0.8716 (ptm-80) REVERT: E 311 LYS cc_start: 0.9046 (mtmt) cc_final: 0.8725 (mmtt) REVERT: E 340 LYS cc_start: 0.8736 (mttt) cc_final: 0.8535 (mtpp) REVERT: E 348 ASP cc_start: 0.8887 (t0) cc_final: 0.8636 (t70) REVERT: E 375 LYS cc_start: 0.8670 (tttt) cc_final: 0.8421 (ttmm) REVERT: F 311 LYS cc_start: 0.8922 (mtmt) cc_final: 0.8253 (tttt) REVERT: F 317 LYS cc_start: 0.8646 (pttt) cc_final: 0.8377 (pttp) REVERT: F 320 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8627 (m) REVERT: F 328 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8810 (mm) REVERT: F 349 ARG cc_start: 0.8876 (ptt-90) cc_final: 0.7300 (mmm160) outliers start: 27 outliers final: 4 residues processed: 131 average time/residue: 0.1220 time to fit residues: 17.5422 Evaluate side-chains 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN E 330 HIS ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.106031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.093247 restraints weight = 5424.148| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.45 r_work: 0.3451 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3498 Z= 0.198 Angle : 0.673 6.942 4680 Z= 0.341 Chirality : 0.051 0.130 528 Planarity : 0.004 0.022 594 Dihedral : 7.263 57.124 473 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.53 % Allowed : 10.61 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.48 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 349 TYR 0.023 0.003 TYR A 310 PHE 0.007 0.001 PHE A 346 HIS 0.006 0.002 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 3498) covalent geometry : angle 0.67332 ( 4680) hydrogen bonds : bond 0.02292 ( 44) hydrogen bonds : angle 5.45709 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8624 (mmtt) REVERT: A 343 LYS cc_start: 0.8348 (mttp) cc_final: 0.8067 (mttp) REVERT: A 349 ARG cc_start: 0.8657 (mtt-85) cc_final: 0.8370 (mtp85) REVERT: B 311 LYS cc_start: 0.8975 (mtmt) cc_final: 0.8197 (tttt) REVERT: C 331 LYS cc_start: 0.8912 (tttm) cc_final: 0.8506 (ttpt) REVERT: C 349 ARG cc_start: 0.8646 (mtt180) cc_final: 0.6904 (mmm160) REVERT: C 375 LYS cc_start: 0.8579 (tttt) cc_final: 0.8150 (ttmm) REVERT: D 311 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8269 (tttt) REVERT: D 320 SER cc_start: 0.8738 (t) cc_final: 0.8073 (m) REVERT: D 368 ASN cc_start: 0.8624 (m110) cc_final: 0.8378 (m-40) REVERT: E 340 LYS cc_start: 0.8765 (mttt) cc_final: 0.8352 (mtpp) REVERT: E 375 LYS cc_start: 0.8649 (tttt) cc_final: 0.8216 (ttmm) REVERT: F 311 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8142 (tttt) REVERT: F 349 ARG cc_start: 0.8360 (ptt-90) cc_final: 0.6625 (mmm160) REVERT: F 350 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8758 (m) outliers start: 10 outliers final: 2 residues processed: 96 average time/residue: 0.0851 time to fit residues: 9.2395 Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 0.0270 chunk 34 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 overall best weight: 1.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.109009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.096166 restraints weight = 5137.403| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.30 r_work: 0.3499 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3498 Z= 0.126 Angle : 0.582 5.805 4680 Z= 0.289 Chirality : 0.048 0.124 528 Planarity : 0.003 0.018 594 Dihedral : 4.831 12.623 462 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.26 % Allowed : 14.65 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.82 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 349 TYR 0.018 0.003 TYR A 310 PHE 0.006 0.001 PHE A 346 HIS 0.005 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3498) covalent geometry : angle 0.58196 ( 4680) hydrogen bonds : bond 0.01688 ( 44) hydrogen bonds : angle 4.99487 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.094 Fit side-chains REVERT: A 311 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8508 (mttm) REVERT: A 348 ASP cc_start: 0.9058 (t0) cc_final: 0.8815 (t0) REVERT: A 349 ARG cc_start: 0.8688 (mtt-85) cc_final: 0.8433 (mtp85) REVERT: B 327 ASN cc_start: 0.9276 (m-40) cc_final: 0.9000 (m-40) REVERT: C 349 ARG cc_start: 0.8762 (mtt180) cc_final: 0.7056 (mmm160) REVERT: C 375 LYS cc_start: 0.8624 (tttt) cc_final: 0.8196 (ttmm) REVERT: D 320 SER cc_start: 0.8681 (t) cc_final: 0.8082 (m) REVERT: D 368 ASN cc_start: 0.8698 (m110) cc_final: 0.8311 (m-40) REVERT: E 311 LYS cc_start: 0.8758 (mtmt) cc_final: 0.8385 (mttt) REVERT: E 340 LYS cc_start: 0.8721 (mttt) cc_final: 0.8501 (mttm) REVERT: E 375 LYS cc_start: 0.8593 (tttt) cc_final: 0.8200 (ttmm) REVERT: F 311 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8177 (tttt) REVERT: F 349 ARG cc_start: 0.8320 (ptt-90) cc_final: 0.6477 (mmm160) REVERT: F 350 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8678 (m) outliers start: 5 outliers final: 3 residues processed: 76 average time/residue: 0.0797 time to fit residues: 6.9963 Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 35 optimal weight: 0.0060 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.106319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.093489 restraints weight = 5218.598| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.30 r_work: 0.3461 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3498 Z= 0.169 Angle : 0.593 5.767 4680 Z= 0.294 Chirality : 0.048 0.120 528 Planarity : 0.003 0.015 594 Dihedral : 4.748 12.305 462 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.017 0.002 TYR A 310 PHE 0.007 0.001 PHE A 346 HIS 0.005 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 3498) covalent geometry : angle 0.59261 ( 4680) hydrogen bonds : bond 0.01627 ( 44) hydrogen bonds : angle 4.90032 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.103 Fit side-chains REVERT: A 311 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8430 (mttm) REVERT: A 348 ASP cc_start: 0.9074 (t0) cc_final: 0.8843 (t0) REVERT: A 349 ARG cc_start: 0.8699 (mtt-85) cc_final: 0.8440 (mtp85) REVERT: B 311 LYS cc_start: 0.8934 (mtmt) cc_final: 0.8227 (tttt) REVERT: C 349 ARG cc_start: 0.8725 (mtt180) cc_final: 0.7002 (mmm160) REVERT: C 375 LYS cc_start: 0.8522 (tttt) cc_final: 0.8102 (ttmm) REVERT: D 320 SER cc_start: 0.8652 (t) cc_final: 0.8050 (m) REVERT: E 311 LYS cc_start: 0.8771 (mtmt) cc_final: 0.8379 (mttt) REVERT: E 375 LYS cc_start: 0.8656 (tttt) cc_final: 0.8245 (ttmm) REVERT: F 311 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8182 (tttt) REVERT: F 349 ARG cc_start: 0.8362 (ptt-90) cc_final: 0.6618 (mmm160) outliers start: 6 outliers final: 4 residues processed: 70 average time/residue: 0.0767 time to fit residues: 6.2402 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 0.0170 chunk 6 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 overall best weight: 4.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.103296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.090594 restraints weight = 5361.272| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.31 r_work: 0.3419 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3498 Z= 0.242 Angle : 0.634 5.607 4680 Z= 0.319 Chirality : 0.049 0.121 528 Planarity : 0.003 0.018 594 Dihedral : 4.908 12.955 462 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.52 % Allowed : 17.17 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.020 0.003 TYR A 310 PHE 0.008 0.002 PHE A 346 HIS 0.006 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 3498) covalent geometry : angle 0.63419 ( 4680) hydrogen bonds : bond 0.01693 ( 44) hydrogen bonds : angle 4.95925 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.085 Fit side-chains REVERT: A 348 ASP cc_start: 0.9090 (t0) cc_final: 0.8866 (t0) REVERT: A 349 ARG cc_start: 0.8754 (mtt-85) cc_final: 0.8465 (mtp85) REVERT: B 311 LYS cc_start: 0.8944 (mtmt) cc_final: 0.8241 (tttt) REVERT: C 349 ARG cc_start: 0.8730 (mtt180) cc_final: 0.7047 (mmm160) REVERT: C 375 LYS cc_start: 0.8617 (tttt) cc_final: 0.8194 (ttmm) REVERT: D 311 LYS cc_start: 0.8859 (mtmt) cc_final: 0.8254 (tttt) REVERT: D 320 SER cc_start: 0.8717 (t) cc_final: 0.8096 (m) REVERT: E 311 LYS cc_start: 0.8820 (mtmt) cc_final: 0.8459 (mttt) REVERT: E 314 ASP cc_start: 0.8660 (t0) cc_final: 0.8445 (t0) REVERT: E 375 LYS cc_start: 0.8683 (tttt) cc_final: 0.8283 (ttmm) REVERT: F 311 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8148 (tttt) REVERT: F 349 ARG cc_start: 0.8429 (ptt-90) cc_final: 0.6577 (mmm160) outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.0863 time to fit residues: 6.8784 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.102391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.089899 restraints weight = 5358.760| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.24 r_work: 0.3404 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3498 Z= 0.274 Angle : 0.646 5.670 4680 Z= 0.329 Chirality : 0.049 0.123 528 Planarity : 0.003 0.025 594 Dihedral : 4.986 12.888 462 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.02 % Allowed : 16.67 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.43 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.018 0.003 TYR A 310 PHE 0.008 0.002 PHE A 346 HIS 0.008 0.002 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00616 ( 3498) covalent geometry : angle 0.64576 ( 4680) hydrogen bonds : bond 0.01692 ( 44) hydrogen bonds : angle 5.02152 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.085 Fit side-chains REVERT: A 348 ASP cc_start: 0.9083 (t0) cc_final: 0.8862 (t0) REVERT: A 375 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8383 (ttmm) REVERT: B 311 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8225 (tttt) REVERT: C 349 ARG cc_start: 0.8713 (mtt180) cc_final: 0.6963 (mmm160) REVERT: C 375 LYS cc_start: 0.8614 (tttt) cc_final: 0.8159 (ttmm) REVERT: D 320 SER cc_start: 0.8747 (t) cc_final: 0.8077 (m) REVERT: E 311 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8461 (mttt) REVERT: E 314 ASP cc_start: 0.8712 (t0) cc_final: 0.8491 (t0) REVERT: E 325 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8083 (tt) REVERT: E 375 LYS cc_start: 0.8664 (tttt) cc_final: 0.8241 (ttmm) REVERT: F 311 LYS cc_start: 0.8811 (mtmt) cc_final: 0.8131 (tttt) REVERT: F 349 ARG cc_start: 0.8437 (ptt-90) cc_final: 0.6577 (mmm160) outliers start: 8 outliers final: 5 residues processed: 67 average time/residue: 0.1082 time to fit residues: 8.2007 Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.101409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.088945 restraints weight = 5493.691| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.27 r_work: 0.3387 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 3498 Z= 0.306 Angle : 0.665 5.243 4680 Z= 0.342 Chirality : 0.050 0.123 528 Planarity : 0.004 0.029 594 Dihedral : 5.091 13.187 462 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.77 % Allowed : 17.68 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 349 TYR 0.018 0.003 TYR A 310 PHE 0.009 0.002 PHE F 378 HIS 0.009 0.002 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00690 ( 3498) covalent geometry : angle 0.66497 ( 4680) hydrogen bonds : bond 0.01766 ( 44) hydrogen bonds : angle 5.04413 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.150 Fit side-chains REVERT: A 311 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8565 (mttm) REVERT: A 375 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8441 (ttmm) REVERT: B 311 LYS cc_start: 0.8994 (mtmt) cc_final: 0.8258 (tttt) REVERT: C 349 ARG cc_start: 0.8741 (mtt180) cc_final: 0.6971 (mmm160) REVERT: C 375 LYS cc_start: 0.8673 (tttt) cc_final: 0.8203 (ttmm) REVERT: D 320 SER cc_start: 0.8795 (t) cc_final: 0.8121 (m) REVERT: E 311 LYS cc_start: 0.8849 (mtmt) cc_final: 0.8457 (mttt) REVERT: E 325 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8097 (tt) REVERT: E 340 LYS cc_start: 0.8618 (mttt) cc_final: 0.8262 (mttm) REVERT: E 375 LYS cc_start: 0.8691 (tttt) cc_final: 0.8272 (ttmm) REVERT: F 311 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8188 (tttt) REVERT: F 349 ARG cc_start: 0.8481 (ptt-90) cc_final: 0.6664 (mmm160) outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.0832 time to fit residues: 6.8809 Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.108252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.095799 restraints weight = 5323.823| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.34 r_work: 0.3501 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3498 Z= 0.200 Angle : 0.618 8.504 4680 Z= 0.307 Chirality : 0.049 0.122 528 Planarity : 0.003 0.029 594 Dihedral : 4.799 12.474 462 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.77 % Allowed : 18.18 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 349 TYR 0.017 0.003 TYR A 310 PHE 0.008 0.002 PHE A 346 HIS 0.005 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 3498) covalent geometry : angle 0.61813 ( 4680) hydrogen bonds : bond 0.01585 ( 44) hydrogen bonds : angle 5.05865 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.125 Fit side-chains REVERT: A 311 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8591 (mttm) REVERT: A 375 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8424 (ttmm) REVERT: B 311 LYS cc_start: 0.8946 (mtmt) cc_final: 0.8230 (tttt) REVERT: C 349 ARG cc_start: 0.8792 (mtt180) cc_final: 0.6990 (mmm160) REVERT: C 375 LYS cc_start: 0.8634 (tttt) cc_final: 0.8182 (ttmm) REVERT: E 311 LYS cc_start: 0.8860 (mtmt) cc_final: 0.8474 (mttt) REVERT: E 325 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.7995 (tt) REVERT: E 349 ARG cc_start: 0.8798 (mmm-85) cc_final: 0.8424 (mmm-85) REVERT: E 375 LYS cc_start: 0.8689 (tttt) cc_final: 0.8278 (ttmm) REVERT: F 311 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8130 (tttt) REVERT: F 349 ARG cc_start: 0.8434 (ptt-90) cc_final: 0.6581 (mmm160) outliers start: 7 outliers final: 5 residues processed: 73 average time/residue: 0.0904 time to fit residues: 7.4739 Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.106271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.093555 restraints weight = 5307.236| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.41 r_work: 0.3470 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3498 Z= 0.262 Angle : 0.661 8.646 4680 Z= 0.331 Chirality : 0.050 0.128 528 Planarity : 0.003 0.029 594 Dihedral : 4.938 12.979 462 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.77 % Allowed : 18.18 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 349 TYR 0.018 0.003 TYR A 310 PHE 0.009 0.002 PHE A 346 HIS 0.007 0.002 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 3498) covalent geometry : angle 0.66108 ( 4680) hydrogen bonds : bond 0.01672 ( 44) hydrogen bonds : angle 5.06720 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.091 Fit side-chains REVERT: A 311 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8576 (mttm) REVERT: A 375 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8413 (ttmm) REVERT: B 311 LYS cc_start: 0.8945 (mtmt) cc_final: 0.8195 (tttt) REVERT: C 349 ARG cc_start: 0.8751 (mtt180) cc_final: 0.6953 (mmm160) REVERT: C 375 LYS cc_start: 0.8678 (tttt) cc_final: 0.8187 (ttmm) REVERT: D 320 SER cc_start: 0.8650 (t) cc_final: 0.7739 (m) REVERT: E 311 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8451 (mttt) REVERT: E 325 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8032 (tt) REVERT: E 375 LYS cc_start: 0.8692 (tttt) cc_final: 0.8248 (ttmm) REVERT: F 311 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8084 (tttt) REVERT: F 349 ARG cc_start: 0.8482 (ptt-90) cc_final: 0.6600 (mmm160) outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.0833 time to fit residues: 6.8276 Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.108541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.095949 restraints weight = 5297.927| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.37 r_work: 0.3505 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3498 Z= 0.185 Angle : 0.622 9.053 4680 Z= 0.306 Chirality : 0.049 0.127 528 Planarity : 0.003 0.028 594 Dihedral : 4.731 12.406 462 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.77 % Allowed : 18.18 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 349 TYR 0.017 0.002 TYR A 310 PHE 0.007 0.002 PHE A 346 HIS 0.005 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 3498) covalent geometry : angle 0.62204 ( 4680) hydrogen bonds : bond 0.01564 ( 44) hydrogen bonds : angle 5.09623 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.135 Fit side-chains REVERT: A 311 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8563 (mttm) REVERT: A 375 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8396 (ttmm) REVERT: B 311 LYS cc_start: 0.8946 (mtmt) cc_final: 0.8195 (tttt) REVERT: C 349 ARG cc_start: 0.8769 (mtt180) cc_final: 0.6916 (mmm160) REVERT: C 375 LYS cc_start: 0.8623 (tttt) cc_final: 0.8153 (ttmm) REVERT: E 311 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8434 (mttt) REVERT: E 325 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7947 (tt) REVERT: E 340 LYS cc_start: 0.8640 (mttt) cc_final: 0.8296 (mttm) REVERT: E 375 LYS cc_start: 0.8685 (tttt) cc_final: 0.8260 (ttmm) REVERT: F 311 LYS cc_start: 0.8788 (mtmt) cc_final: 0.8148 (tttt) REVERT: F 349 ARG cc_start: 0.8479 (ptt-90) cc_final: 0.6593 (mmm160) outliers start: 7 outliers final: 5 residues processed: 74 average time/residue: 0.0927 time to fit residues: 7.8664 Evaluate side-chains 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 329 HIS ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.109088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.095813 restraints weight = 5046.068| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.47 r_work: 0.3473 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3498 Z= 0.148 Angle : 0.602 9.054 4680 Z= 0.292 Chirality : 0.048 0.124 528 Planarity : 0.003 0.029 594 Dihedral : 4.580 12.468 462 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.77 % Allowed : 18.18 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.017 0.002 TYR A 310 PHE 0.007 0.001 PHE A 346 HIS 0.005 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3498) covalent geometry : angle 0.60241 ( 4680) hydrogen bonds : bond 0.01514 ( 44) hydrogen bonds : angle 5.08803 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 880.96 seconds wall clock time: 15 minutes 54.05 seconds (954.05 seconds total)