Starting phenix.real_space_refine on Thu Sep 10 21:07:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hre_0259/09_2026/6hre_0259.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hre_0259/09_2026/6hre_0259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6hre_0259/09_2026/6hre_0259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hre_0259/09_2026/6hre_0259.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hre_0259/09_2026/6hre_0259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hre_0259/09_2026/6hre_0259.map" } resolution = 3.2 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= 0.007 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 2202 2.51 5 N 648 2.21 5 O 666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3522 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, F Time building chain proxies: 0.87, per 1000 atoms: 0.25 Number of scatterers: 3522 At special positions: 0 Unit cell: (128.96, 112.32, 46.8, 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 666 8.00 N 648 7.00 C 2202 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: 0.24 Conformation dependent library (CDL) restraints added in 138.5 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 804 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 43.7% 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 'C' and resid 305 through 308 removed outlier: 6.530A pdb=" N SER A 305 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ILE C 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AA3, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.268A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.451A pdb=" N GLN A 336 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL C 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU A 338 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 343 through 347 removed outlier: 6.351A pdb=" N LEU A 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LYS E 347 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE A 346 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 351 through 356 removed outlier: 6.500A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER C 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY A 355 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER A 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.710A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 367 through 379 removed outlier: 6.213A pdb=" N ASN A 368 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ILE E 371 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LYS A 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR E 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU A 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LYS E 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N HIS A 374 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N THR E 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU A 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ARG E 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE A 378 " --> pdb=" O ARG E 379 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 305 through 308 removed outlier: 6.520A pdb=" N SER B 305 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE D 308 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.276A pdb=" N ILE B 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 336 through 340 removed outlier: 6.442A pdb=" N GLN B 336 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL D 339 " --> pdb=" O GLN B 336 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU B 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 343 through 347 removed outlier: 6.361A pdb=" N LEU B 344 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LYS F 347 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE B 346 " --> pdb=" O LYS F 347 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 351 through 356 removed outlier: 6.492A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER D 356 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N GLY B 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N SER B 356 " --> pdb=" O GLY F 355 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 359 through 362 removed outlier: 6.720A pdb=" N ILE B 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 367 through 379 removed outlier: 6.207A pdb=" N ASN B 368 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE F 371 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LYS B 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N THR F 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU B 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LYS F 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N HIS B 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR F 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU B 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ARG F 379 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE B 378 " --> pdb=" O ARG F 379 " (cutoff:3.500A) 65 hydrogen bonds defined for protein. 195 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: 0.43 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 600 1.31 - 1.44: 812 1.44 - 1.56: 1955 1.56 - 1.68: 203 1.68 - 1.80: 6 Bond restraints: 3576 Sorted by residual: bond pdb=" CA ILE F 354 " pdb=" CB ILE F 354 " ideal model delta sigma weight residual 1.533 1.602 -0.069 1.26e-02 6.30e+03 3.04e+01 bond pdb=" CA ILE D 354 " pdb=" CB ILE D 354 " ideal model delta sigma weight residual 1.533 1.602 -0.069 1.26e-02 6.30e+03 3.03e+01 bond pdb=" CA ILE E 354 " pdb=" CB ILE E 354 " ideal model delta sigma weight residual 1.533 1.602 -0.069 1.26e-02 6.30e+03 3.02e+01 bond pdb=" CA ILE B 354 " pdb=" CB ILE B 354 " ideal model delta sigma weight residual 1.533 1.602 -0.069 1.26e-02 6.30e+03 3.02e+01 bond pdb=" CA ILE A 354 " pdb=" CB ILE A 354 " ideal model delta sigma weight residual 1.533 1.602 -0.069 1.26e-02 6.30e+03 3.00e+01 ... (remaining 3571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 4353 2.16 - 4.32: 327 4.32 - 6.47: 72 6.47 - 8.63: 18 8.63 - 10.79: 12 Bond angle restraints: 4782 Sorted by residual: angle pdb=" C VAL E 363 " pdb=" N PRO E 364 " pdb=" CA PRO E 364 " ideal model delta sigma weight residual 119.76 115.90 3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" C VAL A 363 " pdb=" N PRO A 364 " pdb=" CA PRO A 364 " ideal model delta sigma weight residual 119.76 115.91 3.85 1.00e+00 1.00e+00 1.48e+01 angle pdb=" C VAL C 363 " pdb=" N PRO C 364 " pdb=" CA PRO C 364 " ideal model delta sigma weight residual 119.76 115.92 3.84 1.00e+00 1.00e+00 1.48e+01 angle pdb=" C VAL B 363 " pdb=" N PRO B 364 " pdb=" CA PRO B 364 " ideal model delta sigma weight residual 119.76 115.93 3.83 1.00e+00 1.00e+00 1.47e+01 angle pdb=" C VAL F 363 " pdb=" N PRO F 364 " pdb=" CA PRO F 364 " ideal model delta sigma weight residual 119.76 115.94 3.82 1.00e+00 1.00e+00 1.46e+01 ... (remaining 4777 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 11.04: 1782 11.04 - 22.06: 258 22.06 - 33.09: 78 33.09 - 44.11: 48 44.11 - 55.14: 12 Dihedral angle restraints: 2178 sinusoidal: 912 harmonic: 1266 Sorted by residual: dihedral pdb=" C THR C 377 " pdb=" N THR C 377 " pdb=" CA THR C 377 " pdb=" CB THR C 377 " ideal model delta harmonic sigma weight residual -122.00 -129.71 7.71 0 2.50e+00 1.60e-01 9.52e+00 dihedral pdb=" C THR E 377 " pdb=" N THR E 377 " pdb=" CA THR E 377 " pdb=" CB THR E 377 " ideal model delta harmonic sigma weight residual -122.00 -129.69 7.69 0 2.50e+00 1.60e-01 9.47e+00 dihedral pdb=" C THR F 377 " pdb=" N THR F 377 " pdb=" CA THR F 377 " pdb=" CB THR F 377 " ideal model delta harmonic sigma weight residual -122.00 -129.68 7.68 0 2.50e+00 1.60e-01 9.43e+00 ... (remaining 2175 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.061: 218 0.061 - 0.120: 179 0.120 - 0.179: 83 0.179 - 0.238: 42 0.238 - 0.297: 12 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA ILE C 371 " pdb=" N ILE C 371 " pdb=" C ILE C 371 " pdb=" CB ILE C 371 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA ILE B 371 " pdb=" N ILE B 371 " pdb=" C ILE B 371 " pdb=" CB ILE B 371 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ILE F 371 " pdb=" N ILE F 371 " pdb=" C ILE F 371 " pdb=" CB ILE F 371 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 531 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 346 " 0.010 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE E 346 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE E 346 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 PHE E 346 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE E 346 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE E 346 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 346 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 346 " -0.010 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE F 346 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE F 346 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 PHE F 346 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE F 346 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE F 346 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 346 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 346 " 0.010 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE A 346 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 346 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 PHE A 346 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 346 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE A 346 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 346 " 0.003 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 1308 2.96 - 3.44: 3136 3.44 - 3.93: 5345 3.93 - 4.41: 5628 4.41 - 4.90: 10743 Nonbonded interactions: 26160 Sorted by model distance: nonbonded pdb=" O VAL B 313 " pdb=" OD1 ASP B 314 " model vdw 2.474 3.040 nonbonded pdb=" O VAL E 313 " pdb=" OD1 ASP E 314 " model vdw 2.474 3.040 nonbonded pdb=" O VAL A 313 " pdb=" OD1 ASP A 314 " model vdw 2.474 3.040 nonbonded pdb=" O VAL D 313 " pdb=" OD1 ASP D 314 " model vdw 2.475 3.040 nonbonded pdb=" O VAL F 313 " pdb=" OD1 ASP F 314 " model vdw 2.475 3.040 ... (remaining 26155 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' 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.860 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 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 : 0.019 0.071 3576 Z= 1.228 Angle : 1.469 10.790 4782 Z= 0.757 Chirality : 0.105 0.297 534 Planarity : 0.012 0.062 612 Dihedral : 13.340 55.136 1374 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % 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: -4.17 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 349 TYR 0.040 0.011 TYR C 310 PHE 0.048 0.017 PHE E 346 HIS 0.019 0.006 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.01892 / 1.23 ( 3576) covalent geometry : angle 1.46941 / 0.76 ( 4782) hydrogen bonds : bond 0.18198 / 11.75 ( 65) hydrogen bonds : angle 9.20526 / 6.13 ( 195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7970 (mt0) cc_final: 0.7720 (mp10) REVERT: A 340 LYS cc_start: 0.8053 (mttt) cc_final: 0.7668 (mtpp) REVERT: A 369 LYS cc_start: 0.8889 (ptpt) cc_final: 0.8624 (ptpp) REVERT: B 369 LYS cc_start: 0.8847 (ptpt) cc_final: 0.8521 (ptpp) REVERT: C 369 LYS cc_start: 0.8808 (ptpt) cc_final: 0.8443 (ptpp) REVERT: D 321 LYS cc_start: 0.8700 (mtpt) cc_final: 0.8263 (mmtp) REVERT: D 331 LYS cc_start: 0.8503 (tttt) cc_final: 0.8193 (tttt) REVERT: E 321 LYS cc_start: 0.8461 (mtpt) cc_final: 0.7959 (mmtp) REVERT: F 311 LYS cc_start: 0.8353 (mttt) cc_final: 0.8051 (mmtt) REVERT: F 321 LYS cc_start: 0.8524 (mtpt) cc_final: 0.7988 (mmtp) REVERT: F 369 LYS cc_start: 0.8830 (ptpt) cc_final: 0.8544 (ptpp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1078 time to fit residues: 16.3294 Evaluate side-chains 121 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN C 307 GLN D 362 HIS D 374 HIS E 351 GLN F 374 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.161870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.142346 restraints weight = 4397.632| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 3.13 r_work: 0.3968 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3576 Z= 0.179 Angle : 0.740 10.989 4782 Z= 0.343 Chirality : 0.052 0.129 534 Planarity : 0.004 0.033 612 Dihedral : 5.438 16.092 474 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.24 % Allowed : 11.94 % Favored : 86.82 % 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: -3.64 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.015 0.003 TYR A 310 PHE 0.008 0.002 PHE B 378 HIS 0.005 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 3576) covalent geometry : angle 0.74010 / 0.34 ( 4782) hydrogen bonds : bond 0.02030 / 1.26 ( 65) hydrogen bonds : angle 6.24844 / 4.14 ( 195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7893 (mt0) cc_final: 0.7563 (mp10) REVERT: A 376 LEU cc_start: 0.8605 (tp) cc_final: 0.8370 (tp) REVERT: B 307 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7518 (tm-30) REVERT: B 342 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7717 (mm-30) REVERT: B 349 ARG cc_start: 0.7789 (mtt180) cc_final: 0.7429 (mtm180) REVERT: B 369 LYS cc_start: 0.8658 (ptpt) cc_final: 0.8267 (mtmt) REVERT: C 369 LYS cc_start: 0.8683 (ptpt) cc_final: 0.8303 (ptpp) REVERT: D 321 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8065 (mmtp) REVERT: D 331 LYS cc_start: 0.8423 (tttt) cc_final: 0.8221 (tttt) REVERT: E 311 LYS cc_start: 0.8512 (mtmt) cc_final: 0.7225 (mmmt) REVERT: E 321 LYS cc_start: 0.8043 (mtpt) cc_final: 0.7354 (mmtp) REVERT: E 331 LYS cc_start: 0.8290 (tttp) cc_final: 0.6867 (tptt) REVERT: F 317 LYS cc_start: 0.7672 (ptmt) cc_final: 0.7396 (ptpt) REVERT: F 321 LYS cc_start: 0.8272 (mtpt) cc_final: 0.7643 (mmtp) REVERT: F 327 ASN cc_start: 0.6905 (m-40) cc_final: 0.6625 (p0) REVERT: F 349 ARG cc_start: 0.8048 (mtt180) cc_final: 0.7622 (mtm-85) outliers start: 5 outliers final: 3 residues processed: 133 average time/residue: 0.1153 time to fit residues: 17.3171 Evaluate side-chains 126 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 313 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 0.0370 chunk 28 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS C 368 ASN D 307 GLN D 368 ASN E 374 HIS F 351 GLN F 368 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.154461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.135227 restraints weight = 4466.850| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 3.02 r_work: 0.3895 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3576 Z= 0.279 Angle : 0.818 8.851 4782 Z= 0.385 Chirality : 0.054 0.126 534 Planarity : 0.004 0.029 612 Dihedral : 5.838 17.655 474 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.99 % Allowed : 13.68 % Favored : 83.33 % 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: -3.67 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 379 TYR 0.014 0.003 TYR A 310 PHE 0.012 0.003 PHE C 378 HIS 0.005 0.001 HIS D 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.28 ( 3576) covalent geometry : angle 0.81781 / 0.39 ( 4782) hydrogen bonds : bond 0.02133 / 1.37 ( 65) hydrogen bonds : angle 6.13308 / 4.04 ( 195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.136 Fit side-chains REVERT: A 307 GLN cc_start: 0.7816 (mt0) cc_final: 0.7608 (mp-120) REVERT: A 331 LYS cc_start: 0.8248 (tttt) cc_final: 0.7841 (ttmm) REVERT: A 340 LYS cc_start: 0.8001 (mttt) cc_final: 0.7308 (mtpp) REVERT: B 307 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7409 (tm-30) REVERT: B 369 LYS cc_start: 0.8916 (ptpt) cc_final: 0.8478 (mtmt) REVERT: C 369 LYS cc_start: 0.8799 (ptpt) cc_final: 0.8371 (ptpp) REVERT: D 321 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8183 (mmtp) REVERT: D 331 LYS cc_start: 0.8470 (tttt) cc_final: 0.8169 (tttt) REVERT: E 321 LYS cc_start: 0.8120 (mtpt) cc_final: 0.7410 (mmtp) REVERT: E 377 THR cc_start: 0.7117 (OUTLIER) cc_final: 0.6917 (p) REVERT: F 311 LYS cc_start: 0.8595 (mtmt) cc_final: 0.7951 (mmtt) REVERT: F 317 LYS cc_start: 0.7663 (ptmt) cc_final: 0.7376 (ptpt) REVERT: F 321 LYS cc_start: 0.8463 (mtpt) cc_final: 0.7787 (mmtp) outliers start: 12 outliers final: 6 residues processed: 133 average time/residue: 0.1038 time to fit residues: 15.7040 Evaluate side-chains 129 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 377 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.4980 chunk 35 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN A 368 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.156977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.138435 restraints weight = 4638.828| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 3.09 r_work: 0.3945 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3576 Z= 0.155 Angle : 0.706 7.815 4782 Z= 0.328 Chirality : 0.052 0.127 534 Planarity : 0.004 0.024 612 Dihedral : 5.118 16.713 474 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.99 % Allowed : 16.17 % Favored : 80.85 % 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: -3.42 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.013 0.003 TYR A 310 PHE 0.009 0.002 PHE B 378 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 3576) covalent geometry : angle 0.70579 / 0.33 ( 4782) hydrogen bonds : bond 0.01531 / 0.99 ( 65) hydrogen bonds : angle 5.48102 / 3.63 ( 195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.154 Fit side-chains REVERT: A 307 GLN cc_start: 0.7750 (mt0) cc_final: 0.7452 (mp-120) REVERT: A 311 LYS cc_start: 0.8460 (mttt) cc_final: 0.8168 (mtmt) REVERT: A 340 LYS cc_start: 0.7907 (mttt) cc_final: 0.7219 (mtpp) REVERT: A 348 ASP cc_start: 0.7759 (t0) cc_final: 0.7356 (t70) REVERT: A 357 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8416 (tp) REVERT: B 307 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7382 (tm-30) REVERT: B 342 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7741 (mm-30) REVERT: B 369 LYS cc_start: 0.8755 (ptpt) cc_final: 0.8346 (mtmt) REVERT: C 369 LYS cc_start: 0.8675 (ptpt) cc_final: 0.8251 (ptpp) REVERT: D 321 LYS cc_start: 0.8781 (mtpt) cc_final: 0.8119 (mmtp) REVERT: D 331 LYS cc_start: 0.8405 (tttt) cc_final: 0.8053 (tttt) REVERT: D 342 GLU cc_start: 0.3603 (pm20) cc_final: 0.2827 (mm-30) REVERT: E 321 LYS cc_start: 0.8028 (mtpt) cc_final: 0.7250 (mmtp) REVERT: F 311 LYS cc_start: 0.8546 (mtmt) cc_final: 0.7725 (mmtt) REVERT: F 317 LYS cc_start: 0.7730 (ptmt) cc_final: 0.7473 (ptpp) REVERT: F 321 LYS cc_start: 0.8331 (mtpt) cc_final: 0.7615 (mmtp) REVERT: F 336 GLN cc_start: 0.8299 (tt0) cc_final: 0.7880 (tt0) REVERT: F 375 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7797 (ttmt) outliers start: 12 outliers final: 8 residues processed: 128 average time/residue: 0.1128 time to fit residues: 16.2857 Evaluate side-chains 122 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN D 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.155063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.135641 restraints weight = 4491.656| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 3.04 r_work: 0.3894 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 3576 Z= 0.249 Angle : 0.775 8.483 4782 Z= 0.363 Chirality : 0.053 0.127 534 Planarity : 0.004 0.025 612 Dihedral : 5.596 17.857 474 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.23 % Allowed : 16.42 % Favored : 79.35 % 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: -3.47 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.24), residues: 450 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 0.011 0.003 PHE B 378 HIS 0.004 0.001 HIS D 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.25 ( 3576) covalent geometry : angle 0.77460 / 0.36 ( 4782) hydrogen bonds : bond 0.01909 / 1.23 ( 65) hydrogen bonds : angle 5.74555 / 3.78 ( 195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.137 Fit side-chains REVERT: A 311 LYS cc_start: 0.8503 (mttt) cc_final: 0.8242 (mtmt) REVERT: A 340 LYS cc_start: 0.7987 (mttt) cc_final: 0.7292 (mtpp) REVERT: A 357 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8400 (tp) REVERT: B 307 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7301 (tm-30) REVERT: B 369 LYS cc_start: 0.8777 (ptpt) cc_final: 0.8341 (mtmt) REVERT: C 369 LYS cc_start: 0.8785 (ptpt) cc_final: 0.8329 (ptpp) REVERT: D 321 LYS cc_start: 0.8792 (mtpt) cc_final: 0.8227 (mmtp) REVERT: D 331 LYS cc_start: 0.8402 (tttt) cc_final: 0.8132 (ttmm) REVERT: E 321 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7395 (mmtp) REVERT: E 377 THR cc_start: 0.7141 (OUTLIER) cc_final: 0.6907 (p) REVERT: F 311 LYS cc_start: 0.8533 (mtmt) cc_final: 0.7905 (mmtt) REVERT: F 317 LYS cc_start: 0.7839 (ptmt) cc_final: 0.7608 (ptpp) REVERT: F 321 LYS cc_start: 0.8497 (mtpt) cc_final: 0.7852 (mmtp) outliers start: 17 outliers final: 12 residues processed: 134 average time/residue: 0.1046 time to fit residues: 15.9900 Evaluate side-chains 132 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 22 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.2487 > 50:) chunk 28 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 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 = 0.4295 r_free = 0.4295 target = 0.155004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.136329 restraints weight = 4748.037| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 3.06 r_work: 0.3924 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3576 Z= 0.182 Angle : 0.715 8.624 4782 Z= 0.333 Chirality : 0.052 0.130 534 Planarity : 0.004 0.032 612 Dihedral : 5.258 16.899 474 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.73 % Allowed : 19.15 % Favored : 77.11 % 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: -3.46 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.012 0.003 TYR B 310 PHE 0.010 0.002 PHE B 378 HIS 0.003 0.001 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 ( 3576) covalent geometry : angle 0.71463 / 0.33 ( 4782) hydrogen bonds : bond 0.01658 / 1.03 ( 65) hydrogen bonds : angle 5.43370 / 3.59 ( 195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.086 Fit side-chains REVERT: A 311 LYS cc_start: 0.8535 (mttt) cc_final: 0.8246 (mtmt) REVERT: A 343 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8429 (mtpp) REVERT: A 348 ASP cc_start: 0.7828 (t0) cc_final: 0.7436 (t70) REVERT: A 357 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8382 (tp) REVERT: A 376 LEU cc_start: 0.8639 (tp) cc_final: 0.8421 (tp) REVERT: B 307 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7386 (tm-30) REVERT: B 369 LYS cc_start: 0.8761 (ptpt) cc_final: 0.8349 (mtmt) REVERT: C 369 LYS cc_start: 0.8742 (ptpt) cc_final: 0.8289 (ptpp) REVERT: D 321 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8267 (mmtp) REVERT: D 331 LYS cc_start: 0.8387 (tttt) cc_final: 0.8110 (ttmm) REVERT: E 311 LYS cc_start: 0.8638 (mtmt) cc_final: 0.8180 (mmtt) REVERT: E 321 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7371 (mmtp) REVERT: F 311 LYS cc_start: 0.8552 (mtmt) cc_final: 0.7812 (mmtt) REVERT: F 317 LYS cc_start: 0.7830 (ptmt) cc_final: 0.7623 (ptpp) REVERT: F 321 LYS cc_start: 0.8564 (mtpt) cc_final: 0.7913 (mmtp) REVERT: F 336 GLN cc_start: 0.8360 (tt0) cc_final: 0.8139 (tt0) REVERT: F 375 LYS cc_start: 0.8196 (ttpt) cc_final: 0.7845 (ttmt) outliers start: 15 outliers final: 10 residues processed: 126 average time/residue: 0.1069 time to fit residues: 15.2277 Evaluate side-chains 122 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** 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 = 0.4260 r_free = 0.4260 target = 0.152190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.133500 restraints weight = 4873.915| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 3.09 r_work: 0.3880 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 3576 Z= 0.258 Angle : 0.784 9.263 4782 Z= 0.366 Chirality : 0.053 0.131 534 Planarity : 0.004 0.038 612 Dihedral : 5.640 18.083 474 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 3.98 % Allowed : 20.90 % Favored : 75.12 % 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: -3.58 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.013 0.003 TYR A 310 PHE 0.011 0.002 PHE B 378 HIS 0.004 0.001 HIS D 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.26 ( 3576) covalent geometry : angle 0.78385 / 0.37 ( 4782) hydrogen bonds : bond 0.01871 / 1.18 ( 65) hydrogen bonds : angle 5.62026 / 3.69 ( 195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.143 Fit side-chains REVERT: A 311 LYS cc_start: 0.8557 (mttt) cc_final: 0.8289 (mtmt) REVERT: A 357 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8539 (tp) REVERT: B 307 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7336 (tm-30) REVERT: B 369 LYS cc_start: 0.8785 (ptpt) cc_final: 0.8365 (mtmt) REVERT: C 369 LYS cc_start: 0.8791 (ptpt) cc_final: 0.8417 (ptpp) REVERT: D 321 LYS cc_start: 0.8807 (mtpt) cc_final: 0.8265 (mmtp) REVERT: D 331 LYS cc_start: 0.8388 (tttt) cc_final: 0.8186 (tttt) REVERT: E 311 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8257 (mttt) REVERT: E 321 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7460 (mmtp) REVERT: F 311 LYS cc_start: 0.8533 (mtmt) cc_final: 0.7926 (mmtt) REVERT: F 321 LYS cc_start: 0.8576 (mtpt) cc_final: 0.7947 (mmtp) REVERT: F 375 LYS cc_start: 0.8092 (ttpt) cc_final: 0.7734 (ttmt) outliers start: 16 outliers final: 14 residues processed: 134 average time/residue: 0.1068 time to fit residues: 16.2206 Evaluate side-chains 136 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 20 optimal weight: 0.3980 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 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 = 0.4299 r_free = 0.4299 target = 0.154804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.136086 restraints weight = 4799.513| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 3.10 r_work: 0.3922 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3576 Z= 0.170 Angle : 0.707 9.051 4782 Z= 0.329 Chirality : 0.051 0.128 534 Planarity : 0.004 0.041 612 Dihedral : 5.214 17.185 474 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.23 % Allowed : 23.13 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.59 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.013 0.003 TYR B 310 PHE 0.009 0.002 PHE B 378 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 3576) covalent geometry : angle 0.70658 / 0.33 ( 4782) hydrogen bonds : bond 0.01606 / 1.00 ( 65) hydrogen bonds : angle 5.25623 / 3.47 ( 195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.134 Fit side-chains REVERT: A 311 LYS cc_start: 0.8515 (mttt) cc_final: 0.8262 (mtmt) REVERT: A 357 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8392 (tp) REVERT: A 376 LEU cc_start: 0.8670 (tp) cc_final: 0.8441 (tp) REVERT: B 307 GLN cc_start: 0.8000 (tm-30) cc_final: 0.7335 (tm-30) REVERT: B 369 LYS cc_start: 0.8759 (ptpt) cc_final: 0.8363 (mtmt) REVERT: C 369 LYS cc_start: 0.8728 (ptpt) cc_final: 0.8271 (ptpp) REVERT: D 321 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8266 (mmtp) REVERT: D 331 LYS cc_start: 0.8366 (tttt) cc_final: 0.8104 (ttmm) REVERT: E 311 LYS cc_start: 0.8651 (mtmt) cc_final: 0.8200 (mttt) REVERT: E 321 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7419 (mmtp) REVERT: F 311 LYS cc_start: 0.8555 (mtmt) cc_final: 0.7825 (mmtt) REVERT: F 321 LYS cc_start: 0.8544 (mtpt) cc_final: 0.7908 (mmtp) REVERT: F 336 GLN cc_start: 0.8355 (tt0) cc_final: 0.8051 (tt0) REVERT: F 375 LYS cc_start: 0.8130 (ttpt) cc_final: 0.7774 (ttmt) outliers start: 13 outliers final: 12 residues processed: 120 average time/residue: 0.1085 time to fit residues: 14.6449 Evaluate side-chains 123 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 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 = 0.4288 r_free = 0.4288 target = 0.154058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.135520 restraints weight = 4703.901| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 3.03 r_work: 0.3910 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3576 Z= 0.200 Angle : 0.730 9.254 4782 Z= 0.340 Chirality : 0.051 0.128 534 Planarity : 0.004 0.043 612 Dihedral : 5.322 17.242 474 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.73 % Allowed : 22.14 % Favored : 74.13 % 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: -3.65 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.013 0.003 TYR A 310 PHE 0.009 0.002 PHE B 378 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 ( 3576) covalent geometry : angle 0.72995 / 0.34 ( 4782) hydrogen bonds : bond 0.01684 / 1.07 ( 65) hydrogen bonds : angle 5.33403 / 3.49 ( 195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.148 Fit side-chains REVERT: A 311 LYS cc_start: 0.8577 (mttt) cc_final: 0.8327 (mtmt) REVERT: A 357 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8395 (tp) REVERT: B 307 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7386 (tm-30) REVERT: B 369 LYS cc_start: 0.8800 (ptpt) cc_final: 0.8399 (mtmt) REVERT: C 369 LYS cc_start: 0.8756 (ptpt) cc_final: 0.8388 (ptpp) REVERT: D 321 LYS cc_start: 0.8811 (mtpt) cc_final: 0.8286 (mmtp) REVERT: D 331 LYS cc_start: 0.8374 (tttt) cc_final: 0.8099 (ttmm) REVERT: E 311 LYS cc_start: 0.8661 (mtmt) cc_final: 0.8227 (mttt) REVERT: E 321 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7487 (mmtp) REVERT: F 311 LYS cc_start: 0.8542 (mtmt) cc_final: 0.7902 (mmtt) REVERT: F 321 LYS cc_start: 0.8550 (mtpt) cc_final: 0.7930 (mmtp) outliers start: 15 outliers final: 13 residues processed: 124 average time/residue: 0.1046 time to fit residues: 14.7307 Evaluate side-chains 126 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 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 = 0.4306 r_free = 0.4306 target = 0.155194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.136533 restraints weight = 4788.504| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 3.10 r_work: 0.3930 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3576 Z= 0.171 Angle : 0.699 9.342 4782 Z= 0.326 Chirality : 0.051 0.128 534 Planarity : 0.004 0.046 612 Dihedral : 5.145 16.486 474 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.23 % Allowed : 22.39 % Favored : 74.38 % 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: -3.61 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.012 0.003 TYR A 310 PHE 0.009 0.002 PHE B 378 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 ( 3576) covalent geometry : angle 0.69906 / 0.33 ( 4782) hydrogen bonds : bond 0.01597 / 1.01 ( 65) hydrogen bonds : angle 5.17122 / 3.40 ( 195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.146 Fit side-chains REVERT: A 311 LYS cc_start: 0.8553 (mttt) cc_final: 0.8304 (mtmt) REVERT: A 357 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8400 (tp) REVERT: B 307 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7341 (tm-30) REVERT: B 369 LYS cc_start: 0.8759 (ptpt) cc_final: 0.8426 (mtmt) REVERT: C 369 LYS cc_start: 0.8745 (ptpt) cc_final: 0.8288 (ptpp) REVERT: D 321 LYS cc_start: 0.8800 (mtpt) cc_final: 0.8263 (mmtp) REVERT: D 331 LYS cc_start: 0.8340 (tttt) cc_final: 0.8075 (ttmm) REVERT: E 321 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7468 (mmtp) REVERT: E 376 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8390 (tp) REVERT: F 311 LYS cc_start: 0.8551 (mtmt) cc_final: 0.7824 (mmtt) REVERT: F 321 LYS cc_start: 0.8557 (mtpt) cc_final: 0.7913 (mmtp) REVERT: F 336 GLN cc_start: 0.8332 (tt0) cc_final: 0.8025 (tt0) REVERT: F 375 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7765 (ttmt) outliers start: 13 outliers final: 11 residues processed: 120 average time/residue: 0.1151 time to fit residues: 15.5429 Evaluate side-chains 123 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 0.1980 chunk 3 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 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 = 0.4340 r_free = 0.4340 target = 0.158382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.139550 restraints weight = 4678.874| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 3.15 r_work: 0.3968 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3576 Z= 0.121 Angle : 0.650 9.128 4782 Z= 0.301 Chirality : 0.050 0.126 534 Planarity : 0.004 0.046 612 Dihedral : 4.696 14.613 474 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.99 % Allowed : 24.13 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.43 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 379 TYR 0.012 0.003 TYR E 310 PHE 0.008 0.001 PHE F 346 HIS 0.002 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 3576) covalent geometry : angle 0.64952 / 0.30 ( 4782) hydrogen bonds : bond 0.01390 / 0.88 ( 65) hydrogen bonds : angle 4.90206 / 3.23 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 988.03 seconds wall clock time: 17 minutes 42.56 seconds (1062.56 seconds total)