Starting phenix.real_space_refine on Fri Aug 22 13:48:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hre_0259/08_2025/6hre_0259.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hre_0259/08_2025/6hre_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_0259/08_2025/6hre_0259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hre_0259/08_2025/6hre_0259.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hre_0259/08_2025/6hre_0259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hre_0259/08_2025/6hre_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-2.0-5787/lib/python3.9/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: 0.62, per 1000 atoms: 0.18 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: 0.28 Conformation dependent library (CDL) restraints added in 115.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.09 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: 0.33 Time building geometry restraints manager: 0.37 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: 1.440 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.170 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 aren 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 covalent geometry : bond 0.01892 ( 3576) covalent geometry : angle 1.46941 ( 4782) hydrogen bonds : bond 0.18198 ( 65) hydrogen bonds : angle 9.20526 ( 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 : 0.144 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: 0.8809 (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: 0.0937 time to fit residues: 14.1896 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 : 0.084 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7551 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 aren 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 covalent geometry : bond 0.00412 ( 3576) covalent geometry : angle 0.74010 ( 4782) hydrogen bonds : bond 0.02030 ( 65) hydrogen bonds : angle 6.24844 ( 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 : 0.084 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: 0.0811 time to fit residues: 12.1704 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 : 0.108 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.7683 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 aren 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 covalent geometry : bond 0.00631 ( 3576) covalent geometry : angle 0.81781 ( 4782) hydrogen bonds : bond 0.02133 ( 65) hydrogen bonds : angle 6.13308 ( 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 : 0.107 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: 0.7938 (tm-30) cc_final: 0.7408 (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: 0.0955 time to fit residues: 14.3964 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 : 0.145 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.7532 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 aren 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 covalent geometry : bond 0.00345 ( 3576) covalent geometry : angle 0.70579 ( 4782) hydrogen bonds : bond 0.01531 ( 65) hydrogen bonds : angle 5.48102 ( 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 : 0.117 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: 0.1062 time to fit residues: 15.2229 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 : 0.106 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7627 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 aren 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 covalent geometry : bond 0.00554 ( 3576) covalent geometry : angle 0.77460 ( 4782) hydrogen bonds : bond 0.01909 ( 65) hydrogen bonds : angle 5.74555 ( 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 : 0.090 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: 0.8330 (ptpp) REVERT: D 321 LYS cc_start: 0.8791 (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: 0.0851 time to fit residues: 12.9967 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 : 0.130 ------------------------------------------------------------------------------- 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2487 > 50: distance: 75 - 80: 34.560 distance: 80 - 81: 63.439 distance: 81 - 82: 13.773 distance: 81 - 84: 26.789 distance: 82 - 83: 8.477 distance: 82 - 87: 65.245 distance: 84 - 85: 42.577 distance: 84 - 86: 30.085 distance: 87 - 88: 40.006 distance: 88 - 89: 37.341 distance: 88 - 91: 3.019 distance: 89 - 90: 23.128 distance: 89 - 95: 13.461 distance: 91 - 92: 21.175 distance: 92 - 93: 20.564 distance: 92 - 94: 21.926 distance: 95 - 96: 15.824 distance: 96 - 97: 39.803 distance: 96 - 99: 49.783 distance: 97 - 98: 21.845 distance: 97 - 103: 35.312 distance: 99 - 100: 26.622 distance: 100 - 101: 43.484 distance: 100 - 102: 11.719 distance: 103 - 104: 21.954 distance: 104 - 105: 50.290 distance: 104 - 107: 22.756 distance: 105 - 106: 33.596 distance: 105 - 109: 13.954 distance: 107 - 108: 53.848 distance: 109 - 110: 31.370 distance: 110 - 111: 34.994 distance: 110 - 113: 25.470 distance: 111 - 112: 30.078 distance: 111 - 118: 33.790 distance: 113 - 114: 27.681 distance: 114 - 115: 15.784 distance: 115 - 116: 21.504 distance: 116 - 117: 9.639 distance: 118 - 119: 31.967 distance: 119 - 120: 47.340 distance: 119 - 122: 12.585 distance: 120 - 125: 5.685 distance: 122 - 123: 29.733 distance: 122 - 124: 36.593 distance: 125 - 126: 50.462 distance: 126 - 127: 32.528 distance: 126 - 129: 20.190 distance: 127 - 128: 7.074 distance: 127 - 132: 43.373 distance: 129 - 131: 42.578 distance: 132 - 133: 14.646 distance: 133 - 134: 10.296 distance: 133 - 136: 9.837 distance: 134 - 135: 4.442 distance: 134 - 138: 14.662 distance: 136 - 137: 38.400 distance: 138 - 139: 9.227 distance: 139 - 140: 31.352 distance: 139 - 142: 26.601 distance: 140 - 141: 25.545 distance: 140 - 147: 27.047 distance: 142 - 143: 28.433 distance: 143 - 144: 17.302 distance: 144 - 145: 38.357 distance: 145 - 146: 19.350 distance: 147 - 148: 3.072 distance: 148 - 149: 12.570 distance: 148 - 151: 11.286 distance: 149 - 150: 7.817 distance: 149 - 153: 31.288 distance: 151 - 152: 38.466