Starting phenix.real_space_refine on Wed Mar 5 20:46:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hre_0259/03_2025/6hre_0259.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hre_0259/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6hre_0259/03_2025/6hre_0259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hre_0259/03_2025/6hre_0259.map" model { file = "/net/cci-nas-00/data/ceres_data/6hre_0259/03_2025/6hre_0259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hre_0259/03_2025/6hre_0259.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: C, B, E, D, F Time building chain proxies: 2.20, per 1000 atoms: 0.62 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: 0.82 Conformation dependent library (CDL) restraints added in 463.7 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: 0.85 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: 0.84 Time building geometry restraints manager: 0.98 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 0.890 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.530 Find NCS groups from input model: 0.080 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.590 ------------------------------------------------------------------------------- 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= 1.226 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.019 0.006 HIS E 374 PHE 0.048 0.017 PHE E 346 TYR 0.040 0.011 TYR C 310 ARG 0.003 0.001 ARG E 349 *********************** 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 : 0.439 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: 0.2700 time to fit residues: 40.7475 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 : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN F 374 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.160868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.142516 restraints weight = 4599.360| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 3.04 r_work: 0.3933 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3576 Z= 0.355 Angle : 0.786 11.112 4782 Z= 0.367 Chirality : 0.053 0.130 534 Planarity : 0.005 0.034 612 Dihedral : 5.735 17.415 474 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.49 % Allowed : 11.19 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 330 PHE 0.009 0.002 PHE B 378 TYR 0.017 0.003 TYR A 310 ARG 0.002 0.001 ARG F 379 *********************** 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 143 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7821 (mt0) cc_final: 0.7530 (mp10) REVERT: A 331 LYS cc_start: 0.8087 (tttt) cc_final: 0.7854 (ttmm) REVERT: A 376 LEU cc_start: 0.8578 (tp) cc_final: 0.8372 (tp) REVERT: B 307 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7521 (tm-30) REVERT: B 342 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7752 (mm-30) REVERT: B 349 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7471 (mtm180) REVERT: B 369 LYS cc_start: 0.8769 (ptpt) cc_final: 0.8386 (mtmt) REVERT: C 340 LYS cc_start: 0.8719 (mttt) cc_final: 0.8496 (mttm) REVERT: C 369 LYS cc_start: 0.8743 (ptpt) cc_final: 0.8342 (ptpp) REVERT: D 321 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8171 (mmtp) REVERT: D 331 LYS cc_start: 0.8440 (tttt) cc_final: 0.8239 (tttt) REVERT: E 321 LYS cc_start: 0.8034 (mtpt) cc_final: 0.7402 (mmtp) REVERT: E 331 LYS cc_start: 0.8291 (tttp) cc_final: 0.6795 (tptt) REVERT: F 317 LYS cc_start: 0.7647 (ptmt) cc_final: 0.7337 (ptpt) REVERT: F 321 LYS cc_start: 0.8293 (mtpt) cc_final: 0.7655 (mmtp) REVERT: F 349 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7656 (mtm-85) outliers start: 6 outliers final: 4 residues processed: 141 average time/residue: 0.2596 time to fit residues: 41.2131 Evaluate side-chains 131 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B 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 9 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 36 optimal weight: 0.0050 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- 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 368 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN D 307 GLN D 368 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.156848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.137593 restraints weight = 4374.508| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 3.00 r_work: 0.3922 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3576 Z= 0.325 Angle : 0.767 10.074 4782 Z= 0.356 Chirality : 0.053 0.130 534 Planarity : 0.004 0.027 612 Dihedral : 5.510 16.969 474 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.49 % Allowed : 14.68 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 329 PHE 0.010 0.002 PHE B 378 TYR 0.014 0.003 TYR A 310 ARG 0.002 0.000 ARG C 379 *********************** 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 132 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.389 Fit side-chains REVERT: A 307 GLN cc_start: 0.7842 (mt0) cc_final: 0.7568 (mp-120) REVERT: B 307 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7519 (tm-30) REVERT: B 342 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7688 (mm-30) REVERT: B 369 LYS cc_start: 0.8792 (ptpt) cc_final: 0.8400 (mtmt) REVERT: C 340 LYS cc_start: 0.8546 (mttt) cc_final: 0.8300 (mttm) REVERT: C 342 GLU cc_start: 0.5128 (pm20) cc_final: 0.4804 (pm20) REVERT: C 369 LYS cc_start: 0.8743 (ptpt) cc_final: 0.8310 (ptpp) REVERT: D 321 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8146 (mmtp) REVERT: D 331 LYS cc_start: 0.8415 (tttt) cc_final: 0.8143 (tttt) REVERT: E 321 LYS cc_start: 0.8098 (mtpt) cc_final: 0.7346 (mmtp) REVERT: F 311 LYS cc_start: 0.8593 (mtmt) cc_final: 0.7921 (mmtt) REVERT: F 317 LYS cc_start: 0.7684 (ptmt) cc_final: 0.7369 (ptpt) REVERT: F 321 LYS cc_start: 0.8422 (mtpt) cc_final: 0.7769 (mmtp) REVERT: F 336 GLN cc_start: 0.8354 (tt0) cc_final: 0.8003 (tt0) outliers start: 10 outliers final: 8 residues processed: 131 average time/residue: 0.2471 time to fit residues: 36.4561 Evaluate side-chains 127 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 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 377 THR Chi-restraints excluded: chain F residue 331 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 8 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- 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 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN D 307 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.154837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.136177 restraints weight = 4687.677| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 3.08 r_work: 0.3906 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4070 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= 0.294 Angle : 0.739 8.779 4782 Z= 0.344 Chirality : 0.052 0.127 534 Planarity : 0.004 0.024 612 Dihedral : 5.339 17.584 474 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.48 % Allowed : 15.42 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.010 0.002 PHE B 378 TYR 0.015 0.003 TYR A 310 ARG 0.001 0.000 ARG C 379 *********************** 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 131 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.409 Fit side-chains REVERT: A 307 GLN cc_start: 0.7738 (mt0) cc_final: 0.7443 (mp-120) REVERT: A 311 LYS cc_start: 0.8504 (mttt) cc_final: 0.8126 (mttt) REVERT: A 342 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7952 (mm-30) REVERT: A 357 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8373 (tp) REVERT: B 307 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7413 (tm-30) REVERT: B 342 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7766 (mm-30) REVERT: B 369 LYS cc_start: 0.8773 (ptpt) cc_final: 0.8355 (mtmt) REVERT: C 340 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8218 (mttm) REVERT: C 369 LYS cc_start: 0.8708 (ptpt) cc_final: 0.8256 (ptpp) REVERT: D 321 LYS cc_start: 0.8854 (mtpt) cc_final: 0.8156 (mmtp) REVERT: D 331 LYS cc_start: 0.8414 (tttt) cc_final: 0.8062 (tttt) REVERT: E 321 LYS cc_start: 0.8047 (mtpt) cc_final: 0.7282 (mmtp) REVERT: E 342 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6995 (mm-30) REVERT: F 311 LYS cc_start: 0.8549 (mtmt) cc_final: 0.7751 (mmtt) REVERT: F 317 LYS cc_start: 0.7748 (ptmt) cc_final: 0.7494 (ptpp) REVERT: F 321 LYS cc_start: 0.8444 (mtpt) cc_final: 0.7751 (mmtp) REVERT: F 336 GLN cc_start: 0.8326 (tt0) cc_final: 0.8065 (tt0) outliers start: 14 outliers final: 9 residues processed: 130 average time/residue: 0.2456 time to fit residues: 36.0359 Evaluate side-chains 126 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 340 LYS 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 331 LYS 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 2 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 ASN ** F 368 ASN ** 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 = 0.4280 r_free = 0.4280 target = 0.153542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.134191 restraints weight = 4577.633| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 3.03 r_work: 0.3887 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 3576 Z= 0.437 Angle : 0.813 8.614 4782 Z= 0.384 Chirality : 0.054 0.129 534 Planarity : 0.004 0.029 612 Dihedral : 5.864 19.315 474 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 4.48 % Allowed : 16.42 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (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 HIS 0.005 0.001 HIS D 329 PHE 0.012 0.003 PHE B 378 TYR 0.014 0.003 TYR A 310 ARG 0.002 0.000 ARG A 349 *********************** 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 145 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.405 Fit side-chains REVERT: A 311 LYS cc_start: 0.8546 (mttt) cc_final: 0.8286 (mtmt) REVERT: B 307 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7366 (tm-30) REVERT: B 369 LYS cc_start: 0.8841 (ptpt) cc_final: 0.8389 (mtmt) REVERT: C 369 LYS cc_start: 0.8828 (ptpt) cc_final: 0.8453 (ptpp) REVERT: D 321 LYS cc_start: 0.8755 (mtpt) cc_final: 0.8270 (mmtp) REVERT: D 331 LYS cc_start: 0.8431 (tttt) cc_final: 0.8147 (ttmm) REVERT: E 321 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7509 (mmtp) REVERT: F 321 LYS cc_start: 0.8575 (mtpt) cc_final: 0.7960 (mmtp) REVERT: F 369 LYS cc_start: 0.8889 (ptpt) cc_final: 0.8408 (ptmt) outliers start: 18 outliers final: 11 residues processed: 141 average time/residue: 0.2398 time to fit residues: 38.2379 Evaluate side-chains 135 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 377 THR 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 F residue 331 LYS Chi-restraints excluded: chain F residue 359 ASN 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-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.4766 > 50: distance: 75 - 80: 33.231 distance: 80 - 81: 47.009 distance: 81 - 82: 16.314 distance: 81 - 84: 24.788 distance: 82 - 87: 57.174 distance: 84 - 85: 42.951 distance: 84 - 86: 26.667 distance: 87 - 88: 45.258 distance: 88 - 89: 30.001 distance: 88 - 91: 30.889 distance: 89 - 90: 44.893 distance: 89 - 95: 50.406 distance: 92 - 93: 27.256 distance: 92 - 94: 13.379 distance: 95 - 96: 33.802 distance: 96 - 97: 16.308 distance: 96 - 99: 52.738 distance: 97 - 98: 8.983 distance: 97 - 103: 50.468 distance: 99 - 100: 29.579 distance: 100 - 101: 52.793 distance: 100 - 102: 5.764 distance: 103 - 104: 21.431 distance: 104 - 105: 26.535 distance: 104 - 107: 26.174 distance: 105 - 106: 16.697 distance: 105 - 109: 20.080 distance: 107 - 108: 38.339 distance: 109 - 110: 19.976 distance: 110 - 111: 21.411 distance: 110 - 113: 17.530 distance: 111 - 112: 7.335 distance: 111 - 118: 16.939 distance: 113 - 114: 13.798 distance: 114 - 115: 11.975 distance: 115 - 116: 13.909 distance: 116 - 117: 6.058 distance: 118 - 119: 16.753 distance: 119 - 120: 34.399 distance: 119 - 122: 9.376 distance: 120 - 121: 3.944 distance: 120 - 125: 17.679 distance: 122 - 123: 20.171 distance: 122 - 124: 20.164 distance: 125 - 126: 33.154 distance: 126 - 127: 29.325 distance: 126 - 129: 19.933 distance: 127 - 128: 14.246 distance: 127 - 132: 44.436 distance: 129 - 130: 4.565 distance: 129 - 131: 38.972 distance: 132 - 133: 10.208 distance: 133 - 134: 9.854 distance: 133 - 136: 13.350 distance: 134 - 138: 14.349 distance: 136 - 137: 18.600 distance: 138 - 139: 19.348 distance: 139 - 140: 22.625 distance: 139 - 142: 26.770 distance: 140 - 141: 18.156 distance: 140 - 147: 25.526 distance: 142 - 143: 17.464 distance: 143 - 144: 17.194 distance: 144 - 145: 21.239 distance: 145 - 146: 15.155 distance: 147 - 148: 4.327 distance: 148 - 149: 8.083 distance: 148 - 151: 6.504 distance: 149 - 150: 22.166 distance: 151 - 152: 20.237