Starting phenix.real_space_refine on Mon Jan 13 15:00:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8caq_16532/01_2025/8caq_16532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8caq_16532/01_2025/8caq_16532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8caq_16532/01_2025/8caq_16532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8caq_16532/01_2025/8caq_16532.map" model { file = "/net/cci-nas-00/data/ceres_data/8caq_16532/01_2025/8caq_16532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8caq_16532/01_2025/8caq_16532.cif" } resolution = 2.3 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 1800 2.51 5 N 530 2.21 5 O 535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 2870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Restraints were copied for chains: C, B, E, D Time building chain proxies: 2.78, per 1000 atoms: 0.97 Number of scatterers: 2870 At special positions: 0 Unit cell: (139.256, 119.48, 32.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 535 8.00 N 530 7.00 C 1800 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: 0.59 Conformation dependent library (CDL) restraints added in 318.4 milliseconds 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 56.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.367A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.822A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 322 removed outlier: 6.403A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N SER B 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR A 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N CYS B 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS A 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 325 through 330 removed outlier: 8.567A pdb=" N LEU A 325 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N ILE B 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN A 327 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS B 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS A 329 " --> pdb=" O HIS B 330 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY A 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN E 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 346 removed outlier: 6.861A pdb=" N LEU A 344 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP B 345 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE A 346 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU E 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LYS A 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N PHE E 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 357 removed outlier: 6.411A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N SER B 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY A 355 " --> pdb=" O SER B 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.229A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 369 through 378 removed outlier: 6.825A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AB1, first strand: chain 'C' and resid 313 through 314 Processing sheet with id=AB2, first strand: chain 'C' and resid 317 through 322 Processing sheet with id=AB3, first strand: chain 'C' and resid 325 through 330 removed outlier: 6.806A pdb=" N GLY C 326 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN D 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 337 through 346 removed outlier: 6.316A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLU D 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER C 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU D 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LYS C 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N PHE D 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 350 through 357 Processing sheet with id=AB6, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.229A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 369 through 378 66 hydrogen bonds defined for protein. 198 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: 0.58 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 681 1.34 - 1.46: 697 1.46 - 1.57: 1532 1.57 - 1.69: 0 1.69 - 1.81: 5 Bond restraints: 2915 Sorted by residual: bond pdb=" CG HIS C 362 " pdb=" CD2 HIS C 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.44e+00 bond pdb=" CG HIS A 362 " pdb=" CD2 HIS A 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.44e+00 bond pdb=" CG HIS B 362 " pdb=" CD2 HIS B 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.43e+00 bond pdb=" CG HIS D 362 " pdb=" CD2 HIS D 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.42e+00 bond pdb=" CG HIS E 362 " pdb=" CD2 HIS E 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.39e+00 ... (remaining 2910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 2935 1.22 - 2.44: 780 2.44 - 3.66: 140 3.66 - 4.89: 40 4.89 - 6.11: 5 Bond angle restraints: 3900 Sorted by residual: angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 110.42 116.53 -6.11 1.49e+00 4.50e-01 1.68e+01 angle pdb=" N GLY B 326 " pdb=" CA GLY B 326 " pdb=" C GLY B 326 " ideal model delta sigma weight residual 110.42 116.52 -6.10 1.49e+00 4.50e-01 1.68e+01 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.42 116.52 -6.10 1.49e+00 4.50e-01 1.67e+01 angle pdb=" N GLY E 326 " pdb=" CA GLY E 326 " pdb=" C GLY E 326 " ideal model delta sigma weight residual 110.42 116.51 -6.09 1.49e+00 4.50e-01 1.67e+01 angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.42 116.51 -6.09 1.49e+00 4.50e-01 1.67e+01 ... (remaining 3895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 1645 15.14 - 30.28: 95 30.28 - 45.42: 25 45.42 - 60.55: 10 60.55 - 75.69: 5 Dihedral angle restraints: 1780 sinusoidal: 745 harmonic: 1035 Sorted by residual: dihedral pdb=" CA GLY B 335 " pdb=" C GLY B 335 " pdb=" N GLN B 336 " pdb=" CA GLN B 336 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLY E 335 " pdb=" C GLY E 335 " pdb=" N GLN E 336 " pdb=" CA GLN E 336 " ideal model delta harmonic sigma weight residual 180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLY A 335 " pdb=" C GLY A 335 " pdb=" N GLN A 336 " pdb=" CA GLN A 336 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 1777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 163 0.043 - 0.085: 173 0.085 - 0.127: 79 0.127 - 0.169: 20 0.169 - 0.212: 5 Chirality restraints: 440 Sorted by residual: chirality pdb=" CA LYS B 369 " pdb=" N LYS B 369 " pdb=" C LYS B 369 " pdb=" CB LYS B 369 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LYS E 369 " pdb=" N LYS E 369 " pdb=" C LYS E 369 " pdb=" CB LYS E 369 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LYS D 369 " pdb=" N LYS D 369 " pdb=" C LYS D 369 " pdb=" CB LYS D 369 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 437 not shown) Planarity restraints: 495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " 0.017 2.00e-02 2.50e+03 1.13e-02 2.56e+00 pdb=" CG TYR D 310 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.017 2.00e-02 2.50e+03 1.13e-02 2.55e+00 pdb=" CG TYR A 310 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.017 2.00e-02 2.50e+03 1.13e-02 2.54e+00 pdb=" CG TYR C 310 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.004 2.00e-02 2.50e+03 ... (remaining 492 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.06: 1590 3.06 - 3.52: 2604 3.52 - 3.98: 4241 3.98 - 4.44: 4342 4.44 - 4.90: 8817 Nonbonded interactions: 21594 Sorted by model distance: nonbonded pdb=" N ASP B 348 " pdb=" O ASP B 348 " model vdw 2.606 2.496 nonbonded pdb=" N ASP A 348 " pdb=" O ASP A 348 " model vdw 2.606 2.496 nonbonded pdb=" N ASP C 348 " pdb=" O ASP C 348 " model vdw 2.607 2.496 nonbonded pdb=" N ASP D 348 " pdb=" O ASP D 348 " model vdw 2.607 2.496 nonbonded pdb=" N ASP E 348 " pdb=" O ASP E 348 " model vdw 2.607 2.496 ... (remaining 21589 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 2.870 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.230 Find NCS groups from input model: 0.060 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:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 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 : 0.007 0.042 2915 Z= 0.497 Angle : 1.178 6.107 3900 Z= 0.758 Chirality : 0.071 0.212 440 Planarity : 0.007 0.031 495 Dihedral : 12.141 75.692 1120 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.52 % Allowed : 3.03 % Favored : 95.45 % 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: -3.61 (0.31), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.24), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS E 362 PHE 0.008 0.003 PHE B 378 TYR 0.026 0.007 TYR D 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.388 Fit side-chains REVERT: B 349 ARG cc_start: 0.9009 (mtt180) cc_final: 0.6996 (pmt-80) REVERT: B 379 ARG cc_start: 0.8324 (mtt180) cc_final: 0.7517 (pmt170) REVERT: C 349 ARG cc_start: 0.9022 (mtt180) cc_final: 0.7029 (pmt170) REVERT: C 379 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7436 (pmt170) REVERT: D 311 LYS cc_start: 0.8725 (mtmt) cc_final: 0.8389 (mmtt) REVERT: D 349 ARG cc_start: 0.8992 (mtt180) cc_final: 0.7199 (mmm160) REVERT: E 307 GLN cc_start: 0.8274 (tt0) cc_final: 0.7991 (mt0) REVERT: E 311 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8461 (mmtt) REVERT: E 349 ARG cc_start: 0.8975 (mtt180) cc_final: 0.7581 (mmp-170) outliers start: 5 outliers final: 0 residues processed: 110 average time/residue: 1.5186 time to fit residues: 170.1654 Evaluate side-chains 71 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 0.0970 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 351 GLN C 351 GLN C 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.106448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.096529 restraints weight = 4424.402| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.99 r_work: 0.3692 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2915 Z= 0.222 Angle : 0.585 6.314 3900 Z= 0.289 Chirality : 0.048 0.127 440 Planarity : 0.004 0.025 495 Dihedral : 5.100 15.670 385 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.94 % Allowed : 12.42 % Favored : 83.64 % 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: -2.69 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.26), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.004 0.001 PHE A 346 TYR 0.012 0.003 TYR C 310 ARG 0.003 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.353 Fit side-chains REVERT: A 338 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: B 338 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8316 (tm-30) REVERT: B 348 ASP cc_start: 0.8962 (t0) cc_final: 0.7484 (p0) REVERT: B 349 ARG cc_start: 0.8793 (mtt180) cc_final: 0.6507 (pmt-80) REVERT: B 379 ARG cc_start: 0.7905 (mtt180) cc_final: 0.7529 (pmt170) REVERT: C 338 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8421 (tm-30) REVERT: C 349 ARG cc_start: 0.8882 (mtt180) cc_final: 0.6539 (pmt-80) REVERT: C 379 ARG cc_start: 0.7828 (mtt180) cc_final: 0.7367 (pmt170) REVERT: D 349 ARG cc_start: 0.8803 (mtt180) cc_final: 0.6701 (mmm160) REVERT: D 379 ARG cc_start: 0.4957 (OUTLIER) cc_final: 0.3334 (mmt180) REVERT: E 349 ARG cc_start: 0.8772 (mtt180) cc_final: 0.6831 (mmm160) outliers start: 13 outliers final: 1 residues processed: 79 average time/residue: 1.4755 time to fit residues: 118.8992 Evaluate side-chains 72 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 25 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.100705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.090927 restraints weight = 4497.542| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.97 r_work: 0.3619 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 2915 Z= 0.484 Angle : 0.662 6.283 3900 Z= 0.341 Chirality : 0.052 0.138 440 Planarity : 0.004 0.022 495 Dihedral : 5.194 16.216 385 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.42 % Allowed : 14.85 % Favored : 82.73 % 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: -2.30 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.006 0.001 PHE E 346 TYR 0.020 0.005 TYR C 310 ARG 0.004 0.001 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.381 Fit side-chains REVERT: A 338 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8310 (tt0) REVERT: B 314 ASP cc_start: 0.8853 (t70) cc_final: 0.8543 (t0) REVERT: B 338 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8364 (tm-30) REVERT: B 348 ASP cc_start: 0.8995 (t0) cc_final: 0.7537 (p0) REVERT: B 349 ARG cc_start: 0.8820 (mtt180) cc_final: 0.6379 (pmt-80) REVERT: B 379 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7540 (pmt170) REVERT: C 338 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8463 (tm-30) REVERT: C 349 ARG cc_start: 0.8903 (mtt180) cc_final: 0.6582 (pmt170) REVERT: C 379 ARG cc_start: 0.7947 (mtt180) cc_final: 0.7381 (pmt170) REVERT: D 349 ARG cc_start: 0.8774 (mtt180) cc_final: 0.6666 (mmm160) REVERT: D 379 ARG cc_start: 0.5312 (OUTLIER) cc_final: 0.3463 (mmt180) REVERT: E 349 ARG cc_start: 0.8764 (mtt180) cc_final: 0.6770 (mmm160) outliers start: 8 outliers final: 0 residues processed: 76 average time/residue: 1.5194 time to fit residues: 117.8420 Evaluate side-chains 71 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 362 HIS C 307 GLN C 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.103301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.093659 restraints weight = 4589.659| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.99 r_work: 0.3660 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2915 Z= 0.305 Angle : 0.596 5.573 3900 Z= 0.298 Chirality : 0.049 0.132 440 Planarity : 0.003 0.016 495 Dihedral : 4.998 16.650 385 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.42 % Allowed : 16.06 % Favored : 81.52 % 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: -2.15 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 330 PHE 0.005 0.001 PHE E 346 TYR 0.014 0.003 TYR C 310 ARG 0.003 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.343 Fit side-chains REVERT: A 338 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: B 314 ASP cc_start: 0.8928 (t70) cc_final: 0.8630 (t0) REVERT: B 338 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8346 (tm-30) REVERT: B 348 ASP cc_start: 0.8996 (t0) cc_final: 0.7548 (p0) REVERT: B 349 ARG cc_start: 0.8818 (mtt180) cc_final: 0.6517 (pmt-80) REVERT: B 379 ARG cc_start: 0.8033 (mtt180) cc_final: 0.7590 (pmt170) REVERT: C 338 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8416 (tm-30) REVERT: C 349 ARG cc_start: 0.8901 (mtt180) cc_final: 0.6659 (pmt-80) REVERT: C 379 ARG cc_start: 0.7954 (mtt180) cc_final: 0.7404 (pmt170) REVERT: D 349 ARG cc_start: 0.8799 (mtt180) cc_final: 0.6680 (mmm160) REVERT: D 379 ARG cc_start: 0.5357 (OUTLIER) cc_final: 0.3531 (mmt180) REVERT: E 349 ARG cc_start: 0.8776 (mtt180) cc_final: 0.6792 (mmm160) REVERT: E 379 ARG cc_start: 0.5218 (OUTLIER) cc_final: 0.3179 (mmt180) outliers start: 8 outliers final: 0 residues processed: 75 average time/residue: 1.5951 time to fit residues: 121.8866 Evaluate side-chains 74 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 28 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.102289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.092643 restraints weight = 4551.351| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.97 r_work: 0.3645 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2915 Z= 0.357 Angle : 0.612 5.660 3900 Z= 0.309 Chirality : 0.050 0.134 440 Planarity : 0.003 0.015 495 Dihedral : 5.019 16.470 385 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.12 % Allowed : 15.76 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.09 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.005 0.001 PHE D 378 TYR 0.015 0.004 TYR E 310 ARG 0.003 0.001 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.374 Fit side-chains REVERT: A 338 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8370 (tt0) REVERT: B 314 ASP cc_start: 0.8949 (t70) cc_final: 0.8647 (t0) REVERT: B 338 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8258 (tm-30) REVERT: B 348 ASP cc_start: 0.9002 (t0) cc_final: 0.7575 (p0) REVERT: B 349 ARG cc_start: 0.8816 (mtt180) cc_final: 0.6538 (pmt-80) REVERT: B 379 ARG cc_start: 0.8073 (mtt180) cc_final: 0.7629 (pmt170) REVERT: C 338 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8419 (tm-30) REVERT: C 349 ARG cc_start: 0.8918 (mtt180) cc_final: 0.6650 (pmt-80) REVERT: C 379 ARG cc_start: 0.8023 (mtt180) cc_final: 0.7472 (pmt170) REVERT: D 338 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8239 (tm-30) REVERT: D 349 ARG cc_start: 0.8768 (mtt180) cc_final: 0.6609 (mmm160) REVERT: D 379 ARG cc_start: 0.5417 (OUTLIER) cc_final: 0.3499 (mmt180) REVERT: E 349 ARG cc_start: 0.8781 (mtt180) cc_final: 0.6795 (mmm160) REVERT: E 379 ARG cc_start: 0.4997 (OUTLIER) cc_final: 0.3001 (mmt180) outliers start: 7 outliers final: 0 residues processed: 73 average time/residue: 1.5803 time to fit residues: 117.5728 Evaluate side-chains 75 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.105887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.096391 restraints weight = 4523.267| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.98 r_work: 0.3705 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2915 Z= 0.188 Angle : 0.542 5.879 3900 Z= 0.266 Chirality : 0.049 0.126 440 Planarity : 0.002 0.017 495 Dihedral : 4.739 16.012 385 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.82 % Allowed : 17.27 % Favored : 80.91 % 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: -2.01 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 362 PHE 0.004 0.001 PHE A 346 TYR 0.009 0.002 TYR C 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.396 Fit side-chains REVERT: A 338 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8367 (tt0) REVERT: B 314 ASP cc_start: 0.8948 (t70) cc_final: 0.8694 (t0) REVERT: B 338 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8264 (tm-30) REVERT: B 348 ASP cc_start: 0.8946 (t0) cc_final: 0.7489 (p0) REVERT: B 349 ARG cc_start: 0.8812 (mtt180) cc_final: 0.6538 (pmt-80) REVERT: B 379 ARG cc_start: 0.8062 (mtt180) cc_final: 0.7667 (pmt170) REVERT: C 338 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8405 (tm-30) REVERT: C 349 ARG cc_start: 0.8917 (mtt180) cc_final: 0.6642 (pmt-80) REVERT: C 379 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7479 (pmt170) REVERT: D 349 ARG cc_start: 0.8775 (mtt180) cc_final: 0.6664 (mmm160) REVERT: E 349 ARG cc_start: 0.8778 (mtt180) cc_final: 0.6758 (mmm160) REVERT: E 379 ARG cc_start: 0.4945 (OUTLIER) cc_final: 0.3089 (mmt180) outliers start: 6 outliers final: 1 residues processed: 73 average time/residue: 1.5769 time to fit residues: 117.3457 Evaluate side-chains 75 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 57.3931 > 50: distance: 4 - 9: 12.968 distance: 9 - 10: 6.544 distance: 9 - 212: 11.823 distance: 10 - 11: 5.994 distance: 10 - 13: 7.588 distance: 11 - 12: 4.326 distance: 13 - 14: 7.007 distance: 14 - 15: 6.039 distance: 14 - 16: 5.148 distance: 17 - 18: 10.065 distance: 18 - 19: 10.356 distance: 18 - 21: 3.128 distance: 19 - 20: 8.652 distance: 19 - 25: 8.010 distance: 21 - 22: 3.768 distance: 22 - 23: 5.917 distance: 22 - 24: 11.618 distance: 25 - 26: 15.076 distance: 26 - 27: 19.096 distance: 26 - 29: 14.202 distance: 27 - 28: 20.368 distance: 27 - 31: 11.567 distance: 29 - 30: 28.952 distance: 31 - 32: 5.411 distance: 32 - 33: 18.815 distance: 32 - 35: 11.792 distance: 33 - 34: 13.705 distance: 33 - 40: 20.896 distance: 35 - 36: 10.866 distance: 36 - 37: 18.403 distance: 37 - 38: 12.640 distance: 38 - 39: 28.682 distance: 40 - 41: 14.954 distance: 40 - 238: 20.513 distance: 41 - 42: 11.687 distance: 41 - 44: 13.881 distance: 42 - 43: 7.511 distance: 42 - 47: 23.026 distance: 43 - 251: 23.812 distance: 44 - 45: 11.451 distance: 44 - 46: 11.337 distance: 47 - 48: 20.562 distance: 48 - 49: 47.071 distance: 48 - 51: 29.170 distance: 49 - 50: 15.818 distance: 49 - 54: 31.436 distance: 51 - 52: 20.255 distance: 51 - 53: 20.993 distance: 54 - 55: 14.513 distance: 54 - 254: 19.768 distance: 55 - 56: 23.982 distance: 55 - 58: 18.412 distance: 56 - 57: 28.841 distance: 56 - 60: 12.410 distance: 57 - 264: 27.414 distance: 58 - 59: 12.873 distance: 60 - 61: 14.774 distance: 61 - 62: 18.842 distance: 61 - 64: 4.689 distance: 62 - 63: 4.839 distance: 62 - 69: 31.017 distance: 64 - 65: 6.947 distance: 66 - 67: 16.621 distance: 67 - 68: 21.464 distance: 69 - 70: 6.985 distance: 69 - 267: 8.556 distance: 70 - 71: 8.905 distance: 70 - 73: 11.756 distance: 71 - 72: 7.280 distance: 71 - 75: 19.411 distance: 73 - 74: 13.834 distance: 75 - 76: 9.151 distance: 76 - 77: 9.422 distance: 77 - 78: 38.771 distance: 77 - 79: 19.123