Starting phenix.real_space_refine on Thu Nov 14 00:22:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgh_16643/11_2024/8cgh_16643.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgh_16643/11_2024/8cgh_16643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgh_16643/11_2024/8cgh_16643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgh_16643/11_2024/8cgh_16643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgh_16643/11_2024/8cgh_16643.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgh_16643/11_2024/8cgh_16643.cif" } resolution = 2.68 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= 0.004 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 40 5.16 5 C 1590 2.51 5 N 530 2.21 5 O 550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2710 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 542 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Restraints were copied for chains: C, B, U, D Time building chain proxies: 1.55, per 1000 atoms: 0.57 Number of scatterers: 2710 At special positions: 0 Unit cell: (72.24, 69.66, 45.58, 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 40 16.00 O 550 8.00 N 530 7.00 C 1590 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: 0.65 Conformation dependent library (CDL) restraints added in 381.9 milliseconds 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 590 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 38.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 297 through 303 removed outlier: 9.185A pdb=" N GLY A 298 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 10.464A pdb=" N ASN B 301 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLY A 300 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLN B 303 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASN A 302 " --> pdb=" O GLN B 303 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY B 298 " --> pdb=" O ALA U 297 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU U 299 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLY B 300 " --> pdb=" O LEU U 299 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN U 301 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N GLY U 298 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 10.464A pdb=" N ASN C 301 " --> pdb=" O GLY U 298 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLY U 300 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLN C 303 " --> pdb=" O GLY U 300 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASN U 302 " --> pdb=" O GLN C 303 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N GLY C 298 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 10.464A pdb=" N ASN D 301 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLY C 300 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLN D 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASN C 302 " --> pdb=" O GLN D 303 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 306 through 308 removed outlier: 6.660A pdb=" N ASN U 306 " --> pdb=" O MET B 307 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.698A pdb=" N MET A 311 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N GLY B 314 " --> pdb=" O MET A 311 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE A 313 " --> pdb=" O GLY B 314 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N PHE B 316 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N ALA A 315 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ILE B 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N SER A 317 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER B 317 " --> pdb=" O PHE U 316 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE U 318 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N MET U 311 " --> pdb=" O ASN C 312 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N GLY C 314 " --> pdb=" O MET U 311 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE U 313 " --> pdb=" O GLY C 314 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N PHE C 316 " --> pdb=" O PHE U 313 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N ALA U 315 " --> pdb=" O PHE C 316 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ILE C 318 " --> pdb=" O ALA U 315 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N SER U 317 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N MET C 311 " --> pdb=" O ASN D 312 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N GLY D 314 " --> pdb=" O MET C 311 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE C 313 " --> pdb=" O GLY D 314 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N PHE D 316 " --> pdb=" O PHE C 313 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N ALA C 315 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE D 318 " --> pdb=" O ALA C 315 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N SER C 317 " --> pdb=" O ILE D 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 327 removed outlier: 6.762A pdb=" N ALA A 321 " --> pdb=" O MET B 322 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N ALA B 324 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N MET A 323 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ALA B 326 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA A 325 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA U 321 " --> pdb=" O MET C 322 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N ALA C 324 " --> pdb=" O ALA U 321 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N MET U 323 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ALA C 326 " --> pdb=" O MET U 323 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA U 325 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA C 321 " --> pdb=" O MET D 322 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ALA D 324 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N MET C 323 " --> pdb=" O ALA D 324 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ALA D 326 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA C 325 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 330 through 331 removed outlier: 6.634A pdb=" N LEU U 330 " --> pdb=" O GLN B 331 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 334 through 336 removed outlier: 7.059A pdb=" N MET B 336 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N TRP U 334 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET C 336 " --> pdb=" O GLY U 335 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N MET D 336 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 342 through 347 removed outlier: 7.086A pdb=" N GLN B 343 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLN A 344 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLN U 343 " --> pdb=" O GLN B 344 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N GLN B 346 " --> pdb=" O GLN U 343 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASN U 345 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLN C 343 " --> pdb=" O SER U 342 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLN U 344 " --> pdb=" O GLN C 343 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLN D 343 " --> pdb=" O SER C 342 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLN C 344 " --> pdb=" O GLN D 343 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.839A pdb=" N ASN U 353 " --> pdb=" O GLN B 354 " (cutoff:3.500A) 40 hydrogen bonds defined for protein. 120 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: 0.62 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1001 1.35 - 1.48: 649 1.48 - 1.61: 1015 1.61 - 1.74: 0 1.74 - 1.87: 80 Bond restraints: 2745 Sorted by residual: bond pdb=" CG MET C 359 " pdb=" SD MET C 359 " ideal model delta sigma weight residual 1.803 1.866 -0.063 2.50e-02 1.60e+03 6.35e+00 bond pdb=" CG MET A 359 " pdb=" SD MET A 359 " ideal model delta sigma weight residual 1.803 1.866 -0.063 2.50e-02 1.60e+03 6.26e+00 bond pdb=" CG MET D 359 " pdb=" SD MET D 359 " ideal model delta sigma weight residual 1.803 1.866 -0.063 2.50e-02 1.60e+03 6.26e+00 bond pdb=" CG MET B 359 " pdb=" SD MET B 359 " ideal model delta sigma weight residual 1.803 1.865 -0.062 2.50e-02 1.60e+03 6.25e+00 bond pdb=" CG MET U 359 " pdb=" SD MET U 359 " ideal model delta sigma weight residual 1.803 1.865 -0.062 2.50e-02 1.60e+03 6.22e+00 ... (remaining 2740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 2325 1.30 - 2.61: 1022 2.61 - 3.91: 233 3.91 - 5.21: 41 5.21 - 6.52: 29 Bond angle restraints: 3650 Sorted by residual: angle pdb=" N SER D 333 " pdb=" CA SER D 333 " pdb=" C SER D 333 " ideal model delta sigma weight residual 108.52 114.81 -6.29 1.52e+00 4.33e-01 1.71e+01 angle pdb=" N SER U 333 " pdb=" CA SER U 333 " pdb=" C SER U 333 " ideal model delta sigma weight residual 108.52 114.79 -6.27 1.52e+00 4.33e-01 1.70e+01 angle pdb=" N SER A 333 " pdb=" CA SER A 333 " pdb=" C SER A 333 " ideal model delta sigma weight residual 108.52 114.78 -6.26 1.52e+00 4.33e-01 1.70e+01 angle pdb=" N SER B 333 " pdb=" CA SER B 333 " pdb=" C SER B 333 " ideal model delta sigma weight residual 108.52 114.78 -6.26 1.52e+00 4.33e-01 1.70e+01 angle pdb=" N SER C 333 " pdb=" CA SER C 333 " pdb=" C SER C 333 " ideal model delta sigma weight residual 108.52 114.77 -6.25 1.52e+00 4.33e-01 1.69e+01 ... (remaining 3645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.23: 1325 14.23 - 28.47: 155 28.47 - 42.70: 45 42.70 - 56.93: 15 56.93 - 71.16: 20 Dihedral angle restraints: 1560 sinusoidal: 575 harmonic: 985 Sorted by residual: dihedral pdb=" CA GLN C 327 " pdb=" C GLN C 327 " pdb=" N ALA C 328 " pdb=" CA ALA C 328 " ideal model delta harmonic sigma weight residual -180.00 -156.02 -23.98 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA GLN B 327 " pdb=" C GLN B 327 " pdb=" N ALA B 328 " pdb=" CA ALA B 328 " ideal model delta harmonic sigma weight residual 180.00 -156.08 -23.92 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA GLN U 327 " pdb=" C GLN U 327 " pdb=" N ALA U 328 " pdb=" CA ALA U 328 " ideal model delta harmonic sigma weight residual -180.00 -156.09 -23.91 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 1557 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.042: 88 0.042 - 0.083: 116 0.083 - 0.124: 91 0.124 - 0.165: 5 0.165 - 0.206: 15 Chirality restraints: 315 Sorted by residual: chirality pdb=" CA LEU D 299 " pdb=" N LEU D 299 " pdb=" C LEU D 299 " pdb=" CB LEU D 299 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA LEU C 299 " pdb=" N LEU C 299 " pdb=" C LEU C 299 " pdb=" CB LEU C 299 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA LEU B 299 " pdb=" N LEU B 299 " pdb=" C LEU B 299 " pdb=" CB LEU B 299 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 312 not shown) Planarity restraints: 545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 334 " -0.024 2.00e-02 2.50e+03 1.66e-02 6.92e+00 pdb=" CG TRP D 334 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP D 334 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP D 334 " 0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP D 334 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP D 334 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP D 334 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 334 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 334 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 334 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 334 " -0.024 2.00e-02 2.50e+03 1.66e-02 6.89e+00 pdb=" CG TRP C 334 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 334 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP C 334 " 0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP C 334 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP C 334 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 334 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 334 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 334 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 334 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 334 " -0.024 2.00e-02 2.50e+03 1.66e-02 6.88e+00 pdb=" CG TRP B 334 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 334 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 334 " 0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP B 334 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 334 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 334 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 334 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 334 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 334 " -0.000 2.00e-02 2.50e+03 ... (remaining 542 not shown) Histogram of nonbonded interaction distances: 2.63 - 3.08: 1695 3.08 - 3.54: 2462 3.54 - 3.99: 3975 3.99 - 4.45: 4792 4.45 - 4.90: 7592 Nonbonded interactions: 20516 Sorted by model distance: nonbonded pdb=" N MET B 337 " pdb=" O MET B 337 " model vdw 2.629 2.496 nonbonded pdb=" N MET U 337 " pdb=" O MET U 337 " model vdw 2.629 2.496 nonbonded pdb=" N MET C 337 " pdb=" O MET C 337 " model vdw 2.629 2.496 nonbonded pdb=" N MET A 337 " pdb=" O MET A 337 " model vdw 2.629 2.496 nonbonded pdb=" N MET D 337 " pdb=" O MET D 337 " model vdw 2.630 2.496 ... (remaining 20511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'U' } 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: 0.860 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.830 Find NCS groups from input model: 0.090 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:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9106 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 : 0.011 0.063 2745 Z= 0.719 Angle : 1.540 6.517 3650 Z= 1.009 Chirality : 0.082 0.206 315 Planarity : 0.007 0.035 545 Dihedral : 16.669 71.159 970 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 2.56 % Allowed : 5.13 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % 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: -5.57 (0.17), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.24 (0.13), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.012 TRP C 334 PHE 0.014 0.005 PHE A 289 ARG 0.000 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.295 Fit side-chains REVERT: B 337 MET cc_start: 0.8612 (mtp) cc_final: 0.8269 (mtt) REVERT: D 359 MET cc_start: 0.9168 (ttm) cc_final: 0.8910 (ttm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 1.1150 time to fit residues: 64.1618 Evaluate side-chains 51 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2745 Z= 0.306 Angle : 0.898 6.322 3650 Z= 0.478 Chirality : 0.048 0.159 315 Planarity : 0.003 0.015 545 Dihedral : 6.037 18.668 400 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.80 % Allowed : 7.60 % Favored : 91.60 % 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: -5.17 (0.18), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.14), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP A 334 PHE 0.009 0.002 PHE D 289 ARG 0.000 0.000 ARG U 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.266 Fit side-chains REVERT: B 337 MET cc_start: 0.8694 (mtp) cc_final: 0.8329 (mtt) outliers start: 2 outliers final: 0 residues processed: 47 average time/residue: 1.2851 time to fit residues: 61.8594 Evaluate side-chains 47 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 36 optimal weight: 0.0470 chunk 39 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2745 Z= 0.252 Angle : 0.818 7.245 3650 Z= 0.433 Chirality : 0.045 0.137 315 Planarity : 0.003 0.019 545 Dihedral : 5.548 17.782 400 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.80 % Allowed : 8.40 % Favored : 90.80 % 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: -5.04 (0.18), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.14), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 334 PHE 0.018 0.002 PHE C 283 ARG 0.000 0.000 ARG U 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.287 Fit side-chains REVERT: B 337 MET cc_start: 0.8672 (mtp) cc_final: 0.8373 (mtt) outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 1.3342 time to fit residues: 66.9751 Evaluate side-chains 48 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 2745 Z= 0.438 Angle : 1.009 9.057 3650 Z= 0.538 Chirality : 0.049 0.158 315 Planarity : 0.004 0.030 545 Dihedral : 6.061 20.159 400 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.80 % Allowed : 10.00 % Favored : 89.20 % 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: -5.09 (0.18), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.14), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP B 334 PHE 0.014 0.003 PHE B 289 ARG 0.001 0.000 ARG U 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.305 Fit side-chains REVERT: B 337 MET cc_start: 0.8731 (mtp) cc_final: 0.8337 (mtt) outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 1.2322 time to fit residues: 64.4708 Evaluate side-chains 52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 340 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2745 Z= 0.370 Angle : 0.938 8.667 3650 Z= 0.500 Chirality : 0.047 0.149 315 Planarity : 0.003 0.031 545 Dihedral : 5.860 19.124 400 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.40 % Allowed : 12.80 % Favored : 86.80 % 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: -5.05 (0.18), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.14), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP B 334 PHE 0.025 0.003 PHE A 283 ARG 0.000 0.000 ARG U 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.313 Fit side-chains REVERT: B 337 MET cc_start: 0.8687 (mtp) cc_final: 0.8426 (mtm) outliers start: 1 outliers final: 1 residues processed: 51 average time/residue: 1.2166 time to fit residues: 63.6532 Evaluate side-chains 52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 340 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 2745 Z= 0.395 Angle : 0.965 8.929 3650 Z= 0.515 Chirality : 0.047 0.154 315 Planarity : 0.004 0.031 545 Dihedral : 5.945 19.461 400 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.80 % Allowed : 14.80 % Favored : 84.40 % 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: -5.04 (0.18), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.14), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP B 334 PHE 0.021 0.003 PHE C 283 ARG 0.001 0.000 ARG U 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.290 Fit side-chains REVERT: B 337 MET cc_start: 0.8711 (mtp) cc_final: 0.8336 (mtt) outliers start: 2 outliers final: 1 residues processed: 50 average time/residue: 1.2415 time to fit residues: 63.6733 Evaluate side-chains 51 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 38 optimal weight: 0.1980 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2745 Z= 0.180 Angle : 0.723 7.626 3650 Z= 0.379 Chirality : 0.042 0.121 315 Planarity : 0.003 0.025 545 Dihedral : 5.212 16.200 400 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.40 % Allowed : 15.20 % Favored : 84.40 % 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: -4.91 (0.18), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.14), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 334 PHE 0.025 0.002 PHE A 283 ARG 0.000 0.000 ARG U 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.313 Fit side-chains REVERT: B 337 MET cc_start: 0.8618 (mtp) cc_final: 0.8354 (mtm) outliers start: 1 outliers final: 1 residues processed: 51 average time/residue: 1.1499 time to fit residues: 60.1936 Evaluate side-chains 51 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 overall best weight: 5.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2745 Z= 0.347 Angle : 0.903 9.242 3650 Z= 0.481 Chirality : 0.046 0.142 315 Planarity : 0.003 0.028 545 Dihedral : 5.736 19.115 400 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.80 % Allowed : 14.40 % Favored : 84.80 % 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: -4.96 (0.18), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.14), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 334 PHE 0.027 0.003 PHE A 283 ARG 0.000 0.000 ARG U 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.290 Fit side-chains REVERT: B 337 MET cc_start: 0.8683 (mtp) cc_final: 0.8444 (mtm) outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 1.1455 time to fit residues: 61.1422 Evaluate side-chains 54 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.0000 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 overall best weight: 4.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2745 Z= 0.307 Angle : 0.872 9.056 3650 Z= 0.462 Chirality : 0.045 0.139 315 Planarity : 0.003 0.029 545 Dihedral : 5.642 18.577 400 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.40 % Allowed : 15.20 % Favored : 84.40 % 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: -4.95 (0.18), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.14), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 334 PHE 0.024 0.002 PHE C 283 ARG 0.000 0.000 ARG U 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.331 Fit side-chains REVERT: B 337 MET cc_start: 0.8662 (mtp) cc_final: 0.8274 (mtt) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 1.1851 time to fit residues: 64.4836 Evaluate side-chains 54 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2745 Z= 0.362 Angle : 0.929 9.389 3650 Z= 0.494 Chirality : 0.047 0.147 315 Planarity : 0.003 0.029 545 Dihedral : 5.798 19.249 400 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.80 % Allowed : 15.20 % Favored : 84.00 % 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: -4.97 (0.18), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.14), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP B 334 PHE 0.028 0.003 PHE A 283 ARG 0.001 0.000 ARG U 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.293 Fit side-chains REVERT: B 337 MET cc_start: 0.8667 (mtp) cc_final: 0.8426 (mtm) outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 1.2086 time to fit residues: 65.6850 Evaluate side-chains 55 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain D residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.104659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.084195 restraints weight = 2992.131| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.01 r_work: 0.3043 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2745 Z= 0.236 Angle : 0.799 8.789 3650 Z= 0.421 Chirality : 0.044 0.129 315 Planarity : 0.003 0.028 545 Dihedral : 5.420 17.324 400 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.40 % Allowed : 15.60 % Favored : 84.00 % 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: -4.90 (0.18), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.14), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 334 PHE 0.023 0.002 PHE C 283 ARG 0.000 0.000 ARG U 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1513.05 seconds wall clock time: 27 minutes 37.03 seconds (1657.03 seconds total)