Starting phenix.real_space_refine on Sun Mar 10 15:12:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgh_16643/03_2024/8cgh_16643.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgh_16643/03_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_16643/03_2024/8cgh_16643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgh_16643/03_2024/8cgh_16643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgh_16643/03_2024/8cgh_16643.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgh_16643/03_2024/8cgh_16643.pdb" } 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 Residue "U PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 293": "NH1" <-> "NH2" Residue "A PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 293": "NH1" <-> "NH2" Residue "C PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 293": "NH1" <-> "NH2" Residue "D PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 293": "NH1" <-> "NH2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2710 Number of models: 1 Model: "" Number of chains: 5 Chain: "U" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 542 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} 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} Chain: "B" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 542 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "C" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 542 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "D" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 542 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Time building chain proxies: 1.71, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 0.96 Conformation dependent library (CDL) restraints added in 541.0 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: 0.38 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: 0.61 Time building geometry restraints manager: 1.05 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: 100.01 - 106.94: 120 106.94 - 113.87: 1191 113.87 - 120.79: 1295 120.79 - 127.72: 1029 127.72 - 134.65: 15 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 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: 0.720 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: 3.480 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.130 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.240 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.287 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: 1.0839 time to fit residues: 62.3832 Evaluate side-chains 51 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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: 7.9990 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 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: 0.9035 moved from start: 0.1616 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= 0.307 Angle : 0.896 6.352 3650 Z= 0.477 Chirality : 0.048 0.159 315 Planarity : 0.003 0.015 545 Dihedral : 6.027 18.633 400 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % 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: -5.16 (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 0.020 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 fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.293 Fit side-chains REVERT: B 337 MET cc_start: 0.8693 (mtp) cc_final: 0.8330 (mtt) outliers start: 2 outliers final: 0 residues processed: 47 average time/residue: 1.2613 time to fit residues: 60.7393 Evaluate side-chains 47 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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: 9.9990 chunk 24 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 36 optimal weight: 0.0980 chunk 39 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- 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: 0.9029 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2745 Z= 0.282 Angle : 0.853 7.438 3650 Z= 0.453 Chirality : 0.046 0.143 315 Planarity : 0.003 0.021 545 Dihedral : 5.656 18.270 400 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.40 % Allowed : 9.20 % Favored : 90.40 % 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: -5.07 (0.18), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.14), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 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 fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.297 Fit side-chains REVERT: B 337 MET cc_start: 0.8676 (mtp) cc_final: 0.8278 (mtt) outliers start: 1 outliers final: 0 residues processed: 50 average time/residue: 1.1711 time to fit residues: 60.0556 Evaluate side-chains 49 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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: 2.9990 chunk 17 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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: 0.9043 moved from start: 0.1851 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= 0.343 Angle : 0.918 8.619 3650 Z= 0.488 Chirality : 0.047 0.148 315 Planarity : 0.003 0.027 545 Dihedral : 5.833 19.087 400 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.40 % Allowed : 11.60 % Favored : 88.00 % 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: -5.08 (0.18), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.14), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP B 334 PHE 0.013 0.002 PHE B 289 ARG 0.000 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 51 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.295 Fit side-chains REVERT: B 337 MET cc_start: 0.8672 (mtp) cc_final: 0.8433 (mtm) outliers start: 1 outliers final: 0 residues processed: 50 average time/residue: 1.1824 time to fit residues: 60.6584 Evaluate side-chains 50 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- 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: 0.9045 moved from start: 0.1949 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= 0.348 Angle : 0.915 8.671 3650 Z= 0.487 Chirality : 0.046 0.147 315 Planarity : 0.003 0.029 545 Dihedral : 5.800 19.065 400 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.40 % Allowed : 13.20 % Favored : 86.40 % 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 : -3.83 (0.14), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 334 PHE 0.022 0.003 PHE C 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 51 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.306 Fit side-chains REVERT: B 337 MET cc_start: 0.8691 (mtp) cc_final: 0.8450 (mtm) outliers start: 1 outliers final: 1 residues processed: 50 average time/residue: 1.1808 time to fit residues: 60.5824 Evaluate side-chains 51 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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: 0.3980 chunk 38 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 37 optimal weight: 0.0010 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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: 0.8978 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2745 Z= 0.155 Angle : 0.684 7.563 3650 Z= 0.357 Chirality : 0.041 0.116 315 Planarity : 0.002 0.021 545 Dihedral : 5.044 15.344 400 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.40 % Allowed : 13.60 % Favored : 86.00 % 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: -4.93 (0.18), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.14), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 334 PHE 0.021 0.001 PHE C 283 ARG 0.000 0.000 ARG A 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 50 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.279 Fit side-chains REVERT: B 337 MET cc_start: 0.8617 (mtp) cc_final: 0.8352 (mtm) outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 1.1842 time to fit residues: 59.5021 Evaluate side-chains 48 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 38 optimal weight: 0.1980 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.0370 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 overall best weight: 1.6062 ------------------------------------------------------------------------------- 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: 0.8967 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2745 Z= 0.144 Angle : 0.655 8.010 3650 Z= 0.340 Chirality : 0.040 0.116 315 Planarity : 0.002 0.019 545 Dihedral : 4.780 14.729 400 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 14.40 % Favored : 85.60 % 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: -4.85 (0.18), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.14), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 334 PHE 0.023 0.002 PHE D 283 ARG 0.000 0.000 ARG B 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 50 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.278 Fit side-chains REVERT: B 337 MET cc_start: 0.8566 (mtp) cc_final: 0.8340 (mtm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 1.1718 time to fit residues: 60.1298 Evaluate side-chains 50 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.0370 chunk 30 optimal weight: 9.9990 chunk 35 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.0264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2745 Z= 0.163 Angle : 0.681 7.986 3650 Z= 0.356 Chirality : 0.041 0.116 315 Planarity : 0.002 0.021 545 Dihedral : 4.872 15.641 400 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.40 % Allowed : 13.60 % Favored : 86.00 % 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: -4.85 (0.18), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.14), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 334 PHE 0.023 0.002 PHE C 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 50 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.283 Fit side-chains REVERT: B 337 MET cc_start: 0.8578 (mtp) cc_final: 0.8357 (mtm) outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 1.2045 time to fit residues: 60.5181 Evaluate side-chains 49 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 0.0370 chunk 24 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.2105 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= 0.327 Angle : 0.871 8.992 3650 Z= 0.464 Chirality : 0.045 0.140 315 Planarity : 0.003 0.025 545 Dihedral : 5.542 19.029 400 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.40 % Allowed : 14.00 % Favored : 85.60 % 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: -4.93 (0.18), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.14), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 334 PHE 0.023 0.003 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 53 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.232 Fit side-chains REVERT: B 337 MET cc_start: 0.8660 (mtp) cc_final: 0.8268 (mtt) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 1.1509 time to fit residues: 61.3438 Evaluate side-chains 52 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- 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: 0.9032 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2745 Z= 0.302 Angle : 0.858 9.016 3650 Z= 0.456 Chirality : 0.045 0.138 315 Planarity : 0.003 0.023 545 Dihedral : 5.525 18.637 400 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 0.78 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: -4.93 (0.18), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.14), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 334 PHE 0.027 0.003 PHE D 283 ARG 0.000 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 fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.281 Fit side-chains REVERT: B 337 MET cc_start: 0.8660 (mtp) cc_final: 0.8260 (mtt) outliers start: 1 outliers final: 1 residues processed: 54 average time/residue: 1.1159 time to fit residues: 61.9044 Evaluate side-chains 54 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.102459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.082206 restraints weight = 2900.325| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.96 r_work: 0.2998 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.2104 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= 0.351 Angle : 0.913 9.283 3650 Z= 0.486 Chirality : 0.046 0.145 315 Planarity : 0.003 0.024 545 Dihedral : 5.694 18.965 400 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.40 % Allowed : 16.40 % Favored : 83.20 % 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: -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 0.029 0.003 PHE A 283 ARG 0.001 0.000 ARG U 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1449.19 seconds wall clock time: 26 minutes 24.73 seconds (1584.73 seconds total)