Starting phenix.real_space_refine on Wed Mar 4 08:11:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w3y_32296/03_2026/7w3y_32296.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w3y_32296/03_2026/7w3y_32296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w3y_32296/03_2026/7w3y_32296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w3y_32296/03_2026/7w3y_32296.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w3y_32296/03_2026/7w3y_32296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w3y_32296/03_2026/7w3y_32296.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 80 5.16 5 C 7876 2.51 5 N 1996 2.21 5 O 2136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12088 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3022 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 14, 'TRANS': 358} Chain breaks: 1 Restraints were copied for chains: B, C, D Time building chain proxies: 2.43, per 1000 atoms: 0.20 Number of scatterers: 12088 At special positions: 0 Unit cell: (116.61, 116.61, 125.736, 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 80 16.00 O 2136 8.00 N 1996 7.00 C 7876 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: 0.75 Conformation dependent library (CDL) restraints added in 485.6 milliseconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2824 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 4 sheets defined 74.0% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 69 through 75 removed outlier: 3.598A pdb=" N GLU A 72 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.522A pdb=" N VAL A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 121 Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 129 through 132 Processing helix chain 'A' and resid 133 through 147 Processing helix chain 'A' and resid 165 through 175 removed outlier: 4.094A pdb=" N GLU A 174 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 203 removed outlier: 3.856A pdb=" N VAL A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 222 through 247 removed outlier: 3.761A pdb=" N LEU A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 257 removed outlier: 3.530A pdb=" N ILE A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.551A pdb=" N ILE A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) Proline residue: A 269 - end of helix removed outlier: 3.711A pdb=" N GLY A 273 " --> pdb=" O PRO A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 293 Processing helix chain 'A' and resid 294 through 302 removed outlier: 4.340A pdb=" N LYS A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 316 removed outlier: 4.190A pdb=" N ARG A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 343 Processing helix chain 'A' and resid 353 through 366 removed outlier: 4.138A pdb=" N TRP A 359 " --> pdb=" O PRO A 355 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 396 removed outlier: 3.543A pdb=" N LEU A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 426 removed outlier: 4.615A pdb=" N VAL A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 69 through 75 removed outlier: 3.598A pdb=" N GLU B 72 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 101 removed outlier: 3.522A pdb=" N VAL B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 121 Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 133 through 147 Processing helix chain 'B' and resid 165 through 175 removed outlier: 4.094A pdb=" N GLU B 174 " --> pdb=" O TRP B 170 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 203 removed outlier: 3.856A pdb=" N VAL B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 222 through 247 removed outlier: 3.761A pdb=" N LEU B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 removed outlier: 3.530A pdb=" N ILE B 255 " --> pdb=" O ARG B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.552A pdb=" N ILE B 261 " --> pdb=" O SER B 257 " (cutoff:3.500A) Proline residue: B 269 - end of helix removed outlier: 3.711A pdb=" N GLY B 273 " --> pdb=" O PRO B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 Processing helix chain 'B' and resid 294 through 302 removed outlier: 4.340A pdb=" N LYS B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 300 " --> pdb=" O ILE B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 316 removed outlier: 4.189A pdb=" N ARG B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 343 Processing helix chain 'B' and resid 353 through 366 removed outlier: 4.137A pdb=" N TRP B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 366 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 396 removed outlier: 3.543A pdb=" N LEU B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 426 removed outlier: 4.615A pdb=" N VAL B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 69 through 75 removed outlier: 3.598A pdb=" N GLU C 72 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 removed outlier: 3.522A pdb=" N VAL C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 121 Processing helix chain 'C' and resid 124 through 128 Processing helix chain 'C' and resid 129 through 132 Processing helix chain 'C' and resid 133 through 147 Processing helix chain 'C' and resid 165 through 175 removed outlier: 4.094A pdb=" N GLU C 174 " --> pdb=" O TRP C 170 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 203 removed outlier: 3.856A pdb=" N VAL C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 192 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE C 193 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 222 through 247 removed outlier: 3.761A pdb=" N LEU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 257 removed outlier: 3.530A pdb=" N ILE C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 276 removed outlier: 3.551A pdb=" N ILE C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) Proline residue: C 269 - end of helix removed outlier: 3.711A pdb=" N GLY C 273 " --> pdb=" O PRO C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 293 Processing helix chain 'C' and resid 294 through 302 removed outlier: 4.340A pdb=" N LYS C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE C 300 " --> pdb=" O ILE C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 316 removed outlier: 4.190A pdb=" N ARG C 308 " --> pdb=" O SER C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 343 Processing helix chain 'C' and resid 353 through 366 removed outlier: 4.138A pdb=" N TRP C 359 " --> pdb=" O PRO C 355 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR C 360 " --> pdb=" O ALA C 356 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C 366 " --> pdb=" O ILE C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 396 removed outlier: 3.543A pdb=" N LEU C 389 " --> pdb=" O SER C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 426 removed outlier: 4.615A pdb=" N VAL C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 69 through 75 removed outlier: 3.598A pdb=" N GLU D 72 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.522A pdb=" N VAL D 94 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 121 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 129 through 132 Processing helix chain 'D' and resid 133 through 147 Processing helix chain 'D' and resid 165 through 175 removed outlier: 4.094A pdb=" N GLU D 174 " --> pdb=" O TRP D 170 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 203 removed outlier: 3.856A pdb=" N VAL D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE D 192 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 Processing helix chain 'D' and resid 222 through 247 removed outlier: 3.761A pdb=" N LEU D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 257 removed outlier: 3.530A pdb=" N ILE D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 276 removed outlier: 3.551A pdb=" N ILE D 261 " --> pdb=" O SER D 257 " (cutoff:3.500A) Proline residue: D 269 - end of helix removed outlier: 3.711A pdb=" N GLY D 273 " --> pdb=" O PRO D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 293 Processing helix chain 'D' and resid 294 through 302 removed outlier: 4.340A pdb=" N LYS D 299 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE D 300 " --> pdb=" O ILE D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 316 removed outlier: 4.190A pdb=" N ARG D 308 " --> pdb=" O SER D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 343 Processing helix chain 'D' and resid 353 through 366 removed outlier: 4.138A pdb=" N TRP D 359 " --> pdb=" O PRO D 355 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR D 360 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR D 366 " --> pdb=" O ILE D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 396 removed outlier: 3.543A pdb=" N LEU D 389 " --> pdb=" O SER D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 426 removed outlier: 4.615A pdb=" N VAL D 401 " --> pdb=" O LEU D 397 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 46 Processing sheet with id=AA2, first strand: chain 'B' and resid 41 through 46 Processing sheet with id=AA3, first strand: chain 'C' and resid 41 through 46 Processing sheet with id=AA4, first strand: chain 'D' and resid 41 through 46 732 hydrogen bonds defined for protein. 2064 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: 1.86 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3744 1.34 - 1.46: 3128 1.46 - 1.58: 5396 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 12388 Sorted by residual: bond pdb=" C PHE A 292 " pdb=" N ARG A 293 " ideal model delta sigma weight residual 1.333 1.310 0.023 1.56e-02 4.11e+03 2.26e+00 bond pdb=" C PHE D 292 " pdb=" N ARG D 293 " ideal model delta sigma weight residual 1.333 1.310 0.023 1.56e-02 4.11e+03 2.26e+00 bond pdb=" C PHE C 292 " pdb=" N ARG C 293 " ideal model delta sigma weight residual 1.333 1.310 0.023 1.56e-02 4.11e+03 2.26e+00 bond pdb=" C PHE B 292 " pdb=" N ARG B 293 " ideal model delta sigma weight residual 1.333 1.310 0.023 1.56e-02 4.11e+03 2.23e+00 bond pdb=" CA VAL B 205 " pdb=" CB VAL B 205 " ideal model delta sigma weight residual 1.537 1.521 0.016 1.29e-02 6.01e+03 1.53e+00 ... (remaining 12383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 16479 2.09 - 4.19: 261 4.19 - 6.28: 20 6.28 - 8.37: 0 8.37 - 10.47: 4 Bond angle restraints: 16764 Sorted by residual: angle pdb=" N TYR A 108 " pdb=" CA TYR A 108 " pdb=" C TYR A 108 " ideal model delta sigma weight residual 111.28 114.88 -3.60 1.09e+00 8.42e-01 1.09e+01 angle pdb=" N TYR C 108 " pdb=" CA TYR C 108 " pdb=" C TYR C 108 " ideal model delta sigma weight residual 111.28 114.88 -3.60 1.09e+00 8.42e-01 1.09e+01 angle pdb=" N TYR D 108 " pdb=" CA TYR D 108 " pdb=" C TYR D 108 " ideal model delta sigma weight residual 111.28 114.88 -3.60 1.09e+00 8.42e-01 1.09e+01 angle pdb=" C PRO A 398 " pdb=" N VAL A 399 " pdb=" CA VAL A 399 " ideal model delta sigma weight residual 120.43 123.59 -3.16 9.60e-01 1.09e+00 1.08e+01 angle pdb=" C PRO C 398 " pdb=" N VAL C 399 " pdb=" CA VAL C 399 " ideal model delta sigma weight residual 120.43 123.59 -3.16 9.60e-01 1.09e+00 1.08e+01 ... (remaining 16759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.49: 6391 14.49 - 28.98: 709 28.98 - 43.46: 172 43.46 - 57.95: 36 57.95 - 72.44: 8 Dihedral angle restraints: 7316 sinusoidal: 2924 harmonic: 4392 Sorted by residual: dihedral pdb=" CA ARG C 107 " pdb=" C ARG C 107 " pdb=" N TYR C 108 " pdb=" CA TYR C 108 " ideal model delta harmonic sigma weight residual 180.00 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ARG D 107 " pdb=" C ARG D 107 " pdb=" N TYR D 108 " pdb=" CA TYR D 108 " ideal model delta harmonic sigma weight residual 180.00 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ARG A 107 " pdb=" C ARG A 107 " pdb=" N TYR A 108 " pdb=" CA TYR A 108 " ideal model delta harmonic sigma weight residual -180.00 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 7313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 879 0.027 - 0.055: 609 0.055 - 0.082: 252 0.082 - 0.109: 111 0.109 - 0.137: 21 Chirality restraints: 1872 Sorted by residual: chirality pdb=" CA PHE D 383 " pdb=" N PHE D 383 " pdb=" C PHE D 383 " pdb=" CB PHE D 383 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA PHE A 383 " pdb=" N PHE A 383 " pdb=" C PHE A 383 " pdb=" CB PHE A 383 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA PHE C 383 " pdb=" N PHE C 383 " pdb=" C PHE C 383 " pdb=" CB PHE C 383 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 1869 not shown) Planarity restraints: 2096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 354 " 0.029 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO B 355 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 355 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 355 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 355 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 354 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO C 355 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 355 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 355 " 0.024 5.00e-02 4.00e+02 ... (remaining 2093 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 203 2.67 - 3.23: 13004 3.23 - 3.79: 19104 3.79 - 4.34: 25124 4.34 - 4.90: 40817 Nonbonded interactions: 98252 Sorted by model distance: nonbonded pdb=" OG SER A 68 " pdb=" OE1 GLU A 70 " model vdw 2.117 3.040 nonbonded pdb=" OG SER C 68 " pdb=" OE1 GLU C 70 " model vdw 2.117 3.040 nonbonded pdb=" OG SER D 68 " pdb=" OE1 GLU D 70 " model vdw 2.117 3.040 nonbonded pdb=" OG SER B 68 " pdb=" OE1 GLU B 70 " model vdw 2.117 3.040 nonbonded pdb=" OG1 THR B 231 " pdb=" OH TYR B 270 " model vdw 2.170 3.040 ... (remaining 98247 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.070 Find NCS groups from input model: 0.090 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:9.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 : 0.006 0.039 12388 Z= 0.267 Angle : 0.684 10.467 16764 Z= 0.405 Chirality : 0.044 0.137 1872 Planarity : 0.004 0.043 2096 Dihedral : 13.233 72.441 4492 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.91 % Allowed : 6.36 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.20), residues: 1476 helix: -1.61 (0.15), residues: 992 sheet: -5.29 (0.29), residues: 40 loop : -2.99 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 426 TYR 0.019 0.001 TYR C 186 PHE 0.013 0.001 PHE B 383 TRP 0.009 0.002 TRP B 170 HIS 0.002 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00602 (12388) covalent geometry : angle 0.68356 (16764) hydrogen bonds : bond 0.13820 ( 732) hydrogen bonds : angle 5.31814 ( 2064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 264 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.6943 (t80) cc_final: 0.6537 (t80) REVERT: A 104 HIS cc_start: 0.8100 (m-70) cc_final: 0.7698 (m-70) REVERT: A 140 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8357 (ptmt) REVERT: A 259 MET cc_start: 0.8075 (mmm) cc_final: 0.7682 (mmm) REVERT: A 263 ASP cc_start: 0.8436 (m-30) cc_final: 0.8118 (m-30) REVERT: B 91 PHE cc_start: 0.6852 (t80) cc_final: 0.6512 (t80) REVERT: B 104 HIS cc_start: 0.8134 (m-70) cc_final: 0.7591 (m-70) REVERT: B 140 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8481 (ptmt) REVERT: B 259 MET cc_start: 0.8045 (mmm) cc_final: 0.7631 (mmm) REVERT: B 263 ASP cc_start: 0.8346 (m-30) cc_final: 0.8036 (m-30) REVERT: C 91 PHE cc_start: 0.6975 (t80) cc_final: 0.6566 (t80) REVERT: C 104 HIS cc_start: 0.8121 (m-70) cc_final: 0.7756 (m-70) REVERT: C 140 LYS cc_start: 0.8575 (mtmt) cc_final: 0.8369 (ptmt) REVERT: C 259 MET cc_start: 0.8090 (mmm) cc_final: 0.7679 (mmm) REVERT: C 263 ASP cc_start: 0.8421 (m-30) cc_final: 0.8102 (m-30) REVERT: D 91 PHE cc_start: 0.6964 (t80) cc_final: 0.6561 (t80) REVERT: D 104 HIS cc_start: 0.8099 (m-70) cc_final: 0.7696 (m-70) REVERT: D 140 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8365 (ptmt) REVERT: D 259 MET cc_start: 0.8091 (mmm) cc_final: 0.7679 (mmm) REVERT: D 263 ASP cc_start: 0.8453 (m-30) cc_final: 0.8132 (m-30) outliers start: 12 outliers final: 6 residues processed: 268 average time/residue: 0.6599 time to fit residues: 189.4437 Evaluate side-chains 198 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 192 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 275 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 ASN A 143 ASN B 76 ASN B 96 ASN B 143 ASN B 405 ASN B 413 ASN C 45 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 143 ASN C 413 ASN D 45 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN D 143 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.153854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.092596 restraints weight = 20502.674| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.71 r_work: 0.3094 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12388 Z= 0.183 Angle : 0.620 9.572 16764 Z= 0.327 Chirality : 0.043 0.145 1872 Planarity : 0.005 0.054 2096 Dihedral : 4.734 34.661 1688 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.20 % Allowed : 17.42 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.22), residues: 1476 helix: -0.45 (0.16), residues: 1000 sheet: None (None), residues: 0 loop : -2.36 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 139 TYR 0.020 0.002 TYR C 186 PHE 0.021 0.001 PHE B 185 TRP 0.009 0.002 TRP C 359 HIS 0.002 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00425 (12388) covalent geometry : angle 0.61970 (16764) hydrogen bonds : bond 0.04529 ( 732) hydrogen bonds : angle 4.18960 ( 2064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 210 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7046 (t80) cc_final: 0.6668 (t80) REVERT: A 104 HIS cc_start: 0.7994 (m-70) cc_final: 0.7507 (m-70) REVERT: A 133 TYR cc_start: 0.4985 (t80) cc_final: 0.4725 (t80) REVERT: A 235 MET cc_start: 0.8242 (ttm) cc_final: 0.7976 (ttp) REVERT: A 240 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8071 (tm-30) REVERT: A 259 MET cc_start: 0.8347 (mmm) cc_final: 0.7875 (mmm) REVERT: A 263 ASP cc_start: 0.8940 (m-30) cc_final: 0.8634 (m-30) REVERT: B 91 PHE cc_start: 0.6896 (t80) cc_final: 0.6656 (t80) REVERT: B 104 HIS cc_start: 0.7978 (m-70) cc_final: 0.7449 (m-70) REVERT: B 133 TYR cc_start: 0.5006 (t80) cc_final: 0.4674 (t80) REVERT: B 136 TYR cc_start: 0.8343 (t80) cc_final: 0.8083 (t80) REVERT: B 240 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8061 (tm-30) REVERT: B 259 MET cc_start: 0.8350 (mmm) cc_final: 0.7897 (mmm) REVERT: B 263 ASP cc_start: 0.8890 (m-30) cc_final: 0.8617 (m-30) REVERT: B 412 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7642 (tm-30) REVERT: C 91 PHE cc_start: 0.7094 (t80) cc_final: 0.6751 (t80) REVERT: C 104 HIS cc_start: 0.8116 (m-70) cc_final: 0.7631 (m-70) REVERT: C 133 TYR cc_start: 0.4985 (t80) cc_final: 0.4731 (t80) REVERT: C 240 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8046 (tm-30) REVERT: C 259 MET cc_start: 0.8364 (mmm) cc_final: 0.7970 (mmm) REVERT: C 263 ASP cc_start: 0.8942 (m-30) cc_final: 0.8684 (m-30) REVERT: C 410 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.7779 (t80) REVERT: D 91 PHE cc_start: 0.7085 (t80) cc_final: 0.6743 (t80) REVERT: D 104 HIS cc_start: 0.8040 (m-70) cc_final: 0.7537 (m-70) REVERT: D 133 TYR cc_start: 0.4971 (t80) cc_final: 0.4735 (t80) REVERT: D 240 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8074 (tm-30) REVERT: D 259 MET cc_start: 0.8365 (mmm) cc_final: 0.7970 (mmm) REVERT: D 263 ASP cc_start: 0.8955 (m-30) cc_final: 0.8697 (m-30) REVERT: D 410 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7626 (t80) outliers start: 29 outliers final: 16 residues processed: 230 average time/residue: 0.6282 time to fit residues: 155.1951 Evaluate side-chains 196 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 410 TYR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 410 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 4 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 413 ASN C 76 ASN C 413 ASN D 76 ASN D 413 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.153043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.091782 restraints weight = 20636.853| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.63 r_work: 0.3077 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12388 Z= 0.196 Angle : 0.629 9.655 16764 Z= 0.327 Chirality : 0.043 0.145 1872 Planarity : 0.006 0.105 2096 Dihedral : 4.639 36.504 1684 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.94 % Allowed : 19.55 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.22), residues: 1476 helix: 0.01 (0.17), residues: 984 sheet: None (None), residues: 0 loop : -2.08 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 415 TYR 0.022 0.002 TYR C 186 PHE 0.022 0.001 PHE B 185 TRP 0.009 0.002 TRP A 359 HIS 0.003 0.000 HIS C 411 Details of bonding type rmsd covalent geometry : bond 0.00471 (12388) covalent geometry : angle 0.62943 (16764) hydrogen bonds : bond 0.04271 ( 732) hydrogen bonds : angle 4.02062 ( 2064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 182 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.5428 (OUTLIER) cc_final: 0.5109 (m-80) REVERT: A 91 PHE cc_start: 0.7067 (t80) cc_final: 0.6814 (t80) REVERT: A 104 HIS cc_start: 0.8029 (m-70) cc_final: 0.7518 (m-70) REVERT: A 169 MET cc_start: 0.8226 (ptp) cc_final: 0.7921 (ptt) REVERT: A 174 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8568 (mp0) REVERT: A 235 MET cc_start: 0.8259 (ttm) cc_final: 0.7974 (ttp) REVERT: A 240 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7888 (tm-30) REVERT: A 259 MET cc_start: 0.8355 (mmm) cc_final: 0.7924 (mmm) REVERT: A 263 ASP cc_start: 0.8961 (m-30) cc_final: 0.8667 (m-30) REVERT: A 410 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7801 (t80) REVERT: A 413 ASN cc_start: 0.8832 (m110) cc_final: 0.8458 (t0) REVERT: B 89 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8217 (mm-30) REVERT: B 91 PHE cc_start: 0.7010 (t80) cc_final: 0.6737 (t80) REVERT: B 104 HIS cc_start: 0.8009 (m-70) cc_final: 0.7495 (m-70) REVERT: B 133 TYR cc_start: 0.4768 (t80) cc_final: 0.4413 (t80) REVERT: B 169 MET cc_start: 0.8242 (ptp) cc_final: 0.7905 (ptt) REVERT: B 174 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8590 (mp0) REVERT: B 235 MET cc_start: 0.8278 (ttm) cc_final: 0.8004 (ttp) REVERT: B 240 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8030 (tm-30) REVERT: B 259 MET cc_start: 0.8363 (mmm) cc_final: 0.7859 (mmm) REVERT: B 263 ASP cc_start: 0.8932 (m-30) cc_final: 0.8632 (m-30) REVERT: B 343 GLU cc_start: 0.8597 (mm-30) cc_final: 0.7858 (tp30) REVERT: B 410 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.7780 (t80) REVERT: C 74 PHE cc_start: 0.5449 (OUTLIER) cc_final: 0.5113 (m-80) REVERT: C 91 PHE cc_start: 0.6963 (t80) cc_final: 0.6600 (t80) REVERT: C 104 HIS cc_start: 0.8119 (m-70) cc_final: 0.7614 (m-70) REVERT: C 169 MET cc_start: 0.8229 (ptp) cc_final: 0.7928 (ptt) REVERT: C 174 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8524 (mp0) REVERT: C 240 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7919 (tm-30) REVERT: C 259 MET cc_start: 0.8355 (mmm) cc_final: 0.7912 (mmm) REVERT: C 263 ASP cc_start: 0.8949 (m-30) cc_final: 0.8651 (m-30) REVERT: C 410 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7727 (t80) REVERT: D 74 PHE cc_start: 0.5466 (OUTLIER) cc_final: 0.5123 (m-80) REVERT: D 91 PHE cc_start: 0.7124 (t80) cc_final: 0.6861 (t80) REVERT: D 104 HIS cc_start: 0.8037 (m-70) cc_final: 0.7533 (m-70) REVERT: D 169 MET cc_start: 0.8266 (ptp) cc_final: 0.7963 (ptt) REVERT: D 174 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8524 (mp0) REVERT: D 240 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7866 (tm-30) REVERT: D 259 MET cc_start: 0.8365 (mmm) cc_final: 0.7929 (mmm) REVERT: D 263 ASP cc_start: 0.8977 (m-30) cc_final: 0.8691 (m-30) REVERT: D 410 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.7828 (t80) outliers start: 52 outliers final: 29 residues processed: 222 average time/residue: 0.5850 time to fit residues: 140.3337 Evaluate side-chains 206 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 410 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 410 TYR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 410 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 106 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.153678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.092316 restraints weight = 20309.240| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.60 r_work: 0.3086 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12388 Z= 0.179 Angle : 0.614 10.468 16764 Z= 0.316 Chirality : 0.042 0.142 1872 Planarity : 0.005 0.072 2096 Dihedral : 4.443 35.605 1682 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.32 % Allowed : 21.14 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.23), residues: 1476 helix: 0.29 (0.17), residues: 984 sheet: None (None), residues: 0 loop : -1.79 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 415 TYR 0.023 0.002 TYR B 136 PHE 0.022 0.001 PHE B 185 TRP 0.008 0.002 TRP B 359 HIS 0.001 0.000 HIS C 411 Details of bonding type rmsd covalent geometry : bond 0.00428 (12388) covalent geometry : angle 0.61409 (16764) hydrogen bonds : bond 0.04077 ( 732) hydrogen bonds : angle 3.91911 ( 2064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 180 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7096 (t80) cc_final: 0.6841 (t80) REVERT: A 104 HIS cc_start: 0.8067 (m-70) cc_final: 0.7559 (m-70) REVERT: A 169 MET cc_start: 0.8323 (ptp) cc_final: 0.8054 (ptt) REVERT: A 174 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8597 (mp0) REVERT: A 235 MET cc_start: 0.8272 (ttm) cc_final: 0.7981 (ttp) REVERT: A 240 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7998 (tm-30) REVERT: A 259 MET cc_start: 0.8374 (mmm) cc_final: 0.7936 (mmm) REVERT: A 263 ASP cc_start: 0.8924 (m-30) cc_final: 0.8649 (m-30) REVERT: A 410 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7844 (t80) REVERT: A 413 ASN cc_start: 0.8883 (m110) cc_final: 0.8510 (t0) REVERT: B 91 PHE cc_start: 0.7060 (t80) cc_final: 0.6819 (t80) REVERT: B 104 HIS cc_start: 0.8002 (m-70) cc_final: 0.7500 (m-70) REVERT: B 169 MET cc_start: 0.8316 (ptp) cc_final: 0.8030 (ptt) REVERT: B 174 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8599 (mp0) REVERT: B 235 MET cc_start: 0.8300 (ttm) cc_final: 0.8019 (ttp) REVERT: B 240 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7977 (tm-30) REVERT: B 259 MET cc_start: 0.8391 (mmm) cc_final: 0.7914 (mmm) REVERT: B 263 ASP cc_start: 0.8913 (m-30) cc_final: 0.8666 (m-30) REVERT: C 91 PHE cc_start: 0.6942 (t80) cc_final: 0.6600 (t80) REVERT: C 104 HIS cc_start: 0.8121 (m-70) cc_final: 0.7622 (m-70) REVERT: C 169 MET cc_start: 0.8305 (ptp) cc_final: 0.8040 (ptt) REVERT: C 174 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8565 (mp0) REVERT: C 240 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8003 (tm-30) REVERT: C 259 MET cc_start: 0.8333 (mmm) cc_final: 0.7915 (mmm) REVERT: C 263 ASP cc_start: 0.8923 (m-30) cc_final: 0.8669 (m-30) REVERT: C 410 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7689 (t80) REVERT: C 413 ASN cc_start: 0.8806 (m110) cc_final: 0.8485 (t0) REVERT: D 91 PHE cc_start: 0.7039 (t80) cc_final: 0.6802 (t80) REVERT: D 104 HIS cc_start: 0.8068 (m-70) cc_final: 0.7556 (m-70) REVERT: D 169 MET cc_start: 0.8320 (ptp) cc_final: 0.8035 (ptt) REVERT: D 174 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8552 (mp0) REVERT: D 240 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7987 (tm-30) REVERT: D 259 MET cc_start: 0.8331 (mmm) cc_final: 0.7920 (mmm) REVERT: D 263 ASP cc_start: 0.8928 (m-30) cc_final: 0.8678 (m-30) REVERT: D 410 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.7750 (t80) REVERT: D 413 ASN cc_start: 0.8827 (m110) cc_final: 0.8456 (t0) outliers start: 57 outliers final: 28 residues processed: 228 average time/residue: 0.5090 time to fit residues: 126.6034 Evaluate side-chains 210 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 410 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 410 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 141 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN D 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.155843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.095004 restraints weight = 20390.280| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.64 r_work: 0.3128 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12388 Z= 0.126 Angle : 0.592 10.726 16764 Z= 0.299 Chirality : 0.040 0.143 1872 Planarity : 0.005 0.055 2096 Dihedral : 4.278 37.629 1682 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.02 % Allowed : 21.97 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.23), residues: 1476 helix: 0.55 (0.17), residues: 984 sheet: -3.48 (0.57), residues: 40 loop : -1.55 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 415 TYR 0.024 0.001 TYR A 136 PHE 0.023 0.001 PHE B 185 TRP 0.007 0.001 TRP A 359 HIS 0.001 0.000 HIS C 411 Details of bonding type rmsd covalent geometry : bond 0.00292 (12388) covalent geometry : angle 0.59238 (16764) hydrogen bonds : bond 0.03606 ( 732) hydrogen bonds : angle 3.84551 ( 2064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 194 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7060 (t80) cc_final: 0.6734 (t80) REVERT: A 104 HIS cc_start: 0.8060 (m-70) cc_final: 0.7516 (m-70) REVERT: A 169 MET cc_start: 0.8380 (ptp) cc_final: 0.8074 (ptt) REVERT: A 174 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8576 (mp0) REVERT: A 235 MET cc_start: 0.8255 (ttm) cc_final: 0.7968 (ttp) REVERT: A 240 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7915 (tm-30) REVERT: A 259 MET cc_start: 0.8332 (mmm) cc_final: 0.7943 (mmm) REVERT: A 263 ASP cc_start: 0.8886 (m-30) cc_final: 0.8636 (m-30) REVERT: A 413 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8429 (t0) REVERT: B 91 PHE cc_start: 0.7170 (t80) cc_final: 0.6803 (t80) REVERT: B 104 HIS cc_start: 0.8025 (m-70) cc_final: 0.7512 (m-70) REVERT: B 169 MET cc_start: 0.8374 (ptp) cc_final: 0.8048 (ptt) REVERT: B 174 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8577 (mp0) REVERT: B 235 MET cc_start: 0.8233 (ttm) cc_final: 0.7939 (ttp) REVERT: B 240 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7947 (tm-30) REVERT: B 259 MET cc_start: 0.8347 (mmm) cc_final: 0.7914 (mmm) REVERT: B 263 ASP cc_start: 0.8865 (m-30) cc_final: 0.8634 (m-30) REVERT: B 343 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8145 (mt-10) REVERT: C 91 PHE cc_start: 0.6979 (t80) cc_final: 0.6661 (t80) REVERT: C 104 HIS cc_start: 0.8103 (m-70) cc_final: 0.7607 (m-70) REVERT: C 169 MET cc_start: 0.8386 (ptp) cc_final: 0.8081 (ptt) REVERT: C 174 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8540 (mp0) REVERT: C 240 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7898 (tm-30) REVERT: C 259 MET cc_start: 0.8335 (mmm) cc_final: 0.7962 (mmm) REVERT: C 263 ASP cc_start: 0.8880 (m-30) cc_final: 0.8645 (m-30) REVERT: C 413 ASN cc_start: 0.8796 (m110) cc_final: 0.8401 (t0) REVERT: D 91 PHE cc_start: 0.7087 (t80) cc_final: 0.6873 (t80) REVERT: D 104 HIS cc_start: 0.8076 (m-70) cc_final: 0.7581 (m-70) REVERT: D 169 MET cc_start: 0.8343 (ptp) cc_final: 0.8047 (ptt) REVERT: D 174 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8558 (mp0) REVERT: D 228 CYS cc_start: 0.9117 (m) cc_final: 0.8607 (t) REVERT: D 240 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7914 (tm-30) REVERT: D 259 MET cc_start: 0.8281 (mmm) cc_final: 0.7912 (mmm) REVERT: D 263 ASP cc_start: 0.8870 (m-30) cc_final: 0.8638 (m-30) REVERT: D 410 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7819 (t80) REVERT: D 413 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8406 (t0) outliers start: 53 outliers final: 33 residues processed: 233 average time/residue: 0.4818 time to fit residues: 123.0736 Evaluate side-chains 223 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 410 TYR Chi-restraints excluded: chain D residue 413 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 38 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 94 optimal weight: 0.3980 chunk 47 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN D 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.153679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.093235 restraints weight = 20407.972| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.55 r_work: 0.3075 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12388 Z= 0.171 Angle : 0.612 10.675 16764 Z= 0.313 Chirality : 0.042 0.139 1872 Planarity : 0.005 0.049 2096 Dihedral : 4.232 35.895 1682 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.94 % Allowed : 21.21 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.23), residues: 1476 helix: 0.68 (0.17), residues: 984 sheet: -3.10 (0.61), residues: 40 loop : -1.40 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 99 TYR 0.032 0.002 TYR A 136 PHE 0.022 0.001 PHE B 185 TRP 0.008 0.001 TRP D 359 HIS 0.001 0.000 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00413 (12388) covalent geometry : angle 0.61202 (16764) hydrogen bonds : bond 0.03873 ( 732) hydrogen bonds : angle 3.80191 ( 2064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.6982 (t80) cc_final: 0.6759 (t80) REVERT: A 104 HIS cc_start: 0.8085 (m-70) cc_final: 0.7586 (m-70) REVERT: A 169 MET cc_start: 0.8540 (ptp) cc_final: 0.8257 (ptt) REVERT: A 174 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8805 (mp0) REVERT: A 235 MET cc_start: 0.8275 (ttm) cc_final: 0.7970 (ttp) REVERT: A 240 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8018 (tm-30) REVERT: A 259 MET cc_start: 0.8612 (mmm) cc_final: 0.8228 (mmm) REVERT: A 263 ASP cc_start: 0.8939 (m-30) cc_final: 0.8704 (m-30) REVERT: B 91 PHE cc_start: 0.7145 (t80) cc_final: 0.6878 (t80) REVERT: B 104 HIS cc_start: 0.8082 (m-70) cc_final: 0.7604 (m-70) REVERT: B 169 MET cc_start: 0.8565 (ptp) cc_final: 0.8244 (ptt) REVERT: B 174 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8671 (mp0) REVERT: B 235 MET cc_start: 0.8262 (ttm) cc_final: 0.7970 (ttp) REVERT: B 240 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7996 (tm-30) REVERT: B 259 MET cc_start: 0.8577 (mmm) cc_final: 0.8143 (mmm) REVERT: B 263 ASP cc_start: 0.8945 (m-30) cc_final: 0.8728 (m-30) REVERT: B 343 GLU cc_start: 0.8602 (mm-30) cc_final: 0.7890 (tt0) REVERT: C 91 PHE cc_start: 0.7093 (t80) cc_final: 0.6810 (t80) REVERT: C 104 HIS cc_start: 0.8125 (m-70) cc_final: 0.7670 (m-70) REVERT: C 133 TYR cc_start: 0.4890 (t80) cc_final: 0.4602 (t80) REVERT: C 169 MET cc_start: 0.8535 (ptp) cc_final: 0.8225 (ptt) REVERT: C 174 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8732 (mp0) REVERT: C 240 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8003 (tm-30) REVERT: C 259 MET cc_start: 0.8598 (mmm) cc_final: 0.8152 (mmm) REVERT: C 263 ASP cc_start: 0.8934 (m-30) cc_final: 0.8705 (m-30) REVERT: C 410 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.7897 (t80) REVERT: C 413 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8451 (t0) REVERT: D 89 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8081 (mm-30) REVERT: D 91 PHE cc_start: 0.7232 (t80) cc_final: 0.7021 (t80) REVERT: D 104 HIS cc_start: 0.8121 (m-70) cc_final: 0.7655 (m-70) REVERT: D 169 MET cc_start: 0.8573 (ptp) cc_final: 0.8277 (ptt) REVERT: D 174 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8693 (mp0) REVERT: D 240 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7961 (tm-30) REVERT: D 259 MET cc_start: 0.8566 (mmm) cc_final: 0.8123 (mmm) REVERT: D 263 ASP cc_start: 0.8922 (m-30) cc_final: 0.8687 (m-30) REVERT: D 413 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8448 (t0) outliers start: 52 outliers final: 32 residues processed: 228 average time/residue: 0.4878 time to fit residues: 121.6349 Evaluate side-chains 216 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 410 TYR Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 413 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 53 optimal weight: 0.2980 chunk 85 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 414 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.155797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.095141 restraints weight = 20447.287| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.57 r_work: 0.3111 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12388 Z= 0.124 Angle : 0.598 10.888 16764 Z= 0.302 Chirality : 0.041 0.223 1872 Planarity : 0.005 0.048 2096 Dihedral : 4.016 17.613 1680 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.64 % Allowed : 21.36 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.23), residues: 1476 helix: 0.90 (0.17), residues: 984 sheet: -2.68 (0.69), residues: 40 loop : -1.31 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 99 TYR 0.036 0.001 TYR B 136 PHE 0.023 0.001 PHE B 185 TRP 0.007 0.001 TRP A 359 HIS 0.001 0.000 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00285 (12388) covalent geometry : angle 0.59827 (16764) hydrogen bonds : bond 0.03462 ( 732) hydrogen bonds : angle 3.72837 ( 2064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7123 (t80) cc_final: 0.6905 (t80) REVERT: A 104 HIS cc_start: 0.8042 (m-70) cc_final: 0.7619 (m-70) REVERT: A 133 TYR cc_start: 0.4977 (t80) cc_final: 0.4652 (t80) REVERT: A 169 MET cc_start: 0.8530 (ptp) cc_final: 0.8261 (ptt) REVERT: A 174 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8752 (mp0) REVERT: A 228 CYS cc_start: 0.9139 (m) cc_final: 0.8671 (t) REVERT: A 235 MET cc_start: 0.8224 (ttm) cc_final: 0.7912 (ttp) REVERT: A 240 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8007 (tm-30) REVERT: A 259 MET cc_start: 0.8607 (mmm) cc_final: 0.8233 (mmm) REVERT: A 263 ASP cc_start: 0.8914 (m-30) cc_final: 0.8699 (m-30) REVERT: B 91 PHE cc_start: 0.7164 (t80) cc_final: 0.6897 (t80) REVERT: B 104 HIS cc_start: 0.8029 (m-70) cc_final: 0.7432 (m-70) REVERT: B 169 MET cc_start: 0.8546 (ptp) cc_final: 0.8246 (ptt) REVERT: B 174 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8601 (mp0) REVERT: B 235 MET cc_start: 0.8196 (ttm) cc_final: 0.7898 (ttp) REVERT: B 240 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8007 (tm-30) REVERT: B 259 MET cc_start: 0.8577 (mmm) cc_final: 0.8158 (mmm) REVERT: C 91 PHE cc_start: 0.7093 (t80) cc_final: 0.6820 (t80) REVERT: C 104 HIS cc_start: 0.8126 (m-70) cc_final: 0.7691 (m-70) REVERT: C 169 MET cc_start: 0.8505 (ptp) cc_final: 0.8244 (ptt) REVERT: C 174 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8711 (mp0) REVERT: C 228 CYS cc_start: 0.9108 (m) cc_final: 0.8622 (t) REVERT: C 240 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7990 (tm-30) REVERT: C 259 MET cc_start: 0.8583 (mmm) cc_final: 0.8147 (mmm) REVERT: C 263 ASP cc_start: 0.8918 (m-30) cc_final: 0.8704 (m-30) REVERT: C 413 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8437 (t0) REVERT: D 91 PHE cc_start: 0.7238 (t80) cc_final: 0.7033 (t80) REVERT: D 104 HIS cc_start: 0.8103 (m-70) cc_final: 0.7673 (m-70) REVERT: D 133 TYR cc_start: 0.4949 (t80) cc_final: 0.4613 (t80) REVERT: D 169 MET cc_start: 0.8551 (ptp) cc_final: 0.8300 (ptt) REVERT: D 174 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8647 (mp0) REVERT: D 228 CYS cc_start: 0.9132 (m) cc_final: 0.8662 (t) REVERT: D 240 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8020 (tm-30) REVERT: D 259 MET cc_start: 0.8571 (mmm) cc_final: 0.8223 (mmm) REVERT: D 263 ASP cc_start: 0.8913 (m-30) cc_final: 0.8705 (m-30) REVERT: D 413 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8401 (t0) outliers start: 48 outliers final: 31 residues processed: 230 average time/residue: 0.4865 time to fit residues: 122.5117 Evaluate side-chains 212 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 413 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 128 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 108 optimal weight: 0.3980 chunk 109 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.155254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.094773 restraints weight = 20384.395| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.52 r_work: 0.3113 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12388 Z= 0.135 Angle : 0.631 11.100 16764 Z= 0.320 Chirality : 0.042 0.185 1872 Planarity : 0.005 0.051 2096 Dihedral : 3.981 23.157 1680 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.11 % Allowed : 22.05 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.23), residues: 1476 helix: 0.97 (0.17), residues: 984 sheet: -2.73 (0.68), residues: 40 loop : -1.26 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 99 TYR 0.038 0.001 TYR B 136 PHE 0.023 0.001 PHE B 185 TRP 0.007 0.001 TRP D 359 HIS 0.001 0.000 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00316 (12388) covalent geometry : angle 0.63123 (16764) hydrogen bonds : bond 0.03503 ( 732) hydrogen bonds : angle 3.74408 ( 2064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7217 (t80) cc_final: 0.7005 (t80) REVERT: A 104 HIS cc_start: 0.8089 (m-70) cc_final: 0.7646 (m-70) REVERT: A 169 MET cc_start: 0.8555 (ptp) cc_final: 0.8278 (ptt) REVERT: A 174 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8753 (mp0) REVERT: A 228 CYS cc_start: 0.9132 (m) cc_final: 0.8671 (t) REVERT: A 235 MET cc_start: 0.8214 (ttm) cc_final: 0.7900 (ttp) REVERT: A 240 GLU cc_start: 0.8445 (tm-30) cc_final: 0.7994 (tm-30) REVERT: A 259 MET cc_start: 0.8640 (mmm) cc_final: 0.8311 (mmm) REVERT: B 91 PHE cc_start: 0.7150 (t80) cc_final: 0.6899 (t80) REVERT: B 104 HIS cc_start: 0.7999 (m-70) cc_final: 0.7582 (m-70) REVERT: B 169 MET cc_start: 0.8561 (ptp) cc_final: 0.8268 (ptt) REVERT: B 174 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8612 (mp0) REVERT: B 235 MET cc_start: 0.8200 (ttm) cc_final: 0.7983 (mtt) REVERT: B 240 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8036 (tm-30) REVERT: C 91 PHE cc_start: 0.7096 (t80) cc_final: 0.6878 (t80) REVERT: C 104 HIS cc_start: 0.8106 (m-70) cc_final: 0.7668 (m-70) REVERT: C 169 MET cc_start: 0.8539 (ptp) cc_final: 0.8260 (ptt) REVERT: C 174 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8690 (mp0) REVERT: C 240 GLU cc_start: 0.8446 (tm-30) cc_final: 0.7998 (tm-30) REVERT: C 259 MET cc_start: 0.8610 (mmm) cc_final: 0.8233 (mmm) REVERT: C 413 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8401 (t0) REVERT: D 104 HIS cc_start: 0.8105 (m-70) cc_final: 0.7438 (m-70) REVERT: D 169 MET cc_start: 0.8554 (ptp) cc_final: 0.8288 (ptt) REVERT: D 174 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8642 (mp0) REVERT: D 228 CYS cc_start: 0.9125 (m) cc_final: 0.8660 (t) REVERT: D 240 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8012 (tm-30) REVERT: D 259 MET cc_start: 0.8612 (mmm) cc_final: 0.8191 (mmm) REVERT: D 413 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8419 (t0) outliers start: 41 outliers final: 29 residues processed: 215 average time/residue: 0.4937 time to fit residues: 116.5130 Evaluate side-chains 211 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 413 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 144 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 0.0470 chunk 25 optimal weight: 0.5980 chunk 44 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 414 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.157606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.099544 restraints weight = 20047.637| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.55 r_work: 0.3211 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12388 Z= 0.125 Angle : 0.632 11.398 16764 Z= 0.319 Chirality : 0.041 0.220 1872 Planarity : 0.004 0.053 2096 Dihedral : 3.914 22.285 1680 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.73 % Allowed : 22.50 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.23), residues: 1476 helix: 1.10 (0.17), residues: 984 sheet: -2.50 (0.70), residues: 40 loop : -1.14 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 99 TYR 0.037 0.001 TYR A 136 PHE 0.025 0.001 PHE B 185 TRP 0.006 0.001 TRP A 359 HIS 0.002 0.000 HIS D 303 Details of bonding type rmsd covalent geometry : bond 0.00286 (12388) covalent geometry : angle 0.63203 (16764) hydrogen bonds : bond 0.03324 ( 732) hydrogen bonds : angle 3.77078 ( 2064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7155 (t80) cc_final: 0.6893 (t80) REVERT: A 104 HIS cc_start: 0.8135 (m-70) cc_final: 0.7624 (m-70) REVERT: A 169 MET cc_start: 0.8505 (ptp) cc_final: 0.8224 (ptt) REVERT: A 174 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8738 (mp0) REVERT: A 228 CYS cc_start: 0.9126 (m) cc_final: 0.8640 (t) REVERT: A 235 MET cc_start: 0.8244 (ttm) cc_final: 0.8004 (mtt) REVERT: A 240 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7959 (tm-30) REVERT: A 292 PHE cc_start: 0.9333 (m-80) cc_final: 0.9083 (m-80) REVERT: B 91 PHE cc_start: 0.7135 (t80) cc_final: 0.6890 (t80) REVERT: B 104 HIS cc_start: 0.8179 (m-70) cc_final: 0.7697 (m-70) REVERT: B 169 MET cc_start: 0.8514 (ptp) cc_final: 0.8220 (ptt) REVERT: B 174 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8646 (mp0) REVERT: B 228 CYS cc_start: 0.9142 (m) cc_final: 0.8631 (t) REVERT: B 240 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7958 (tm-30) REVERT: C 104 HIS cc_start: 0.8102 (m-70) cc_final: 0.7670 (m-70) REVERT: C 169 MET cc_start: 0.8506 (ptp) cc_final: 0.8226 (ptt) REVERT: C 174 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8677 (mp0) REVERT: C 228 CYS cc_start: 0.9117 (m) cc_final: 0.8616 (t) REVERT: C 240 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7933 (tm-30) REVERT: C 413 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8344 (t0) REVERT: D 104 HIS cc_start: 0.8045 (m-70) cc_final: 0.7477 (m-70) REVERT: D 169 MET cc_start: 0.8475 (ptp) cc_final: 0.8196 (ptt) REVERT: D 174 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8659 (mp0) REVERT: D 228 CYS cc_start: 0.9100 (m) cc_final: 0.8603 (t) REVERT: D 240 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7933 (tm-30) REVERT: D 292 PHE cc_start: 0.9330 (m-80) cc_final: 0.9040 (m-80) REVERT: D 413 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8363 (t0) outliers start: 36 outliers final: 23 residues processed: 216 average time/residue: 0.5315 time to fit residues: 125.0682 Evaluate side-chains 199 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 413 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.154315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.093926 restraints weight = 20547.296| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.54 r_work: 0.3087 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12388 Z= 0.170 Angle : 0.679 10.720 16764 Z= 0.348 Chirality : 0.043 0.190 1872 Planarity : 0.005 0.065 2096 Dihedral : 4.020 25.245 1680 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.73 % Allowed : 23.56 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.23), residues: 1476 helix: 0.95 (0.17), residues: 1004 sheet: -2.10 (0.75), residues: 40 loop : -0.99 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 99 TYR 0.036 0.002 TYR A 136 PHE 0.023 0.001 PHE B 185 TRP 0.007 0.001 TRP D 359 HIS 0.001 0.000 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00413 (12388) covalent geometry : angle 0.67860 (16764) hydrogen bonds : bond 0.03718 ( 732) hydrogen bonds : angle 3.88464 ( 2064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.353 Fit side-chains REVERT: A 91 PHE cc_start: 0.7070 (t80) cc_final: 0.6858 (t80) REVERT: A 104 HIS cc_start: 0.8105 (m-70) cc_final: 0.7601 (m-70) REVERT: A 169 MET cc_start: 0.8576 (ptp) cc_final: 0.8299 (ptt) REVERT: A 174 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8802 (mp0) REVERT: A 228 CYS cc_start: 0.9146 (m) cc_final: 0.8680 (t) REVERT: A 235 MET cc_start: 0.8273 (ttm) cc_final: 0.8046 (mtt) REVERT: A 240 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7985 (tm-30) REVERT: B 49 ARG cc_start: 0.5918 (mmm160) cc_final: 0.5692 (mmm160) REVERT: B 91 PHE cc_start: 0.7102 (t80) cc_final: 0.6833 (t80) REVERT: B 104 HIS cc_start: 0.8168 (m-70) cc_final: 0.7702 (m-70) REVERT: B 169 MET cc_start: 0.8603 (ptp) cc_final: 0.8305 (ptt) REVERT: B 174 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8684 (mp0) REVERT: B 240 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7990 (tm-30) REVERT: C 104 HIS cc_start: 0.8153 (m-70) cc_final: 0.7558 (m-70) REVERT: C 169 MET cc_start: 0.8557 (ptp) cc_final: 0.8279 (ptt) REVERT: C 174 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8746 (mp0) REVERT: C 240 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7978 (tm-30) REVERT: C 413 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8363 (t0) REVERT: D 104 HIS cc_start: 0.8028 (m-70) cc_final: 0.7500 (m-70) REVERT: D 169 MET cc_start: 0.8564 (ptp) cc_final: 0.8298 (ptt) REVERT: D 174 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8740 (mp0) REVERT: D 228 CYS cc_start: 0.9136 (m) cc_final: 0.8665 (t) REVERT: D 240 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7988 (tm-30) REVERT: D 413 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8352 (t0) outliers start: 36 outliers final: 23 residues processed: 198 average time/residue: 0.4944 time to fit residues: 107.0303 Evaluate side-chains 188 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 413 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.5980 chunk 129 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.155287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.094927 restraints weight = 20455.641| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.55 r_work: 0.3103 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12388 Z= 0.145 Angle : 0.676 11.282 16764 Z= 0.344 Chirality : 0.042 0.191 1872 Planarity : 0.005 0.057 2096 Dihedral : 4.054 26.401 1680 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.35 % Allowed : 24.17 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.23), residues: 1476 helix: 1.08 (0.17), residues: 984 sheet: -2.05 (0.74), residues: 40 loop : -1.03 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 415 TYR 0.035 0.001 TYR A 136 PHE 0.024 0.001 PHE B 185 TRP 0.007 0.001 TRP C 359 HIS 0.001 0.000 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00349 (12388) covalent geometry : angle 0.67571 (16764) hydrogen bonds : bond 0.03547 ( 732) hydrogen bonds : angle 3.87821 ( 2064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5553.26 seconds wall clock time: 94 minutes 55.62 seconds (5695.62 seconds total)