Starting phenix.real_space_refine on Tue Jun 10 21:48:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w3y_32296/06_2025/7w3y_32296.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w3y_32296/06_2025/7w3y_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7w3y_32296/06_2025/7w3y_32296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w3y_32296/06_2025/7w3y_32296.map" model { file = "/net/cci-nas-00/data/ceres_data/7w3y_32296/06_2025/7w3y_32296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w3y_32296/06_2025/7w3y_32296.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, D Time building chain proxies: 5.93, per 1000 atoms: 0.49 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: 3.11 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.29 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: 3.18 Time building geometry restraints manager: 3.66 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.790 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 27.920 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.400 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (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 TRP 0.009 0.002 TRP B 170 HIS 0.002 0.001 HIS B 303 PHE 0.013 0.001 PHE B 383 TYR 0.019 0.001 TYR C 186 ARG 0.003 0.000 ARG B 426 Details of bonding type rmsd hydrogen bonds : bond 0.13820 ( 732) hydrogen bonds : angle 5.31814 ( 2064) covalent geometry : bond 0.00602 (12388) covalent geometry : angle 0.68356 (16764) *********************** 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 : 1.392 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: 1.3098 time to fit residues: 378.4232 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 : 1.387 ------------------------------------------------------------------------------- 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 124 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 0.5980 chunk 59 optimal weight: 0.3980 chunk 116 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 C 45 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 143 ASN C 405 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.155258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.094246 restraints weight = 20373.765| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.69 r_work: 0.3121 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2188 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= 0.146 Angle : 0.612 9.667 16764 Z= 0.319 Chirality : 0.042 0.143 1872 Planarity : 0.005 0.057 2096 Dihedral : 4.699 36.701 1688 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.97 % Allowed : 16.36 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.22), residues: 1476 helix: -0.26 (0.17), residues: 980 sheet: None (None), residues: 0 loop : -2.33 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 359 HIS 0.002 0.000 HIS B 303 PHE 0.021 0.001 PHE B 185 TYR 0.018 0.002 TYR C 186 ARG 0.008 0.001 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 732) hydrogen bonds : angle 4.13616 ( 2064) covalent geometry : bond 0.00328 (12388) covalent geometry : angle 0.61179 (16764) *********************** 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 249 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 1.265 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: 0.7061 (t80) cc_final: 0.6708 (t80) REVERT: A 104 HIS cc_start: 0.7984 (m-70) cc_final: 0.7490 (m-70) REVERT: A 133 TYR cc_start: 0.5007 (t80) cc_final: 0.4738 (t80) REVERT: A 235 MET cc_start: 0.8230 (ttm) cc_final: 0.7966 (ttp) REVERT: A 240 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8055 (tm-30) REVERT: A 259 MET cc_start: 0.8337 (mmm) cc_final: 0.7961 (mmm) REVERT: A 263 ASP cc_start: 0.8941 (m-30) cc_final: 0.8693 (m-30) REVERT: B 91 PHE cc_start: 0.6889 (t80) cc_final: 0.6654 (t80) REVERT: B 104 HIS cc_start: 0.7979 (m-70) cc_final: 0.7467 (m-70) REVERT: B 133 TYR cc_start: 0.4957 (t80) cc_final: 0.4647 (t80) REVERT: B 136 TYR cc_start: 0.8353 (t80) cc_final: 0.8092 (t80) REVERT: B 240 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8072 (tm-30) REVERT: B 259 MET cc_start: 0.8334 (mmm) cc_final: 0.7919 (mmm) REVERT: B 263 ASP cc_start: 0.8889 (m-30) cc_final: 0.8659 (m-30) REVERT: B 412 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7722 (tm-30) REVERT: C 91 PHE cc_start: 0.7099 (t80) cc_final: 0.6751 (t80) REVERT: C 104 HIS cc_start: 0.8112 (m-70) cc_final: 0.7618 (m-70) REVERT: C 133 TYR cc_start: 0.5004 (t80) cc_final: 0.4715 (t80) REVERT: C 240 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8030 (tm-30) REVERT: C 259 MET cc_start: 0.8348 (mmm) cc_final: 0.7961 (mmm) REVERT: C 263 ASP cc_start: 0.8945 (m-30) cc_final: 0.8699 (m-30) REVERT: D 91 PHE cc_start: 0.7090 (t80) cc_final: 0.6739 (t80) REVERT: D 104 HIS cc_start: 0.8013 (m-70) cc_final: 0.7493 (m-70) REVERT: D 133 TYR cc_start: 0.4985 (t80) cc_final: 0.4716 (t80) REVERT: D 240 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8056 (tm-30) REVERT: D 259 MET cc_start: 0.8353 (mmm) cc_final: 0.8002 (mmm) REVERT: D 263 ASP cc_start: 0.8954 (m-30) cc_final: 0.8735 (m-30) outliers start: 26 outliers final: 12 residues processed: 240 average time/residue: 1.2792 time to fit residues: 331.2964 Evaluate side-chains 195 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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 B residue 70 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 267 ILE 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 D residue 70 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 267 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 114 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 137 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 D 76 ASN D 413 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.152613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.091400 restraints weight = 20606.473| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.62 r_work: 0.3071 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12388 Z= 0.207 Angle : 0.635 9.498 16764 Z= 0.330 Chirality : 0.044 0.148 1872 Planarity : 0.006 0.098 2096 Dihedral : 4.633 38.142 1684 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.94 % Allowed : 19.39 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.22), residues: 1476 helix: 0.07 (0.17), residues: 984 sheet: None (None), residues: 0 loop : -1.99 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 359 HIS 0.002 0.000 HIS C 411 PHE 0.022 0.001 PHE B 185 TYR 0.024 0.002 TYR C 186 ARG 0.010 0.001 ARG D 415 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 732) hydrogen bonds : angle 3.99670 ( 2064) covalent geometry : bond 0.00502 (12388) covalent geometry : angle 0.63456 (16764) *********************** 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 230 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 1.446 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: 0.7080 (t80) cc_final: 0.6847 (t80) REVERT: A 104 HIS cc_start: 0.8022 (m-70) cc_final: 0.7531 (m-70) REVERT: A 169 MET cc_start: 0.8271 (ptp) cc_final: 0.7996 (ptt) REVERT: A 174 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8548 (mp0) REVERT: A 235 MET cc_start: 0.8268 (ttm) cc_final: 0.7981 (ttp) REVERT: A 240 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7968 (tm-30) REVERT: A 259 MET cc_start: 0.8368 (mmm) cc_final: 0.7939 (mmm) REVERT: A 263 ASP cc_start: 0.8963 (m-30) cc_final: 0.8672 (m-30) REVERT: A 410 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.7843 (t80) REVERT: A 413 ASN cc_start: 0.8815 (m110) cc_final: 0.8426 (t0) REVERT: B 91 PHE cc_start: 0.7036 (t80) cc_final: 0.6804 (t80) REVERT: B 104 HIS cc_start: 0.7973 (m-70) cc_final: 0.7453 (m-70) REVERT: B 133 TYR cc_start: 0.4770 (t80) cc_final: 0.4366 (t80) REVERT: B 136 TYR cc_start: 0.8217 (t80) cc_final: 0.8000 (t80) REVERT: B 140 LYS cc_start: 0.8255 (mtmm) cc_final: 0.7663 (mtmm) REVERT: B 169 MET cc_start: 0.8270 (ptp) cc_final: 0.7978 (ptt) REVERT: B 174 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8581 (mp0) REVERT: B 235 MET cc_start: 0.8292 (ttm) cc_final: 0.8018 (ttp) REVERT: B 240 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7887 (tm-30) REVERT: B 259 MET cc_start: 0.8366 (mmm) cc_final: 0.7906 (mmm) REVERT: B 263 ASP cc_start: 0.8949 (m-30) cc_final: 0.8710 (m-30) REVERT: B 343 GLU cc_start: 0.8594 (mm-30) cc_final: 0.7855 (tp30) REVERT: B 410 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7733 (t80) REVERT: C 74 PHE cc_start: 0.5444 (OUTLIER) cc_final: 0.5107 (m-80) REVERT: C 91 PHE cc_start: 0.6983 (t80) cc_final: 0.6716 (t80) REVERT: C 104 HIS cc_start: 0.8123 (m-70) cc_final: 0.7603 (m-70) REVERT: C 169 MET cc_start: 0.8257 (ptp) cc_final: 0.8003 (ptt) REVERT: C 174 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8503 (mp0) REVERT: C 240 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7851 (tm-30) REVERT: C 259 MET cc_start: 0.8365 (mmm) cc_final: 0.7842 (mmm) REVERT: C 263 ASP cc_start: 0.8940 (m-30) cc_final: 0.8648 (m-30) REVERT: D 74 PHE cc_start: 0.5458 (OUTLIER) cc_final: 0.5115 (m-80) REVERT: D 91 PHE cc_start: 0.7122 (t80) cc_final: 0.6891 (t80) REVERT: D 104 HIS cc_start: 0.8058 (m-70) cc_final: 0.7540 (m-70) REVERT: D 169 MET cc_start: 0.8265 (ptp) cc_final: 0.7996 (ptt) REVERT: D 174 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8500 (mp0) REVERT: D 240 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7851 (tm-30) REVERT: D 259 MET cc_start: 0.8369 (mmm) cc_final: 0.7938 (mmm) REVERT: D 263 ASP cc_start: 0.8966 (m-30) cc_final: 0.8687 (m-30) REVERT: D 410 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7839 (t80) REVERT: D 413 ASN cc_start: 0.8843 (m110) cc_final: 0.8435 (t0) outliers start: 52 outliers final: 31 residues processed: 221 average time/residue: 1.1997 time to fit residues: 288.8113 Evaluate side-chains 202 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 1.474 ------------------------------------------------------------------------------- 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 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 250 SER 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 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 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 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 62 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 140 optimal weight: 0.3980 chunk 46 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** D 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 = 0.4132 r_free = 0.4132 target = 0.154355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.093168 restraints weight = 20117.473| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.63 r_work: 0.3101 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12388 Z= 0.156 Angle : 0.597 10.686 16764 Z= 0.306 Chirality : 0.042 0.141 1872 Planarity : 0.005 0.068 2096 Dihedral : 4.382 36.335 1682 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.86 % Allowed : 21.74 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.23), residues: 1476 helix: 0.43 (0.17), residues: 984 sheet: -3.45 (0.58), residues: 40 loop : -1.70 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 359 HIS 0.001 0.000 HIS A 303 PHE 0.022 0.001 PHE B 185 TYR 0.020 0.001 TYR D 136 ARG 0.005 0.001 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 732) hydrogen bonds : angle 3.86530 ( 2064) covalent geometry : bond 0.00375 (12388) covalent geometry : angle 0.59718 (16764) *********************** 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 239 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 1.390 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: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.6974 (t80) cc_final: 0.6753 (t80) REVERT: A 104 HIS cc_start: 0.8068 (m-70) cc_final: 0.7551 (m-70) REVERT: A 133 TYR cc_start: 0.4889 (t80) cc_final: 0.4681 (t80) REVERT: A 169 MET cc_start: 0.8323 (ptp) cc_final: 0.8032 (ptt) REVERT: A 174 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8596 (mp0) REVERT: A 235 MET cc_start: 0.8264 (ttm) cc_final: 0.7969 (ttp) REVERT: A 240 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 259 MET cc_start: 0.8354 (mmm) cc_final: 0.7943 (mmm) REVERT: A 263 ASP cc_start: 0.8913 (m-30) cc_final: 0.8664 (m-30) REVERT: A 413 ASN cc_start: 0.8822 (m110) cc_final: 0.8495 (t0) REVERT: B 91 PHE cc_start: 0.7093 (t80) cc_final: 0.6833 (t80) REVERT: B 104 HIS cc_start: 0.8009 (m-70) cc_final: 0.7475 (m-70) REVERT: B 133 TYR cc_start: 0.4578 (t80) cc_final: 0.4199 (t80) REVERT: B 136 TYR cc_start: 0.8241 (t80) cc_final: 0.7972 (t80) REVERT: B 140 LYS cc_start: 0.8242 (mtmm) cc_final: 0.7741 (mtmm) REVERT: B 169 MET cc_start: 0.8316 (ptp) cc_final: 0.8007 (ptt) REVERT: B 174 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8621 (mp0) REVERT: B 235 MET cc_start: 0.8277 (ttm) cc_final: 0.7992 (ttp) REVERT: B 240 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7991 (tm-30) REVERT: B 259 MET cc_start: 0.8373 (mmm) cc_final: 0.7892 (mmm) REVERT: B 263 ASP cc_start: 0.8898 (m-30) cc_final: 0.8647 (m-30) REVERT: C 91 PHE cc_start: 0.6973 (t80) cc_final: 0.6710 (t80) REVERT: C 104 HIS cc_start: 0.8121 (m-70) cc_final: 0.7615 (m-70) REVERT: C 133 TYR cc_start: 0.4814 (t80) cc_final: 0.4612 (t80) REVERT: C 169 MET cc_start: 0.8317 (ptp) cc_final: 0.8028 (ptt) REVERT: C 174 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8567 (mp0) REVERT: C 240 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8005 (tm-30) REVERT: C 259 MET cc_start: 0.8364 (mmm) cc_final: 0.7862 (mmm) REVERT: C 263 ASP cc_start: 0.8905 (m-30) cc_final: 0.8643 (m-30) REVERT: C 413 ASN cc_start: 0.8788 (m110) cc_final: 0.8465 (t0) REVERT: D 91 PHE cc_start: 0.7016 (t80) cc_final: 0.6792 (t80) REVERT: D 104 HIS cc_start: 0.8057 (m-70) cc_final: 0.7539 (m-70) REVERT: D 133 TYR cc_start: 0.4866 (t80) cc_final: 0.4662 (t80) REVERT: D 169 MET cc_start: 0.8314 (ptp) cc_final: 0.8031 (ptt) REVERT: D 174 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8554 (mp0) REVERT: D 240 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7978 (tm-30) REVERT: D 259 MET cc_start: 0.8309 (mmm) cc_final: 0.7890 (mmm) REVERT: D 263 ASP cc_start: 0.8917 (m-30) cc_final: 0.8663 (m-30) REVERT: D 413 ASN cc_start: 0.8817 (m110) cc_final: 0.8457 (t0) outliers start: 51 outliers final: 33 residues processed: 228 average time/residue: 1.1322 time to fit residues: 282.5913 Evaluate side-chains 221 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 140 LYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 183 LEU 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 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 276 MET Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 183 LEU 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 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 140 LYS Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 276 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 22 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 102 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4153 r_free = 0.4153 target = 0.156033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.095431 restraints weight = 20249.247| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.61 r_work: 0.3139 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12388 Z= 0.124 Angle : 0.584 10.714 16764 Z= 0.294 Chirality : 0.040 0.142 1872 Planarity : 0.005 0.065 2096 Dihedral : 4.222 36.854 1682 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.32 % Allowed : 20.98 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.23), residues: 1476 helix: 0.65 (0.17), residues: 984 sheet: -3.31 (0.60), residues: 40 loop : -1.51 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 359 HIS 0.002 0.000 HIS A 411 PHE 0.022 0.001 PHE B 185 TYR 0.024 0.001 TYR A 136 ARG 0.008 0.001 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 732) hydrogen bonds : angle 3.78008 ( 2064) covalent geometry : bond 0.00287 (12388) covalent geometry : angle 0.58358 (16764) *********************** 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 257 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 200 time to evaluate : 1.393 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: 0.7045 (t80) cc_final: 0.6844 (t80) REVERT: A 104 HIS cc_start: 0.8104 (m-70) cc_final: 0.7599 (m-70) REVERT: A 133 TYR cc_start: 0.4725 (t80) cc_final: 0.4510 (t80) REVERT: A 169 MET cc_start: 0.8344 (ptp) cc_final: 0.8035 (ptt) REVERT: A 174 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8592 (mp0) REVERT: A 228 CYS cc_start: 0.9123 (m) cc_final: 0.8621 (t) REVERT: A 235 MET cc_start: 0.8257 (ttm) cc_final: 0.7967 (ttp) REVERT: A 240 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7913 (tm-30) REVERT: A 259 MET cc_start: 0.8348 (mmm) cc_final: 0.7989 (mmm) REVERT: A 263 ASP cc_start: 0.8872 (m-30) cc_final: 0.8653 (m-30) REVERT: A 410 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7877 (t80) REVERT: A 413 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8413 (t0) REVERT: B 91 PHE cc_start: 0.7185 (t80) cc_final: 0.6785 (t80) REVERT: B 104 HIS cc_start: 0.8021 (m-70) cc_final: 0.7526 (m-70) REVERT: B 133 TYR cc_start: 0.4651 (t80) cc_final: 0.4202 (t80) REVERT: B 136 TYR cc_start: 0.8228 (t80) cc_final: 0.7953 (t80) REVERT: B 140 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7688 (mtmm) REVERT: B 169 MET cc_start: 0.8367 (ptp) cc_final: 0.8059 (ptt) REVERT: B 174 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8597 (mp0) REVERT: B 235 MET cc_start: 0.8201 (ttm) cc_final: 0.7901 (ttp) REVERT: B 240 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7909 (tm-30) REVERT: B 259 MET cc_start: 0.8335 (mmm) cc_final: 0.7899 (mmm) REVERT: B 263 ASP cc_start: 0.8860 (m-30) cc_final: 0.8631 (m-30) REVERT: C 91 PHE cc_start: 0.7029 (t80) cc_final: 0.6787 (t80) REVERT: C 104 HIS cc_start: 0.8099 (m-70) cc_final: 0.7606 (m-70) REVERT: C 169 MET cc_start: 0.8353 (ptp) cc_final: 0.8046 (ptt) REVERT: C 174 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8558 (mp0) REVERT: C 240 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7897 (tm-30) REVERT: C 259 MET cc_start: 0.8338 (mmm) cc_final: 0.7878 (mmm) REVERT: C 263 ASP cc_start: 0.8876 (m-30) cc_final: 0.8640 (m-30) REVERT: C 413 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8388 (t0) REVERT: D 91 PHE cc_start: 0.7164 (t80) cc_final: 0.6932 (t80) REVERT: D 104 HIS cc_start: 0.8083 (m-70) cc_final: 0.7588 (m-70) REVERT: D 133 TYR cc_start: 0.4694 (t80) cc_final: 0.4443 (t80) REVERT: D 169 MET cc_start: 0.8357 (ptp) cc_final: 0.8057 (ptt) REVERT: D 174 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8560 (mp0) REVERT: D 228 CYS cc_start: 0.9060 (m) cc_final: 0.8535 (t) REVERT: D 240 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7918 (tm-30) REVERT: D 259 MET cc_start: 0.8293 (mmm) cc_final: 0.7838 (mmm) REVERT: D 263 ASP cc_start: 0.8868 (m-30) cc_final: 0.8639 (m-30) REVERT: D 413 ASN cc_start: 0.8805 (m110) cc_final: 0.8441 (t0) outliers start: 57 outliers final: 32 residues processed: 243 average time/residue: 1.1487 time to fit residues: 307.0787 Evaluate side-chains 226 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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 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 410 TYR 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 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 95 LEU 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 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 183 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 40 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** D 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 = 0.4101 r_free = 0.4101 target = 0.152476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.091636 restraints weight = 20644.303| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.53 r_work: 0.3051 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12388 Z= 0.220 Angle : 0.640 10.326 16764 Z= 0.331 Chirality : 0.044 0.148 1872 Planarity : 0.005 0.055 2096 Dihedral : 4.279 34.112 1682 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.94 % Allowed : 21.82 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.23), residues: 1476 helix: 0.56 (0.17), residues: 988 sheet: -3.04 (0.61), residues: 40 loop : -1.28 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 359 HIS 0.001 0.000 HIS B 303 PHE 0.022 0.001 PHE B 185 TYR 0.031 0.002 TYR A 136 ARG 0.009 0.001 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.04162 ( 732) hydrogen bonds : angle 3.86334 ( 2064) covalent geometry : bond 0.00535 (12388) covalent geometry : angle 0.63999 (16764) *********************** 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 238 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8143 (mm-30) REVERT: A 91 PHE cc_start: 0.7232 (t80) cc_final: 0.7019 (t80) REVERT: A 104 HIS cc_start: 0.8087 (m-70) cc_final: 0.7548 (m-70) REVERT: A 169 MET cc_start: 0.8551 (ptp) cc_final: 0.8245 (ptt) REVERT: A 174 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8731 (mp0) REVERT: A 235 MET cc_start: 0.8276 (ttm) cc_final: 0.7976 (ttp) REVERT: A 240 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8027 (tm-30) REVERT: A 259 MET cc_start: 0.8637 (mmm) cc_final: 0.8267 (mmm) REVERT: A 263 ASP cc_start: 0.8934 (m-30) cc_final: 0.8706 (m-30) REVERT: A 413 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8439 (t0) REVERT: B 104 HIS cc_start: 0.8084 (m-70) cc_final: 0.7616 (m-70) REVERT: B 133 TYR cc_start: 0.4837 (t80) cc_final: 0.4424 (t80) REVERT: B 136 TYR cc_start: 0.8212 (t80) cc_final: 0.7965 (t80) REVERT: B 140 LYS cc_start: 0.8262 (mtmm) cc_final: 0.7718 (mtmm) REVERT: B 169 MET cc_start: 0.8599 (ptp) cc_final: 0.8275 (ptt) REVERT: B 174 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8691 (mp0) REVERT: B 235 MET cc_start: 0.8283 (ttm) cc_final: 0.7996 (ttp) REVERT: B 240 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8038 (tm-30) REVERT: B 259 MET cc_start: 0.8623 (mmm) cc_final: 0.8215 (mmm) REVERT: B 263 ASP cc_start: 0.8954 (m-30) cc_final: 0.8741 (m-30) REVERT: C 91 PHE cc_start: 0.7114 (t80) cc_final: 0.6865 (t80) REVERT: C 104 HIS cc_start: 0.8129 (m-70) cc_final: 0.7677 (m-70) REVERT: C 169 MET cc_start: 0.8567 (ptp) cc_final: 0.8260 (ptt) REVERT: C 174 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8671 (mp0) REVERT: C 240 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8027 (tm-30) REVERT: C 259 MET cc_start: 0.8639 (mmm) cc_final: 0.8219 (mmm) REVERT: C 263 ASP cc_start: 0.8945 (m-30) cc_final: 0.8729 (m-30) REVERT: C 413 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8407 (t0) REVERT: D 104 HIS cc_start: 0.8143 (m-70) cc_final: 0.7483 (m-70) REVERT: D 169 MET cc_start: 0.8606 (ptp) cc_final: 0.8278 (ptt) REVERT: D 174 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8709 (mp0) REVERT: D 240 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7958 (tm-30) REVERT: D 259 MET cc_start: 0.8593 (mmm) cc_final: 0.8204 (mmm) REVERT: D 263 ASP cc_start: 0.8947 (m-30) cc_final: 0.8700 (m-30) REVERT: D 413 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8497 (t0) outliers start: 52 outliers final: 38 residues processed: 226 average time/residue: 1.2152 time to fit residues: 300.7833 Evaluate side-chains 219 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 A residue 353 SER 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 236 ILE 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 B residue 353 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 95 LEU 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 353 SER 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 183 LEU 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 353 SER 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 106 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 127 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4117 r_free = 0.4117 target = 0.154397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.093409 restraints weight = 20391.194| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.54 r_work: 0.3086 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3369 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= 0.145 Angle : 0.623 10.983 16764 Z= 0.319 Chirality : 0.042 0.222 1872 Planarity : 0.005 0.056 2096 Dihedral : 4.106 18.069 1680 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.71 % Allowed : 21.59 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.23), residues: 1476 helix: 0.77 (0.17), residues: 988 sheet: -2.69 (0.66), residues: 40 loop : -1.19 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 359 HIS 0.001 0.000 HIS B 104 PHE 0.023 0.001 PHE B 185 TYR 0.037 0.002 TYR A 136 ARG 0.008 0.001 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 732) hydrogen bonds : angle 3.81489 ( 2064) covalent geometry : bond 0.00347 (12388) covalent geometry : angle 0.62295 (16764) *********************** 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 234 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7254 (t80) cc_final: 0.7047 (t80) REVERT: A 104 HIS cc_start: 0.8089 (m-70) cc_final: 0.7659 (m-70) REVERT: A 133 TYR cc_start: 0.4999 (t80) cc_final: 0.4568 (t80) REVERT: A 169 MET cc_start: 0.8582 (ptp) cc_final: 0.8323 (ptt) REVERT: A 174 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8670 (mp0) REVERT: A 235 MET cc_start: 0.8223 (ttm) cc_final: 0.7914 (ttp) REVERT: A 240 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7998 (tm-30) REVERT: A 259 MET cc_start: 0.8634 (mmm) cc_final: 0.8282 (mmm) REVERT: A 263 ASP cc_start: 0.8933 (m-30) cc_final: 0.8731 (m-30) REVERT: A 413 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8422 (t0) REVERT: B 104 HIS cc_start: 0.8051 (m-70) cc_final: 0.7562 (m-70) REVERT: B 133 TYR cc_start: 0.4834 (t80) cc_final: 0.4264 (t80) REVERT: B 136 TYR cc_start: 0.8186 (t80) cc_final: 0.7946 (t80) REVERT: B 140 LYS cc_start: 0.8261 (mtmm) cc_final: 0.7654 (mtmm) REVERT: B 169 MET cc_start: 0.8607 (ptp) cc_final: 0.8322 (ptt) REVERT: B 174 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8680 (mp0) REVERT: B 235 MET cc_start: 0.8223 (ttm) cc_final: 0.7929 (ttp) REVERT: B 240 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8020 (tm-30) REVERT: B 259 MET cc_start: 0.8619 (mmm) cc_final: 0.8188 (mmm) REVERT: B 414 GLN cc_start: 0.8235 (mm-40) cc_final: 0.8028 (tp-100) REVERT: C 91 PHE cc_start: 0.7093 (t80) cc_final: 0.6841 (t80) REVERT: C 104 HIS cc_start: 0.8133 (m-70) cc_final: 0.7504 (m-70) REVERT: C 169 MET cc_start: 0.8559 (ptp) cc_final: 0.8300 (ptt) REVERT: C 174 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8608 (mp0) REVERT: C 240 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8012 (tm-30) REVERT: C 259 MET cc_start: 0.8618 (mmm) cc_final: 0.8173 (mmm) REVERT: C 263 ASP cc_start: 0.8933 (m-30) cc_final: 0.8703 (m-30) REVERT: C 413 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8422 (t0) REVERT: D 104 HIS cc_start: 0.8131 (m-70) cc_final: 0.7443 (m-70) REVERT: D 133 TYR cc_start: 0.4989 (t80) cc_final: 0.4581 (t80) REVERT: D 169 MET cc_start: 0.8587 (ptp) cc_final: 0.8323 (ptt) REVERT: D 174 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8678 (mp0) REVERT: D 240 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8011 (tm-30) REVERT: D 259 MET cc_start: 0.8598 (mmm) cc_final: 0.8232 (mmm) REVERT: D 263 ASP cc_start: 0.8922 (m-30) cc_final: 0.8697 (m-30) REVERT: D 413 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8465 (t0) outliers start: 49 outliers final: 31 residues processed: 220 average time/residue: 1.1351 time to fit residues: 274.7907 Evaluate side-chains 216 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 1.449 ------------------------------------------------------------------------------- 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 275 VAL 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 95 LEU Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 188 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 95 LEU 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 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 275 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 86 optimal weight: 7.9990 chunk 16 optimal weight: 0.0470 chunk 124 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 132 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4112 r_free = 0.4112 target = 0.153930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.093035 restraints weight = 20519.802| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.55 r_work: 0.3080 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3472 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= 0.155 Angle : 0.625 11.036 16764 Z= 0.320 Chirality : 0.042 0.195 1872 Planarity : 0.005 0.058 2096 Dihedral : 4.063 23.844 1680 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.79 % Allowed : 21.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.23), residues: 1476 helix: 0.85 (0.17), residues: 988 sheet: -2.38 (0.71), residues: 40 loop : -1.17 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 359 HIS 0.001 0.000 HIS A 303 PHE 0.023 0.001 PHE B 185 TYR 0.035 0.002 TYR D 136 ARG 0.007 0.000 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 732) hydrogen bonds : angle 3.78882 ( 2064) covalent geometry : bond 0.00372 (12388) covalent geometry : angle 0.62521 (16764) *********************** 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 234 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8112 (m-70) cc_final: 0.7457 (m-70) REVERT: A 169 MET cc_start: 0.8596 (ptp) cc_final: 0.8328 (ptt) REVERT: A 174 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8714 (mp0) REVERT: A 235 MET cc_start: 0.8241 (ttm) cc_final: 0.7984 (mtt) REVERT: A 240 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8023 (tm-30) REVERT: A 259 MET cc_start: 0.8640 (mmm) cc_final: 0.8286 (mmm) REVERT: A 263 ASP cc_start: 0.8932 (m-30) cc_final: 0.8722 (m-30) REVERT: A 413 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8429 (t0) REVERT: B 104 HIS cc_start: 0.8020 (m-70) cc_final: 0.7467 (m-70) REVERT: B 133 TYR cc_start: 0.4711 (t80) cc_final: 0.4205 (t80) REVERT: B 136 TYR cc_start: 0.8160 (t80) cc_final: 0.7925 (t80) REVERT: B 140 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7651 (mtmm) REVERT: B 169 MET cc_start: 0.8610 (ptp) cc_final: 0.8333 (ptt) REVERT: B 174 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8731 (mp0) REVERT: B 235 MET cc_start: 0.8225 (ttm) cc_final: 0.8015 (mtt) REVERT: B 240 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8036 (tm-30) REVERT: B 259 MET cc_start: 0.8490 (mmm) cc_final: 0.8270 (mmm) REVERT: B 414 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8160 (tp-100) REVERT: C 91 PHE cc_start: 0.7092 (t80) cc_final: 0.6875 (t80) REVERT: C 104 HIS cc_start: 0.8070 (m-70) cc_final: 0.7595 (m-70) REVERT: C 169 MET cc_start: 0.8591 (ptp) cc_final: 0.8321 (ptt) REVERT: C 174 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8649 (mp0) REVERT: C 240 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8008 (tm-30) REVERT: C 259 MET cc_start: 0.8621 (mmm) cc_final: 0.8218 (mmm) REVERT: C 413 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8442 (t0) REVERT: D 104 HIS cc_start: 0.8227 (m-70) cc_final: 0.7345 (m-70) REVERT: D 169 MET cc_start: 0.8613 (ptp) cc_final: 0.8346 (ptt) REVERT: D 174 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8644 (mp0) REVERT: D 240 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8005 (tm-30) REVERT: D 259 MET cc_start: 0.8617 (mmm) cc_final: 0.8182 (mmm) REVERT: D 413 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8428 (t0) outliers start: 50 outliers final: 34 residues processed: 220 average time/residue: 1.0625 time to fit residues: 256.7817 Evaluate side-chains 220 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 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 275 VAL Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 236 ILE 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 B residue 353 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 70 GLU 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 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 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 275 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 353 SER 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 128 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4122 r_free = 0.4122 target = 0.154696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.094300 restraints weight = 20239.714| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.51 r_work: 0.3104 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12388 Z= 0.133 Angle : 0.636 11.586 16764 Z= 0.324 Chirality : 0.042 0.178 1872 Planarity : 0.005 0.058 2096 Dihedral : 3.963 22.221 1680 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.80 % Allowed : 22.95 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.23), residues: 1476 helix: 0.95 (0.17), residues: 988 sheet: -2.17 (0.72), residues: 40 loop : -1.09 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 359 HIS 0.002 0.000 HIS A 411 PHE 0.024 0.001 PHE B 185 TYR 0.017 0.001 TYR C 136 ARG 0.011 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 732) hydrogen bonds : angle 3.79782 ( 2064) covalent geometry : bond 0.00313 (12388) covalent geometry : angle 0.63610 (16764) *********************** 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 228 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8032 (m-70) cc_final: 0.7536 (m-70) REVERT: A 169 MET cc_start: 0.8568 (ptp) cc_final: 0.8298 (ptt) REVERT: A 174 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8698 (mp0) REVERT: A 228 CYS cc_start: 0.9129 (m) cc_final: 0.8663 (t) REVERT: A 235 MET cc_start: 0.8209 (ttm) cc_final: 0.7962 (mtt) REVERT: A 240 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8028 (tm-30) REVERT: A 259 MET cc_start: 0.8632 (mmm) cc_final: 0.8232 (mmm) REVERT: A 413 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8372 (t0) REVERT: B 104 HIS cc_start: 0.7962 (m-70) cc_final: 0.7494 (m-70) REVERT: B 136 TYR cc_start: 0.8055 (t80) cc_final: 0.7826 (t80) REVERT: B 140 LYS cc_start: 0.8245 (mtmm) cc_final: 0.7651 (mtmm) REVERT: B 169 MET cc_start: 0.8597 (ptp) cc_final: 0.8329 (ptt) REVERT: B 174 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8690 (mp0) REVERT: B 240 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8013 (tm-30) REVERT: C 91 PHE cc_start: 0.7043 (t80) cc_final: 0.6819 (t80) REVERT: C 104 HIS cc_start: 0.8059 (m-70) cc_final: 0.7657 (m-70) REVERT: C 169 MET cc_start: 0.8560 (ptp) cc_final: 0.8290 (ptt) REVERT: C 174 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8648 (mp0) REVERT: C 240 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7988 (tm-30) REVERT: C 413 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8452 (t0) REVERT: D 104 HIS cc_start: 0.8080 (m-70) cc_final: 0.7329 (m-70) REVERT: D 169 MET cc_start: 0.8565 (ptp) cc_final: 0.8303 (ptt) REVERT: D 174 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8647 (mp0) REVERT: D 228 CYS cc_start: 0.9093 (m) cc_final: 0.8612 (t) REVERT: D 240 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7988 (tm-30) REVERT: D 413 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8415 (t0) outliers start: 37 outliers final: 29 residues processed: 215 average time/residue: 1.1283 time to fit residues: 264.6906 Evaluate side-chains 208 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 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 95 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 236 ILE 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 95 LEU 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 276 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 353 SER 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 275 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 69 optimal weight: 1.9990 chunk 119 optimal weight: 0.0070 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4103 r_free = 0.4103 target = 0.153193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.092556 restraints weight = 20404.360| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.54 r_work: 0.3060 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12388 Z= 0.187 Angle : 0.689 11.247 16764 Z= 0.352 Chirality : 0.044 0.188 1872 Planarity : 0.005 0.059 2096 Dihedral : 4.016 22.492 1680 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.73 % Allowed : 23.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.23), residues: 1476 helix: 0.86 (0.17), residues: 1004 sheet: -1.99 (0.74), residues: 40 loop : -0.96 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 359 HIS 0.001 0.000 HIS A 411 PHE 0.023 0.001 PHE B 185 TYR 0.041 0.002 TYR A 136 ARG 0.009 0.001 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03877 ( 732) hydrogen bonds : angle 3.88150 ( 2064) covalent geometry : bond 0.00457 (12388) covalent geometry : angle 0.68900 (16764) ********************** 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 : 1.356 Fit side-chains REVERT: A 104 HIS cc_start: 0.8071 (m-70) cc_final: 0.7637 (m-70) REVERT: A 169 MET cc_start: 0.8594 (ptp) cc_final: 0.8319 (ptt) REVERT: A 174 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8762 (mp0) REVERT: A 235 MET cc_start: 0.8252 (ttm) cc_final: 0.8025 (mtt) REVERT: A 240 GLU cc_start: 0.8485 (tm-30) cc_final: 0.7951 (tm-30) REVERT: A 259 MET cc_start: 0.8530 (mmm) cc_final: 0.8307 (mmm) REVERT: A 413 ASN cc_start: 0.8805 (m110) cc_final: 0.8389 (t0) REVERT: B 104 HIS cc_start: 0.8203 (m-70) cc_final: 0.7674 (m-70) REVERT: B 136 TYR cc_start: 0.8029 (t80) cc_final: 0.7794 (t80) REVERT: B 140 LYS cc_start: 0.8182 (mtmm) cc_final: 0.7592 (mtmm) REVERT: B 169 MET cc_start: 0.8635 (ptp) cc_final: 0.8354 (ptt) REVERT: B 174 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8765 (mp0) REVERT: B 240 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8024 (tm-30) REVERT: C 91 PHE cc_start: 0.7055 (t80) cc_final: 0.6762 (t80) REVERT: C 104 HIS cc_start: 0.8097 (m-70) cc_final: 0.7665 (m-70) REVERT: C 169 MET cc_start: 0.8578 (ptp) cc_final: 0.8302 (ptt) REVERT: C 174 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8704 (mp0) REVERT: C 240 GLU cc_start: 0.8493 (tm-30) cc_final: 0.7999 (tm-30) REVERT: C 413 ASN cc_start: 0.8837 (m110) cc_final: 0.8372 (t0) REVERT: D 49 ARG cc_start: 0.5998 (mmm160) cc_final: 0.5725 (mmm160) REVERT: D 104 HIS cc_start: 0.8159 (m-70) cc_final: 0.7462 (m-70) REVERT: D 169 MET cc_start: 0.8587 (ptp) cc_final: 0.8316 (ptt) REVERT: D 174 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8701 (mp0) REVERT: D 240 GLU cc_start: 0.8470 (tm-30) cc_final: 0.7970 (tm-30) REVERT: D 413 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8400 (t0) outliers start: 36 outliers final: 27 residues processed: 199 average time/residue: 1.2970 time to fit residues: 284.4005 Evaluate side-chains 199 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 1.674 ------------------------------------------------------------------------------- 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 267 ILE Chi-restraints excluded: chain A residue 275 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 188 VAL Chi-restraints excluded: chain B residue 236 ILE 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 95 LEU 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 276 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 353 SER 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 188 VAL Chi-restraints excluded: chain D residue 275 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 39 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 143 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 chunk 79 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.155429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.095438 restraints weight = 20249.517| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.53 r_work: 0.3109 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12388 Z= 0.134 Angle : 0.672 11.730 16764 Z= 0.341 Chirality : 0.042 0.181 1872 Planarity : 0.005 0.058 2096 Dihedral : 4.056 24.724 1680 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.12 % Allowed : 24.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.23), residues: 1476 helix: 1.03 (0.17), residues: 988 sheet: -1.87 (0.75), residues: 40 loop : -0.96 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 359 HIS 0.001 0.000 HIS C 303 PHE 0.024 0.001 PHE B 185 TYR 0.041 0.001 TYR A 136 ARG 0.008 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 732) hydrogen bonds : angle 3.83391 ( 2064) covalent geometry : bond 0.00315 (12388) covalent geometry : angle 0.67236 (16764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11650.91 seconds wall clock time: 204 minutes 45.79 seconds (12285.79 seconds total)