Starting phenix.real_space_refine on Sat Aug 23 03:25:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5k0z_8191/08_2025/5k0z_8191.cif Found real_map, /net/cci-nas-00/data/ceres_data/5k0z_8191/08_2025/5k0z_8191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5k0z_8191/08_2025/5k0z_8191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5k0z_8191/08_2025/5k0z_8191.map" model { file = "/net/cci-nas-00/data/ceres_data/5k0z_8191/08_2025/5k0z_8191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5k0z_8191/08_2025/5k0z_8191.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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 52 5.16 5 C 6196 2.51 5 N 1636 2.21 5 O 1865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9749 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2427 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 307} Chain breaks: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Restraints were copied for chains: B, C, D Time building chain proxies: 1.35, per 1000 atoms: 0.14 Number of scatterers: 9749 At special positions: 0 Unit cell: (73.755, 97.515, 83.655, 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 52 16.00 O 1865 8.00 N 1636 7.00 C 6196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 219.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 12 sheets defined 46.4% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 30 through 41 Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.673A pdb=" N LYS A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 109 through 127 removed outlier: 3.501A pdb=" N ASN A 114 " --> pdb=" O GLN A 110 " (cutoff:3.500A) Proline residue: A 121 - end of helix removed outlier: 3.595A pdb=" N TYR A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 162 through 176 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 226 through 245 removed outlier: 3.999A pdb=" N HIS A 230 " --> pdb=" O TRP A 226 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 264 Processing helix chain 'A' and resid 308 through 327 removed outlier: 3.760A pdb=" N ILE A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 54 through 66 removed outlier: 3.673A pdb=" N LYS B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 109 through 127 removed outlier: 3.501A pdb=" N ASN B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A) Proline residue: B 121 - end of helix removed outlier: 3.595A pdb=" N TYR B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 162 through 176 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 226 through 245 removed outlier: 4.000A pdb=" N HIS B 230 " --> pdb=" O TRP B 226 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR B 238 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 243 " --> pdb=" O GLU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 308 through 327 removed outlier: 3.760A pdb=" N ILE B 325 " --> pdb=" O THR B 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 30 through 41 Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.672A pdb=" N LYS C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 109 through 127 removed outlier: 3.501A pdb=" N ASN C 114 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Proline residue: C 121 - end of helix removed outlier: 3.595A pdb=" N TYR C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 162 through 176 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 226 through 245 removed outlier: 4.000A pdb=" N HIS C 230 " --> pdb=" O TRP C 226 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR C 238 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 243 " --> pdb=" O GLU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 264 Processing helix chain 'C' and resid 308 through 327 removed outlier: 3.760A pdb=" N ILE C 325 " --> pdb=" O THR C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 54 through 66 removed outlier: 3.673A pdb=" N LYS D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 109 through 127 removed outlier: 3.502A pdb=" N ASN D 114 " --> pdb=" O GLN D 110 " (cutoff:3.500A) Proline residue: D 121 - end of helix removed outlier: 3.595A pdb=" N TYR D 126 " --> pdb=" O GLN D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 153 through 155 No H-bonds generated for 'chain 'D' and resid 153 through 155' Processing helix chain 'D' and resid 162 through 176 Processing helix chain 'D' and resid 210 through 214 Processing helix chain 'D' and resid 226 through 245 removed outlier: 3.999A pdb=" N HIS D 230 " --> pdb=" O TRP D 226 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR D 238 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 243 " --> pdb=" O GLU D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 264 Processing helix chain 'D' and resid 308 through 327 removed outlier: 3.760A pdb=" N ILE D 325 " --> pdb=" O THR D 321 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 10 removed outlier: 6.580A pdb=" N VAL C 293 " --> pdb=" O THR C 300 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL C 302 " --> pdb=" O PRO C 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 78 removed outlier: 5.923A pdb=" N LEU A 47 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE A 132 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 190 removed outlier: 10.027A pdb=" N HIS A 185 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER A 201 " --> pdb=" O HIS A 185 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TRP A 187 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 275 removed outlier: 4.830A pdb=" N VAL A 302 " --> pdb=" O PRO A 291 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 293 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 8 through 10 removed outlier: 6.579A pdb=" N VAL D 293 " --> pdb=" O THR D 300 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL D 302 " --> pdb=" O PRO D 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 75 through 78 removed outlier: 5.923A pdb=" N LEU B 47 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE B 132 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 184 through 190 removed outlier: 10.027A pdb=" N HIS B 185 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER B 201 " --> pdb=" O HIS B 185 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TRP B 187 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 268 through 275 removed outlier: 4.830A pdb=" N VAL B 302 " --> pdb=" O PRO B 291 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 293 " --> pdb=" O THR B 300 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 75 through 78 removed outlier: 5.924A pdb=" N LEU C 47 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE C 132 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 184 through 190 removed outlier: 10.027A pdb=" N HIS C 185 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER C 201 " --> pdb=" O HIS C 185 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TRP C 187 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 75 through 78 removed outlier: 5.923A pdb=" N LEU D 47 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE D 132 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 184 through 190 removed outlier: 10.027A pdb=" N HIS D 185 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER D 201 " --> pdb=" O HIS D 185 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TRP D 187 " --> pdb=" O VAL D 199 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2690 1.33 - 1.45: 1393 1.45 - 1.57: 5705 1.57 - 1.68: 0 1.68 - 1.80: 76 Bond restraints: 9864 Sorted by residual: bond pdb=" CB CYS B 184 " pdb=" SG CYS B 184 " ideal model delta sigma weight residual 1.808 1.745 0.063 3.30e-02 9.18e+02 3.66e+00 bond pdb=" CB CYS A 184 " pdb=" SG CYS A 184 " ideal model delta sigma weight residual 1.808 1.745 0.063 3.30e-02 9.18e+02 3.62e+00 bond pdb=" CB CYS C 184 " pdb=" SG CYS C 184 " ideal model delta sigma weight residual 1.808 1.745 0.063 3.30e-02 9.18e+02 3.59e+00 bond pdb=" CB CYS D 184 " pdb=" SG CYS D 184 " ideal model delta sigma weight residual 1.808 1.745 0.063 3.30e-02 9.18e+02 3.59e+00 bond pdb=" CG LEU D 263 " pdb=" CD1 LEU D 263 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.49e+00 ... (remaining 9859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 12500 1.89 - 3.78: 768 3.78 - 5.67: 88 5.67 - 7.56: 16 7.56 - 9.46: 12 Bond angle restraints: 13384 Sorted by residual: angle pdb=" C TYR D 126 " pdb=" N SER D 127 " pdb=" CA SER D 127 " ideal model delta sigma weight residual 122.74 119.03 3.71 1.06e+00 8.90e-01 1.23e+01 angle pdb=" C TYR B 126 " pdb=" N SER B 127 " pdb=" CA SER B 127 " ideal model delta sigma weight residual 122.74 119.05 3.69 1.06e+00 8.90e-01 1.21e+01 angle pdb=" C TYR A 126 " pdb=" N SER A 127 " pdb=" CA SER A 127 " ideal model delta sigma weight residual 122.74 119.07 3.67 1.06e+00 8.90e-01 1.20e+01 angle pdb=" C TYR C 126 " pdb=" N SER C 127 " pdb=" CA SER C 127 " ideal model delta sigma weight residual 122.74 119.08 3.66 1.06e+00 8.90e-01 1.19e+01 angle pdb=" CA GLN B 326 " pdb=" CB GLN B 326 " pdb=" CG GLN B 326 " ideal model delta sigma weight residual 114.10 120.89 -6.79 2.00e+00 2.50e-01 1.15e+01 ... (remaining 13379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 5704 17.61 - 35.22: 180 35.22 - 52.84: 20 52.84 - 70.45: 8 70.45 - 88.06: 12 Dihedral angle restraints: 5924 sinusoidal: 2284 harmonic: 3640 Sorted by residual: dihedral pdb=" CA GLY D 298 " pdb=" C GLY D 298 " pdb=" N LEU D 299 " pdb=" CA LEU D 299 " ideal model delta harmonic sigma weight residual 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA GLY A 298 " pdb=" C GLY A 298 " pdb=" N LEU A 299 " pdb=" CA LEU A 299 " ideal model delta harmonic sigma weight residual 180.00 158.62 21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA GLY C 298 " pdb=" C GLY C 298 " pdb=" N LEU C 299 " pdb=" CA LEU C 299 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 5921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 924 0.044 - 0.087: 505 0.087 - 0.131: 146 0.131 - 0.175: 39 0.175 - 0.218: 18 Chirality restraints: 1632 Sorted by residual: chirality pdb=" CA ASN D 225 " pdb=" N ASN D 225 " pdb=" C ASN D 225 " pdb=" CB ASN D 225 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASN C 225 " pdb=" N ASN C 225 " pdb=" C ASN C 225 " pdb=" CB ASN C 225 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ASN A 225 " pdb=" N ASN A 225 " pdb=" C ASN A 225 " pdb=" CB ASN A 225 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1629 not shown) Planarity restraints: 1652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 118 " 0.023 2.00e-02 2.50e+03 1.81e-02 5.75e+00 pdb=" CG PHE D 118 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE D 118 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE D 118 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE D 118 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 118 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 118 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 118 " 0.023 2.00e-02 2.50e+03 1.80e-02 5.67e+00 pdb=" CG PHE C 118 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE C 118 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 118 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 118 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 118 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 118 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 118 " -0.023 2.00e-02 2.50e+03 1.80e-02 5.66e+00 pdb=" CG PHE A 118 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE A 118 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 118 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 118 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 118 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 118 " -0.006 2.00e-02 2.50e+03 ... (remaining 1649 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 143 2.62 - 3.19: 9617 3.19 - 3.76: 15515 3.76 - 4.33: 23988 4.33 - 4.90: 37950 Nonbonded interactions: 87213 Sorted by model distance: nonbonded pdb=" O THR B 16 " pdb=" CG2 VAL B 17 " model vdw 2.056 3.460 nonbonded pdb=" O THR D 16 " pdb=" CG2 VAL D 17 " model vdw 2.056 3.460 nonbonded pdb=" O THR C 16 " pdb=" CG2 VAL C 17 " model vdw 2.056 3.460 nonbonded pdb=" O THR A 16 " pdb=" CG2 VAL A 17 " model vdw 2.056 3.460 nonbonded pdb=" NZ LYS B 21 " pdb=" O VAL B 84 " model vdw 2.089 3.120 ... (remaining 87208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.820 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.063 9864 Z= 0.473 Angle : 1.038 9.456 13384 Z= 0.572 Chirality : 0.059 0.218 1632 Planarity : 0.006 0.052 1652 Dihedral : 10.637 88.059 3572 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.11 (0.17), residues: 1244 helix: -3.65 (0.13), residues: 536 sheet: -2.52 (0.31), residues: 164 loop : -1.53 (0.20), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 242 TYR 0.022 0.003 TYR D 82 PHE 0.041 0.008 PHE D 118 TRP 0.033 0.005 TRP C 147 HIS 0.010 0.003 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.01108 ( 9864) covalent geometry : angle 1.03780 (13384) hydrogen bonds : bond 0.27044 ( 464) hydrogen bonds : angle 10.61323 ( 1332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 518 time to evaluate : 0.253 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: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.5770 (p0) cc_final: 0.5431 (p0) REVERT: A 328 ASP cc_start: 0.6820 (p0) cc_final: 0.6498 (p0) REVERT: B 55 ASP cc_start: 0.5735 (p0) cc_final: 0.5448 (p0) REVERT: B 328 ASP cc_start: 0.6840 (p0) cc_final: 0.6514 (p0) REVERT: C 55 ASP cc_start: 0.5777 (p0) cc_final: 0.5480 (p0) REVERT: C 328 ASP cc_start: 0.6801 (p0) cc_final: 0.6479 (p0) REVERT: D 55 ASP cc_start: 0.5785 (p0) cc_final: 0.5488 (p0) REVERT: D 328 ASP cc_start: 0.6820 (p0) cc_final: 0.6497 (p0) outliers start: 0 outliers final: 1 residues processed: 518 average time/residue: 0.3542 time to fit residues: 199.3617 Evaluate side-chains 320 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 30.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 40.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 304 ASN B 163 ASN B 304 ASN C 163 ASN C 304 ASN D 304 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.104224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.082843 restraints weight = 24864.614| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 5.14 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9864 Z= 0.211 Angle : 0.893 8.875 13384 Z= 0.466 Chirality : 0.049 0.203 1632 Planarity : 0.006 0.036 1652 Dihedral : 5.461 24.455 1318 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 24.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.27 % Allowed : 22.45 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.21), residues: 1244 helix: -1.15 (0.20), residues: 512 sheet: -2.02 (0.30), residues: 168 loop : -0.71 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG B 156 TYR 0.028 0.003 TYR D 171 PHE 0.018 0.003 PHE C 116 TRP 0.009 0.001 TRP B 249 HIS 0.005 0.002 HIS D 185 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 9864) covalent geometry : angle 0.89285 (13384) hydrogen bonds : bond 0.04912 ( 464) hydrogen bonds : angle 5.88681 ( 1332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 420 time to evaluate : 0.232 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8835 (ttp) cc_final: 0.8564 (ttp) REVERT: A 75 LYS cc_start: 0.9132 (tppp) cc_final: 0.8902 (tppp) REVERT: A 133 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9143 (tm) REVERT: A 170 ARG cc_start: 0.9043 (mtt180) cc_final: 0.8818 (mtt90) REVERT: A 171 TYR cc_start: 0.9162 (t80) cc_final: 0.8837 (t80) REVERT: A 188 ILE cc_start: 0.9140 (mp) cc_final: 0.8870 (mp) REVERT: A 232 GLN cc_start: 0.9214 (tp-100) cc_final: 0.8912 (tp-100) REVERT: A 242 ARG cc_start: 0.9160 (ttm-80) cc_final: 0.8948 (tmm-80) REVERT: A 249 TRP cc_start: 0.8176 (m-90) cc_final: 0.7963 (m-90) REVERT: A 310 ASP cc_start: 0.9280 (p0) cc_final: 0.8554 (p0) REVERT: B 60 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8989 (mm-30) REVERT: B 61 MET cc_start: 0.8818 (ttp) cc_final: 0.8607 (ttp) REVERT: B 170 ARG cc_start: 0.9056 (mtt180) cc_final: 0.8836 (mtt90) REVERT: B 171 TYR cc_start: 0.9166 (t80) cc_final: 0.8828 (t80) REVERT: B 188 ILE cc_start: 0.9136 (mp) cc_final: 0.8863 (mp) REVERT: B 232 GLN cc_start: 0.9257 (tp-100) cc_final: 0.8948 (tp-100) REVERT: B 249 TRP cc_start: 0.8208 (m-90) cc_final: 0.7997 (m-90) REVERT: B 310 ASP cc_start: 0.9276 (p0) cc_final: 0.8790 (p0) REVERT: C 61 MET cc_start: 0.8811 (ttp) cc_final: 0.8547 (ttp) REVERT: C 75 LYS cc_start: 0.9103 (tppp) cc_final: 0.8892 (tppp) REVERT: C 170 ARG cc_start: 0.9058 (mtt180) cc_final: 0.8832 (mtt90) REVERT: C 171 TYR cc_start: 0.9148 (t80) cc_final: 0.8838 (t80) REVERT: C 188 ILE cc_start: 0.9120 (mp) cc_final: 0.8851 (mp) REVERT: C 232 GLN cc_start: 0.9264 (tp-100) cc_final: 0.8957 (tp-100) REVERT: C 242 ARG cc_start: 0.9138 (ttm-80) cc_final: 0.8931 (tmm-80) REVERT: C 249 TRP cc_start: 0.8226 (m-90) cc_final: 0.8006 (m-90) REVERT: C 310 ASP cc_start: 0.9274 (p0) cc_final: 0.8565 (p0) REVERT: D 61 MET cc_start: 0.8791 (ttp) cc_final: 0.8538 (ttp) REVERT: D 75 LYS cc_start: 0.9108 (tppp) cc_final: 0.8894 (tppp) REVERT: D 170 ARG cc_start: 0.9070 (mtt180) cc_final: 0.8842 (mtt90) REVERT: D 171 TYR cc_start: 0.9126 (t80) cc_final: 0.8805 (t80) REVERT: D 188 ILE cc_start: 0.9138 (mp) cc_final: 0.8863 (mp) REVERT: D 232 GLN cc_start: 0.9249 (tp-100) cc_final: 0.8940 (tp-100) REVERT: D 242 ARG cc_start: 0.9105 (ttm-80) cc_final: 0.8897 (tmm-80) REVERT: D 310 ASP cc_start: 0.9283 (p0) cc_final: 0.8575 (p0) outliers start: 25 outliers final: 5 residues processed: 424 average time/residue: 0.3493 time to fit residues: 160.6626 Evaluate side-chains 299 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 293 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 293 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 68 optimal weight: 20.0000 chunk 83 optimal weight: 30.0000 chunk 89 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 59 optimal weight: 40.0000 chunk 99 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 78 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 232 GLN A 305 GLN C 232 GLN C 305 GLN D 232 GLN D 305 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.100842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.081489 restraints weight = 25810.563| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 4.62 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9864 Z= 0.206 Angle : 0.863 9.405 13384 Z= 0.440 Chirality : 0.052 0.301 1632 Planarity : 0.005 0.031 1652 Dihedral : 5.201 13.178 1316 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 24.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.55 % Allowed : 27.64 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.22), residues: 1244 helix: -0.26 (0.22), residues: 516 sheet: -1.91 (0.31), residues: 168 loop : -0.17 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG A 268 TYR 0.020 0.003 TYR A 126 PHE 0.018 0.004 PHE D 169 TRP 0.012 0.002 TRP C 249 HIS 0.004 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 9864) covalent geometry : angle 0.86266 (13384) hydrogen bonds : bond 0.04217 ( 464) hydrogen bonds : angle 5.75556 ( 1332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 376 time to evaluate : 0.289 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: 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: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8949 (ttp) cc_final: 0.8596 (ttp) REVERT: A 65 GLN cc_start: 0.8969 (mt0) cc_final: 0.8766 (pm20) REVERT: A 170 ARG cc_start: 0.9061 (mtt180) cc_final: 0.8730 (mtt-85) REVERT: A 171 TYR cc_start: 0.9151 (t80) cc_final: 0.8729 (t80) REVERT: A 210 LEU cc_start: 0.8778 (mp) cc_final: 0.8448 (mt) REVERT: A 217 MET cc_start: 0.6814 (ptm) cc_final: 0.6533 (ptm) REVERT: A 257 GLU cc_start: 0.8277 (tp30) cc_final: 0.7683 (tp30) REVERT: A 311 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8527 (mt-10) REVERT: B 61 MET cc_start: 0.8975 (ttp) cc_final: 0.8732 (ttp) REVERT: B 170 ARG cc_start: 0.9082 (mtt180) cc_final: 0.8765 (mtt-85) REVERT: B 171 TYR cc_start: 0.9158 (t80) cc_final: 0.8750 (t80) REVERT: B 172 LEU cc_start: 0.9109 (mt) cc_final: 0.8835 (mt) REVERT: B 232 GLN cc_start: 0.9277 (tp-100) cc_final: 0.8935 (tp-100) REVERT: B 257 GLU cc_start: 0.8484 (tp30) cc_final: 0.8028 (tp30) REVERT: B 314 GLN cc_start: 0.8977 (tp-100) cc_final: 0.8751 (tp-100) REVERT: B 317 LYS cc_start: 0.9371 (mtmt) cc_final: 0.9104 (ptpp) REVERT: B 328 ASP cc_start: 0.8940 (p0) cc_final: 0.8417 (p0) REVERT: C 61 MET cc_start: 0.8996 (ttp) cc_final: 0.8734 (ttp) REVERT: C 75 LYS cc_start: 0.9017 (tppp) cc_final: 0.8713 (tppp) REVERT: C 170 ARG cc_start: 0.9064 (mtt180) cc_final: 0.8695 (mtt-85) REVERT: C 171 TYR cc_start: 0.9154 (t80) cc_final: 0.8755 (t80) REVERT: C 172 LEU cc_start: 0.9088 (mt) cc_final: 0.8796 (mt) REVERT: C 217 MET cc_start: 0.6761 (ptm) cc_final: 0.6517 (ptm) REVERT: C 232 GLN cc_start: 0.9239 (tp40) cc_final: 0.8901 (tp-100) REVERT: C 257 GLU cc_start: 0.8540 (tp30) cc_final: 0.8090 (tp30) REVERT: C 311 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8535 (mt-10) REVERT: D 61 MET cc_start: 0.8940 (ttp) cc_final: 0.8567 (ttp) REVERT: D 75 LYS cc_start: 0.8995 (tppp) cc_final: 0.8712 (tppp) REVERT: D 170 ARG cc_start: 0.9084 (mtt180) cc_final: 0.8708 (mtt-85) REVERT: D 171 TYR cc_start: 0.9172 (t80) cc_final: 0.8704 (t80) REVERT: D 172 LEU cc_start: 0.9104 (mt) cc_final: 0.8827 (mt) REVERT: D 232 GLN cc_start: 0.9224 (tp40) cc_final: 0.8892 (tp-100) REVERT: D 257 GLU cc_start: 0.8515 (tp30) cc_final: 0.8118 (tp30) REVERT: D 311 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8544 (mt-10) outliers start: 50 outliers final: 13 residues processed: 394 average time/residue: 0.3604 time to fit residues: 154.0706 Evaluate side-chains 325 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 312 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 107 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 114 optimal weight: 40.0000 chunk 71 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.100820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.079512 restraints weight = 26447.017| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 5.30 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.6292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9864 Z= 0.196 Angle : 0.825 7.792 13384 Z= 0.422 Chirality : 0.049 0.215 1632 Planarity : 0.005 0.054 1652 Dihedral : 5.153 18.437 1316 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 23.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 5.55 % Allowed : 29.09 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.24), residues: 1244 helix: 0.11 (0.22), residues: 508 sheet: -1.49 (0.40), residues: 132 loop : 0.16 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG A 268 TYR 0.020 0.002 TYR B 126 PHE 0.021 0.003 PHE B 70 TRP 0.012 0.002 TRP C 249 HIS 0.008 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 9864) covalent geometry : angle 0.82522 (13384) hydrogen bonds : bond 0.03874 ( 464) hydrogen bonds : angle 5.67054 ( 1332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 344 time to evaluate : 0.251 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9061 (ttp) cc_final: 0.8807 (ttp) REVERT: A 170 ARG cc_start: 0.9003 (mtt180) cc_final: 0.8761 (mtt180) REVERT: A 171 TYR cc_start: 0.9264 (t80) cc_final: 0.8930 (t80) REVERT: A 232 GLN cc_start: 0.9343 (tp-100) cc_final: 0.9028 (tp-100) REVERT: A 257 GLU cc_start: 0.8396 (tp30) cc_final: 0.7794 (tp30) REVERT: A 311 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8586 (mt-10) REVERT: B 61 MET cc_start: 0.9055 (ttp) cc_final: 0.8821 (ttp) REVERT: B 170 ARG cc_start: 0.9009 (mtt180) cc_final: 0.8704 (mtt180) REVERT: B 171 TYR cc_start: 0.9255 (t80) cc_final: 0.8949 (t80) REVERT: B 232 GLN cc_start: 0.9239 (tp40) cc_final: 0.8941 (tp-100) REVERT: B 257 GLU cc_start: 0.8553 (tp30) cc_final: 0.7688 (tp30) REVERT: B 268 ARG cc_start: 0.8950 (ttp-110) cc_final: 0.8536 (ttp80) REVERT: B 294 LEU cc_start: 0.9253 (mp) cc_final: 0.8748 (tm) REVERT: B 311 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8643 (mt-10) REVERT: B 328 ASP cc_start: 0.9045 (p0) cc_final: 0.8708 (p0) REVERT: C 61 MET cc_start: 0.9028 (ttp) cc_final: 0.8775 (ttp) REVERT: C 170 ARG cc_start: 0.9003 (mtt180) cc_final: 0.8709 (mtt180) REVERT: C 171 TYR cc_start: 0.9261 (t80) cc_final: 0.9000 (t80) REVERT: C 232 GLN cc_start: 0.9291 (tp40) cc_final: 0.8969 (tp-100) REVERT: C 257 GLU cc_start: 0.8617 (tp30) cc_final: 0.7751 (tp30) REVERT: C 268 ARG cc_start: 0.8970 (ttp-110) cc_final: 0.8580 (ttp80) REVERT: C 294 LEU cc_start: 0.9226 (mp) cc_final: 0.8735 (tm) REVERT: D 170 ARG cc_start: 0.9008 (mtt180) cc_final: 0.8710 (mtt180) REVERT: D 171 TYR cc_start: 0.9262 (t80) cc_final: 0.8959 (t80) REVERT: D 232 GLN cc_start: 0.9312 (tp40) cc_final: 0.8991 (tp-100) REVERT: D 257 GLU cc_start: 0.8582 (tp30) cc_final: 0.7546 (tp30) REVERT: D 268 ARG cc_start: 0.8837 (ttp-110) cc_final: 0.8463 (ttp80) REVERT: D 311 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8593 (mt-10) outliers start: 61 outliers final: 25 residues processed: 384 average time/residue: 0.3585 time to fit residues: 148.8738 Evaluate side-chains 348 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 323 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 90 optimal weight: 30.0000 chunk 9 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 11 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 113 optimal weight: 50.0000 chunk 39 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 155 HIS ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN B 155 HIS ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN D 155 HIS D 163 ASN ** D 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.097311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.077055 restraints weight = 26171.863| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 4.99 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.6513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 9864 Z= 0.228 Angle : 0.831 8.002 13384 Z= 0.429 Chirality : 0.050 0.255 1632 Planarity : 0.005 0.067 1652 Dihedral : 5.137 19.871 1316 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 24.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.18 % Allowed : 30.45 % Favored : 64.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.24), residues: 1244 helix: 0.27 (0.22), residues: 520 sheet: -1.49 (0.41), residues: 132 loop : 0.33 (0.28), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG A 268 TYR 0.013 0.002 TYR C 171 PHE 0.020 0.003 PHE B 70 TRP 0.014 0.002 TRP D 249 HIS 0.008 0.002 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 9864) covalent geometry : angle 0.83053 (13384) hydrogen bonds : bond 0.04011 ( 464) hydrogen bonds : angle 5.77085 ( 1332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 359 time to evaluate : 0.357 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: 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: symmetry clash REVERT: A 8 ILE cc_start: 0.9002 (mt) cc_final: 0.8743 (pt) REVERT: A 170 ARG cc_start: 0.9003 (mtt180) cc_final: 0.8687 (mtt180) REVERT: A 171 TYR cc_start: 0.9294 (t80) cc_final: 0.8949 (t80) REVERT: A 217 MET cc_start: 0.7412 (ptm) cc_final: 0.7212 (ptm) REVERT: A 232 GLN cc_start: 0.9290 (tp40) cc_final: 0.9037 (tp-100) REVERT: A 257 GLU cc_start: 0.8390 (tp30) cc_final: 0.7849 (tp30) REVERT: A 311 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8601 (mt-10) REVERT: B 61 MET cc_start: 0.9046 (ttp) cc_final: 0.8842 (ttp) REVERT: B 75 LYS cc_start: 0.8947 (ttmm) cc_final: 0.8712 (ttmm) REVERT: B 170 ARG cc_start: 0.9035 (mtt180) cc_final: 0.8719 (mtt180) REVERT: B 171 TYR cc_start: 0.9269 (t80) cc_final: 0.8960 (t80) REVERT: B 249 TRP cc_start: 0.8156 (m-90) cc_final: 0.7638 (m-90) REVERT: B 257 GLU cc_start: 0.8589 (tp30) cc_final: 0.7470 (tp30) REVERT: B 268 ARG cc_start: 0.8852 (ttp-110) cc_final: 0.8504 (ttp80) REVERT: B 311 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8623 (mt-10) REVERT: B 314 GLN cc_start: 0.8911 (tp-100) cc_final: 0.8610 (tp-100) REVERT: B 317 LYS cc_start: 0.9444 (mtmt) cc_final: 0.9230 (ptpp) REVERT: C 61 MET cc_start: 0.9024 (ttp) cc_final: 0.8803 (ttp) REVERT: C 81 ASP cc_start: 0.9033 (p0) cc_final: 0.8813 (p0) REVERT: C 170 ARG cc_start: 0.8999 (mtt180) cc_final: 0.8710 (mtt180) REVERT: C 171 TYR cc_start: 0.9288 (t80) cc_final: 0.9025 (t80) REVERT: C 232 GLN cc_start: 0.9288 (tp40) cc_final: 0.9021 (tp-100) REVERT: C 249 TRP cc_start: 0.8136 (m-90) cc_final: 0.7602 (m-90) REVERT: C 257 GLU cc_start: 0.8687 (tp30) cc_final: 0.7569 (tp30) REVERT: C 264 LYS cc_start: 0.9195 (mmmm) cc_final: 0.8934 (mtpt) REVERT: C 268 ARG cc_start: 0.8813 (ttp-110) cc_final: 0.8580 (ttp80) REVERT: C 311 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8647 (mt-10) REVERT: D 61 MET cc_start: 0.9105 (ttp) cc_final: 0.8635 (tpp) REVERT: D 81 ASP cc_start: 0.9022 (p0) cc_final: 0.8768 (p0) REVERT: D 170 ARG cc_start: 0.9017 (mtt180) cc_final: 0.8711 (mtt180) REVERT: D 171 TYR cc_start: 0.9273 (t80) cc_final: 0.8939 (t80) REVERT: D 217 MET cc_start: 0.7448 (ptm) cc_final: 0.7120 (ptt) REVERT: D 232 GLN cc_start: 0.9306 (tp40) cc_final: 0.8984 (tp-100) REVERT: D 257 GLU cc_start: 0.8689 (tp30) cc_final: 0.7759 (tp30) REVERT: D 262 MET cc_start: 0.8699 (mmm) cc_final: 0.7450 (mmm) REVERT: D 268 ARG cc_start: 0.8883 (ttp-110) cc_final: 0.8607 (ttp80) REVERT: D 294 LEU cc_start: 0.9191 (mp) cc_final: 0.8507 (tp) REVERT: D 311 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8622 (mt-10) outliers start: 57 outliers final: 33 residues processed: 389 average time/residue: 0.3478 time to fit residues: 146.5165 Evaluate side-chains 325 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 292 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 2.9990 chunk 118 optimal weight: 20.0000 chunk 30 optimal weight: 40.0000 chunk 110 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 109 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 63 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN B 20 ASN ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.099773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.079503 restraints weight = 26445.214| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 5.18 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.6925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9864 Z= 0.187 Angle : 0.865 8.319 13384 Z= 0.443 Chirality : 0.051 0.284 1632 Planarity : 0.006 0.072 1652 Dihedral : 5.107 18.394 1316 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.82 % Allowed : 32.73 % Favored : 62.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.24), residues: 1244 helix: 0.45 (0.23), residues: 508 sheet: -1.48 (0.43), residues: 132 loop : 0.38 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 268 TYR 0.013 0.002 TYR D 267 PHE 0.020 0.003 PHE C 70 TRP 0.015 0.002 TRP C 249 HIS 0.006 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 9864) covalent geometry : angle 0.86513 (13384) hydrogen bonds : bond 0.03904 ( 464) hydrogen bonds : angle 5.71310 ( 1332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 350 time to evaluate : 0.358 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ILE cc_start: 0.9007 (mt) cc_final: 0.8735 (pt) REVERT: A 170 ARG cc_start: 0.8934 (mtt180) cc_final: 0.8660 (mtt-85) REVERT: A 171 TYR cc_start: 0.9264 (t80) cc_final: 0.9007 (t80) REVERT: A 232 GLN cc_start: 0.9310 (tp40) cc_final: 0.9058 (tp-100) REVERT: A 257 GLU cc_start: 0.8296 (tp30) cc_final: 0.7325 (tp30) REVERT: A 268 ARG cc_start: 0.8616 (ttp-110) cc_final: 0.8400 (ttp80) REVERT: A 311 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8606 (mt-10) REVERT: B 46 GLU cc_start: 0.8788 (tp30) cc_final: 0.8412 (tp30) REVERT: B 170 ARG cc_start: 0.8970 (mtt180) cc_final: 0.8717 (mtt180) REVERT: B 232 GLN cc_start: 0.9249 (tp-100) cc_final: 0.8945 (tp-100) REVERT: B 257 GLU cc_start: 0.8546 (tp30) cc_final: 0.7609 (tp30) REVERT: B 311 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8663 (mt-10) REVERT: B 314 GLN cc_start: 0.8869 (tp-100) cc_final: 0.8633 (tp-100) REVERT: B 328 ASP cc_start: 0.9068 (p0) cc_final: 0.8743 (p0) REVERT: C 61 MET cc_start: 0.9050 (ttp) cc_final: 0.8652 (ttp) REVERT: C 170 ARG cc_start: 0.8942 (mtt180) cc_final: 0.8678 (mtt180) REVERT: C 171 TYR cc_start: 0.9268 (t80) cc_final: 0.9046 (t80) REVERT: C 232 GLN cc_start: 0.9281 (tp40) cc_final: 0.9056 (tp-100) REVERT: C 249 TRP cc_start: 0.8148 (m-90) cc_final: 0.7597 (m-90) REVERT: C 257 GLU cc_start: 0.8706 (tp30) cc_final: 0.7725 (tp30) REVERT: C 311 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8647 (mt-10) REVERT: D 61 MET cc_start: 0.9083 (ttp) cc_final: 0.8659 (tpp) REVERT: D 170 ARG cc_start: 0.8943 (mtt180) cc_final: 0.8681 (mtt180) REVERT: D 171 TYR cc_start: 0.9280 (t80) cc_final: 0.9024 (t80) REVERT: D 228 GLU cc_start: 0.8446 (pm20) cc_final: 0.8024 (pm20) REVERT: D 232 GLN cc_start: 0.9281 (tp40) cc_final: 0.9073 (tp-100) REVERT: D 257 GLU cc_start: 0.8713 (tp30) cc_final: 0.7728 (tp30) REVERT: D 311 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8628 (mt-10) outliers start: 53 outliers final: 36 residues processed: 376 average time/residue: 0.3567 time to fit residues: 145.5121 Evaluate side-chains 329 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 293 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 118 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 109 optimal weight: 30.0000 chunk 98 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 chunk 111 optimal weight: 0.0770 chunk 33 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 GLN C 314 GLN D 20 ASN D 314 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.100856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.081343 restraints weight = 26253.831| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 4.98 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.7108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9864 Z= 0.182 Angle : 0.899 11.085 13384 Z= 0.457 Chirality : 0.051 0.302 1632 Planarity : 0.006 0.078 1652 Dihedral : 5.135 19.496 1316 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 6.00 % Allowed : 32.55 % Favored : 61.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.24), residues: 1244 helix: 0.45 (0.23), residues: 508 sheet: -1.48 (0.43), residues: 132 loop : 0.45 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG B 268 TYR 0.033 0.002 TYR B 171 PHE 0.023 0.003 PHE B 70 TRP 0.016 0.002 TRP B 226 HIS 0.005 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 9864) covalent geometry : angle 0.89874 (13384) hydrogen bonds : bond 0.03714 ( 464) hydrogen bonds : angle 5.73739 ( 1332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 331 time to evaluate : 0.221 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: 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 81 ASP cc_start: 0.8866 (t0) cc_final: 0.8645 (p0) REVERT: A 170 ARG cc_start: 0.8892 (mtt180) cc_final: 0.8681 (mtt180) REVERT: A 171 TYR cc_start: 0.9257 (t80) cc_final: 0.9052 (t80) REVERT: A 232 GLN cc_start: 0.9259 (tp40) cc_final: 0.9032 (tp-100) REVERT: A 257 GLU cc_start: 0.8275 (tp30) cc_final: 0.7558 (tp30) REVERT: A 294 LEU cc_start: 0.9071 (mp) cc_final: 0.8546 (tp) REVERT: A 311 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8603 (mt-10) REVERT: B 170 ARG cc_start: 0.8912 (mtt180) cc_final: 0.8622 (mtt180) REVERT: B 171 TYR cc_start: 0.9180 (t80) cc_final: 0.8942 (t80) REVERT: B 249 TRP cc_start: 0.8065 (m-90) cc_final: 0.7523 (m-90) REVERT: B 257 GLU cc_start: 0.8432 (tp30) cc_final: 0.8196 (tp30) REVERT: B 311 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8660 (mt-10) REVERT: B 316 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8969 (mtpp) REVERT: B 328 ASP cc_start: 0.8992 (p0) cc_final: 0.8636 (p0) REVERT: C 61 MET cc_start: 0.9035 (ttp) cc_final: 0.8659 (ttp) REVERT: C 170 ARG cc_start: 0.8937 (mtt180) cc_final: 0.8651 (mtt180) REVERT: C 171 TYR cc_start: 0.9225 (t80) cc_final: 0.9008 (t80) REVERT: C 232 GLN cc_start: 0.9259 (tp40) cc_final: 0.8953 (tp-100) REVERT: C 249 TRP cc_start: 0.8009 (m-90) cc_final: 0.7718 (m-90) REVERT: C 257 GLU cc_start: 0.8472 (tp30) cc_final: 0.7581 (tp30) REVERT: C 311 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8640 (mt-10) REVERT: D 61 MET cc_start: 0.9039 (ttp) cc_final: 0.8648 (tpp) REVERT: D 170 ARG cc_start: 0.8946 (mtt180) cc_final: 0.8456 (mtt-85) REVERT: D 232 GLN cc_start: 0.9303 (tp40) cc_final: 0.8949 (tp-100) REVERT: D 257 GLU cc_start: 0.8534 (tp30) cc_final: 0.8199 (tp30) REVERT: D 294 LEU cc_start: 0.9091 (mp) cc_final: 0.8554 (tp) REVERT: D 311 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8627 (mt-10) outliers start: 66 outliers final: 38 residues processed: 367 average time/residue: 0.3347 time to fit residues: 133.5147 Evaluate side-chains 345 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 306 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 5.9990 chunk 42 optimal weight: 40.0000 chunk 112 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 8 optimal weight: 40.0000 chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 92 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 71 optimal weight: 40.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 ASN A 314 GLN B 20 ASN B 232 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.100098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.079273 restraints weight = 27218.396| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 5.10 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.7420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9864 Z= 0.203 Angle : 0.971 13.402 13384 Z= 0.490 Chirality : 0.053 0.302 1632 Planarity : 0.006 0.064 1652 Dihedral : 5.149 20.218 1316 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.45 % Allowed : 35.73 % Favored : 58.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.24), residues: 1244 helix: 0.44 (0.23), residues: 508 sheet: -0.37 (0.54), residues: 92 loop : 0.13 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG C 268 TYR 0.034 0.003 TYR A 246 PHE 0.030 0.004 PHE B 70 TRP 0.024 0.002 TRP A 249 HIS 0.007 0.002 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 9864) covalent geometry : angle 0.97060 (13384) hydrogen bonds : bond 0.03840 ( 464) hydrogen bonds : angle 5.75892 ( 1332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 320 time to evaluate : 0.371 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: 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 170 ARG cc_start: 0.8965 (mtt180) cc_final: 0.8709 (mtt180) REVERT: A 232 GLN cc_start: 0.9255 (tp40) cc_final: 0.8928 (tp-100) REVERT: A 257 GLU cc_start: 0.8146 (tp30) cc_final: 0.7152 (tp30) REVERT: A 268 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8197 (ttp80) REVERT: A 294 LEU cc_start: 0.9075 (mp) cc_final: 0.8544 (tp) REVERT: A 311 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8569 (mt-10) REVERT: B 8 ILE cc_start: 0.8993 (mt) cc_final: 0.8687 (pt) REVERT: B 170 ARG cc_start: 0.8957 (mtt180) cc_final: 0.8457 (mtt-85) REVERT: B 257 GLU cc_start: 0.8399 (tp30) cc_final: 0.7789 (tp30) REVERT: B 311 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8634 (mt-10) REVERT: B 316 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.9015 (mtpp) REVERT: B 328 ASP cc_start: 0.8946 (p0) cc_final: 0.8580 (p0) REVERT: C 61 MET cc_start: 0.8998 (ttp) cc_final: 0.8568 (ttp) REVERT: C 62 MET cc_start: 0.8921 (mtm) cc_final: 0.8721 (ttm) REVERT: C 65 GLN cc_start: 0.9075 (pt0) cc_final: 0.8868 (pt0) REVERT: C 170 ARG cc_start: 0.8971 (mtt180) cc_final: 0.8687 (mtt180) REVERT: C 171 TYR cc_start: 0.9216 (t80) cc_final: 0.8983 (t80) REVERT: C 232 GLN cc_start: 0.9245 (tp40) cc_final: 0.8971 (tp-100) REVERT: C 249 TRP cc_start: 0.8064 (m-90) cc_final: 0.7731 (m-90) REVERT: C 257 GLU cc_start: 0.8228 (tp30) cc_final: 0.7721 (tp30) REVERT: C 294 LEU cc_start: 0.9085 (mp) cc_final: 0.8611 (tp) REVERT: C 311 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8611 (mt-10) REVERT: D 61 MET cc_start: 0.8972 (ttp) cc_final: 0.8677 (ttp) REVERT: D 170 ARG cc_start: 0.8899 (mtt180) cc_final: 0.8454 (mtt-85) REVERT: D 217 MET cc_start: 0.7717 (ptm) cc_final: 0.7494 (ptt) REVERT: D 232 GLN cc_start: 0.9257 (tp40) cc_final: 0.8899 (tp-100) REVERT: D 257 GLU cc_start: 0.8396 (tp30) cc_final: 0.7761 (tp30) REVERT: D 294 LEU cc_start: 0.9086 (mp) cc_final: 0.8493 (tp) REVERT: D 311 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8609 (mt-10) REVERT: D 328 ASP cc_start: 0.9000 (p0) cc_final: 0.8658 (p0) outliers start: 60 outliers final: 38 residues processed: 349 average time/residue: 0.3594 time to fit residues: 136.4031 Evaluate side-chains 339 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 299 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 303 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 39 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 93 optimal weight: 30.0000 chunk 97 optimal weight: 40.0000 chunk 105 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 HIS B 20 ASN ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 GLN C 20 ASN ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN D 20 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.099656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.079338 restraints weight = 26929.351| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 5.12 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.7554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9864 Z= 0.216 Angle : 1.002 13.994 13384 Z= 0.504 Chirality : 0.054 0.309 1632 Planarity : 0.006 0.066 1652 Dihedral : 5.302 20.406 1316 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 26.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.73 % Allowed : 37.09 % Favored : 58.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.24), residues: 1244 helix: 0.11 (0.23), residues: 524 sheet: -0.35 (0.55), residues: 92 loop : -0.06 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG C 268 TYR 0.039 0.003 TYR D 171 PHE 0.032 0.005 PHE D 70 TRP 0.029 0.002 TRP A 249 HIS 0.006 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 9864) covalent geometry : angle 1.00156 (13384) hydrogen bonds : bond 0.03899 ( 464) hydrogen bonds : angle 5.89906 ( 1332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 320 time to evaluate : 0.363 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: 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 170 ARG cc_start: 0.8915 (mtt180) cc_final: 0.8455 (mtt-85) REVERT: A 171 TYR cc_start: 0.9116 (t80) cc_final: 0.8911 (t80) REVERT: A 257 GLU cc_start: 0.8009 (tp30) cc_final: 0.7006 (tp30) REVERT: A 268 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8008 (ttp-170) REVERT: A 294 LEU cc_start: 0.9027 (mp) cc_final: 0.8496 (tp) REVERT: A 328 ASP cc_start: 0.9050 (p0) cc_final: 0.8793 (p0) REVERT: B 8 ILE cc_start: 0.8993 (mt) cc_final: 0.8692 (pt) REVERT: B 249 TRP cc_start: 0.7917 (m-90) cc_final: 0.7621 (m-90) REVERT: B 257 GLU cc_start: 0.8285 (tp30) cc_final: 0.7738 (tp30) REVERT: B 275 LEU cc_start: 0.8496 (mt) cc_final: 0.8143 (tm) REVERT: B 287 PHE cc_start: 0.8215 (m-80) cc_final: 0.7907 (m-80) REVERT: B 294 LEU cc_start: 0.9120 (mp) cc_final: 0.8559 (tp) REVERT: B 311 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8654 (mt-10) REVERT: B 316 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8961 (mtpp) REVERT: B 328 ASP cc_start: 0.8989 (p0) cc_final: 0.8645 (p0) REVERT: C 170 ARG cc_start: 0.8992 (mtt180) cc_final: 0.8723 (mtt180) REVERT: C 232 GLN cc_start: 0.9238 (tp40) cc_final: 0.8887 (tp-100) REVERT: C 249 TRP cc_start: 0.7865 (m-90) cc_final: 0.7571 (m-90) REVERT: C 275 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8025 (tm) REVERT: C 294 LEU cc_start: 0.9095 (mp) cc_final: 0.8619 (tp) REVERT: C 311 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8609 (mt-10) REVERT: C 328 ASP cc_start: 0.8999 (p0) cc_final: 0.8652 (p0) REVERT: D 61 MET cc_start: 0.8922 (ttp) cc_final: 0.8638 (ttp) REVERT: D 170 ARG cc_start: 0.8869 (mtt180) cc_final: 0.8668 (mtt180) REVERT: D 228 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8265 (pm20) REVERT: D 257 GLU cc_start: 0.8305 (tp30) cc_final: 0.7545 (tp30) REVERT: D 294 LEU cc_start: 0.9049 (mp) cc_final: 0.8438 (tp) REVERT: D 311 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8605 (mt-10) REVERT: D 328 ASP cc_start: 0.8943 (p0) cc_final: 0.8597 (p0) outliers start: 52 outliers final: 38 residues processed: 342 average time/residue: 0.3315 time to fit residues: 123.9810 Evaluate side-chains 312 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 270 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 91 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 31 optimal weight: 50.0000 chunk 85 optimal weight: 0.8980 chunk 113 optimal weight: 30.0000 chunk 17 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 107 optimal weight: 40.0000 chunk 69 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 GLN D 20 ASN D 232 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.100722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.080256 restraints weight = 26865.866| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 5.11 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.7787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9864 Z= 0.207 Angle : 1.055 14.722 13384 Z= 0.528 Chirality : 0.055 0.304 1632 Planarity : 0.006 0.065 1652 Dihedral : 5.386 20.606 1316 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 26.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.64 % Allowed : 37.73 % Favored : 57.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.24), residues: 1244 helix: 0.10 (0.23), residues: 516 sheet: -0.40 (0.56), residues: 92 loop : -0.04 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A 168 TYR 0.038 0.003 TYR D 171 PHE 0.028 0.005 PHE C 169 TRP 0.021 0.002 TRP D 226 HIS 0.006 0.002 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 9864) covalent geometry : angle 1.05514 (13384) hydrogen bonds : bond 0.04001 ( 464) hydrogen bonds : angle 5.95985 ( 1332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 289 time to evaluate : 0.337 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.8783 (mtt180) cc_final: 0.8555 (mtt180) REVERT: A 257 GLU cc_start: 0.8023 (tp30) cc_final: 0.6992 (tp30) REVERT: A 268 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7967 (ttp-170) REVERT: A 275 LEU cc_start: 0.8481 (mt) cc_final: 0.8052 (tm) REVERT: A 294 LEU cc_start: 0.9020 (mp) cc_final: 0.8525 (tp) REVERT: B 61 MET cc_start: 0.8875 (ttp) cc_final: 0.8633 (tpp) REVERT: B 170 ARG cc_start: 0.8938 (mtt180) cc_final: 0.8449 (mtt-85) REVERT: B 249 TRP cc_start: 0.7819 (m-90) cc_final: 0.7443 (m-90) REVERT: B 257 GLU cc_start: 0.8257 (tp30) cc_final: 0.7748 (tp30) REVERT: B 294 LEU cc_start: 0.9134 (mp) cc_final: 0.8599 (tp) REVERT: B 316 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8959 (mtpp) REVERT: B 328 ASP cc_start: 0.8892 (p0) cc_final: 0.8533 (p0) REVERT: C 61 MET cc_start: 0.8960 (ttp) cc_final: 0.8597 (tpp) REVERT: C 65 GLN cc_start: 0.9114 (pt0) cc_final: 0.8672 (pt0) REVERT: C 79 ASP cc_start: 0.8305 (p0) cc_final: 0.7831 (p0) REVERT: C 170 ARG cc_start: 0.8888 (mtt180) cc_final: 0.8619 (mtt180) REVERT: C 171 TYR cc_start: 0.9185 (t80) cc_final: 0.8964 (t80) REVERT: C 232 GLN cc_start: 0.9235 (tp40) cc_final: 0.9029 (tp-100) REVERT: C 275 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8034 (tm) REVERT: C 294 LEU cc_start: 0.9061 (mp) cc_final: 0.8571 (tp) REVERT: D 46 GLU cc_start: 0.8391 (tp30) cc_final: 0.7860 (tp30) REVERT: D 170 ARG cc_start: 0.8641 (mtt180) cc_final: 0.8433 (mtt180) REVERT: D 257 GLU cc_start: 0.8272 (tp30) cc_final: 0.7684 (tp30) REVERT: D 275 LEU cc_start: 0.8462 (mt) cc_final: 0.8045 (tm) REVERT: D 294 LEU cc_start: 0.9086 (mp) cc_final: 0.8428 (tt) REVERT: D 311 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8629 (mt-10) outliers start: 51 outliers final: 36 residues processed: 311 average time/residue: 0.2983 time to fit residues: 101.9120 Evaluate side-chains 305 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 266 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 37 optimal weight: 8.9990 chunk 107 optimal weight: 50.0000 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 232 GLN B 20 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.100442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.079848 restraints weight = 27326.488| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 5.16 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.7784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.299 9864 Z= 0.370 Angle : 1.257 59.198 13384 Z= 0.669 Chirality : 0.058 0.406 1632 Planarity : 0.007 0.080 1652 Dihedral : 5.396 23.050 1316 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 32.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.45 % Allowed : 38.36 % Favored : 57.18 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.24), residues: 1244 helix: 0.04 (0.24), residues: 516 sheet: -0.41 (0.56), residues: 92 loop : -0.04 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.065 0.003 ARG C 176 TYR 0.035 0.003 TYR A 171 PHE 0.023 0.005 PHE B 70 TRP 0.150 0.005 TRP C 226 HIS 0.006 0.002 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00912 ( 9864) covalent geometry : angle 1.25686 (13384) hydrogen bonds : bond 0.04064 ( 464) hydrogen bonds : angle 5.98087 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2785.81 seconds wall clock time: 48 minutes 34.63 seconds (2914.63 seconds total)