Starting phenix.real_space_refine on Thu Feb 13 21:32:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5k0z_8191/02_2025/5k0z_8191.cif Found real_map, /net/cci-nas-00/data/ceres_data/5k0z_8191/02_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_8191/02_2025/5k0z_8191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5k0z_8191/02_2025/5k0z_8191.map" model { file = "/net/cci-nas-00/data/ceres_data/5k0z_8191/02_2025/5k0z_8191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5k0z_8191/02_2025/5k0z_8191.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: C, B, D Time building chain proxies: 4.40, per 1000 atoms: 0.45 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: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.36 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: 3.08 Time building geometry restraints manager: 2.91 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 23.710 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.740 ------------------------------------------------------------------------------- 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= 0.728 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (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 TRP 0.033 0.005 TRP C 147 HIS 0.010 0.003 HIS C 180 PHE 0.041 0.008 PHE D 118 TYR 0.022 0.003 TYR D 82 ARG 0.007 0.001 ARG B 242 *********************** 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 : 1.154 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: A 55 ASP cc_start: 0.5770 (p0) cc_final: 0.5431 (p0) REVERT: A 328 ASP cc_start: 0.6820 (p0) cc_final: 0.6499 (p0) REVERT: B 55 ASP cc_start: 0.5735 (p0) cc_final: 0.5448 (p0) REVERT: B 268 ARG cc_start: 0.6675 (mtp180) cc_final: 0.6461 (mtm180) REVERT: B 328 ASP cc_start: 0.6840 (p0) cc_final: 0.6517 (p0) REVERT: C 55 ASP cc_start: 0.5777 (p0) cc_final: 0.5481 (p0) REVERT: C 328 ASP cc_start: 0.6801 (p0) cc_final: 0.6481 (p0) REVERT: D 55 ASP cc_start: 0.5785 (p0) cc_final: 0.5490 (p0) REVERT: D 328 ASP cc_start: 0.6820 (p0) cc_final: 0.6501 (p0) outliers start: 0 outliers final: 1 residues processed: 518 average time/residue: 0.9846 time to fit residues: 552.9879 Evaluate side-chains 324 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 104 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 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 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 = 0.3685 r_free = 0.3685 target = 0.105238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.083409 restraints weight = 24613.995| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 5.08 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9864 Z= 0.309 Angle : 0.882 8.958 13384 Z= 0.463 Chirality : 0.049 0.197 1632 Planarity : 0.006 0.036 1652 Dihedral : 5.461 24.747 1318 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 23.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.18 % Allowed : 22.64 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.20), residues: 1244 helix: -1.17 (0.20), residues: 512 sheet: -2.00 (0.31), residues: 168 loop : -0.71 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 249 HIS 0.005 0.002 HIS C 185 PHE 0.019 0.003 PHE D 116 TYR 0.027 0.003 TYR C 171 ARG 0.007 0.002 ARG A 111 *********************** 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 453 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 418 time to evaluate : 1.155 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 61 MET cc_start: 0.8721 (ttp) cc_final: 0.8476 (ttp) REVERT: A 75 LYS cc_start: 0.9101 (tppp) cc_final: 0.8879 (tppp) REVERT: A 133 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9099 (tm) REVERT: A 170 ARG cc_start: 0.9055 (mtt180) cc_final: 0.8830 (mtt90) REVERT: A 171 TYR cc_start: 0.9145 (t80) cc_final: 0.8839 (t80) REVERT: A 188 ILE cc_start: 0.9118 (mp) cc_final: 0.8838 (mp) REVERT: A 232 GLN cc_start: 0.9290 (tp-100) cc_final: 0.8970 (tp-100) REVERT: A 249 TRP cc_start: 0.8152 (m-90) cc_final: 0.7936 (m-90) REVERT: A 268 ARG cc_start: 0.8628 (mtm180) cc_final: 0.8017 (ttp80) REVERT: A 310 ASP cc_start: 0.9252 (p0) cc_final: 0.8531 (p0) REVERT: B 61 MET cc_start: 0.8766 (ttp) cc_final: 0.8556 (ttp) REVERT: B 75 LYS cc_start: 0.9105 (tppp) cc_final: 0.8866 (tppp) REVERT: B 170 ARG cc_start: 0.9055 (mtt180) cc_final: 0.8835 (mtt90) REVERT: B 171 TYR cc_start: 0.9162 (t80) cc_final: 0.8856 (t80) REVERT: B 188 ILE cc_start: 0.9099 (mp) cc_final: 0.8827 (mp) REVERT: B 232 GLN cc_start: 0.9341 (tp-100) cc_final: 0.9021 (tp-100) REVERT: B 249 TRP cc_start: 0.8202 (m-90) cc_final: 0.7967 (m-90) REVERT: B 257 GLU cc_start: 0.8437 (tp30) cc_final: 0.8049 (tm-30) REVERT: B 294 LEU cc_start: 0.9122 (mp) cc_final: 0.8642 (tm) REVERT: B 310 ASP cc_start: 0.9206 (p0) cc_final: 0.8606 (p0) REVERT: B 311 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8514 (mt-10) REVERT: C 61 MET cc_start: 0.8743 (ttp) cc_final: 0.8495 (ttp) REVERT: C 75 LYS cc_start: 0.9064 (tppp) cc_final: 0.8860 (tppp) REVERT: C 170 ARG cc_start: 0.9072 (mtt180) cc_final: 0.8848 (mtt90) REVERT: C 171 TYR cc_start: 0.9147 (t80) cc_final: 0.8867 (t80) REVERT: C 188 ILE cc_start: 0.9108 (mp) cc_final: 0.8828 (mp) REVERT: C 232 GLN cc_start: 0.9315 (tp-100) cc_final: 0.8983 (tp-100) REVERT: C 249 TRP cc_start: 0.8143 (m-90) cc_final: 0.7934 (m-90) REVERT: C 268 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7960 (ttp80) REVERT: C 310 ASP cc_start: 0.9295 (p0) cc_final: 0.8590 (p0) REVERT: D 61 MET cc_start: 0.8814 (ttp) cc_final: 0.8561 (ttp) REVERT: D 75 LYS cc_start: 0.9076 (tppp) cc_final: 0.8870 (tppp) REVERT: D 170 ARG cc_start: 0.9054 (mtt180) cc_final: 0.8827 (mtt90) REVERT: D 171 TYR cc_start: 0.9154 (t80) cc_final: 0.8870 (t80) REVERT: D 188 ILE cc_start: 0.9104 (mp) cc_final: 0.8824 (mp) REVERT: D 232 GLN cc_start: 0.9322 (tp-100) cc_final: 0.8996 (tp-100) REVERT: D 249 TRP cc_start: 0.8134 (m-90) cc_final: 0.7931 (m-90) REVERT: D 268 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7731 (ttp80) REVERT: D 310 ASP cc_start: 0.9285 (p0) cc_final: 0.8583 (p0) outliers start: 35 outliers final: 5 residues processed: 426 average time/residue: 0.9913 time to fit residues: 458.1567 Evaluate side-chains 341 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 333 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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 268 ARG Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 268 ARG 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 1 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 113 optimal weight: 50.0000 chunk 109 optimal weight: 30.0000 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 305 GLN C 305 GLN D 305 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.101083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.081360 restraints weight = 25806.129| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 4.84 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.5756 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= 0.310 Angle : 0.845 9.333 13384 Z= 0.433 Chirality : 0.052 0.291 1632 Planarity : 0.005 0.039 1652 Dihedral : 5.203 13.296 1316 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.27 % Allowed : 25.18 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.22), residues: 1244 helix: -0.27 (0.22), residues: 524 sheet: -1.86 (0.32), residues: 168 loop : -0.22 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 249 HIS 0.004 0.001 HIS C 230 PHE 0.017 0.003 PHE A 169 TYR 0.021 0.002 TYR A 126 ARG 0.007 0.002 ARG C 176 *********************** 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 419 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 372 time to evaluate : 1.134 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: 0.8951 (ttp) cc_final: 0.8726 (ttp) REVERT: A 75 LYS cc_start: 0.8974 (tppp) cc_final: 0.8740 (tppp) REVERT: A 170 ARG cc_start: 0.9079 (mtt180) cc_final: 0.8783 (mtt90) REVERT: A 171 TYR cc_start: 0.9174 (t80) cc_final: 0.8777 (t80) REVERT: A 172 LEU cc_start: 0.9093 (mt) cc_final: 0.8833 (mt) REVERT: A 242 ARG cc_start: 0.8764 (ttp-110) cc_final: 0.8338 (ptt-90) REVERT: A 264 LYS cc_start: 0.9019 (mmmm) cc_final: 0.8804 (mtpt) REVERT: A 311 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8589 (mt-10) REVERT: B 170 ARG cc_start: 0.9071 (mtt180) cc_final: 0.8774 (mtt90) REVERT: B 171 TYR cc_start: 0.9179 (t80) cc_final: 0.8705 (t80) REVERT: B 172 LEU cc_start: 0.9093 (mt) cc_final: 0.8815 (mt) REVERT: B 232 GLN cc_start: 0.9231 (tp-100) cc_final: 0.8968 (tp-100) REVERT: B 257 GLU cc_start: 0.8617 (tp30) cc_final: 0.8192 (tm-30) REVERT: C 61 MET cc_start: 0.8980 (ttp) cc_final: 0.8733 (ttp) REVERT: C 170 ARG cc_start: 0.9067 (mtt180) cc_final: 0.8764 (mtt-85) REVERT: C 171 TYR cc_start: 0.9158 (t80) cc_final: 0.8777 (t80) REVERT: C 232 GLN cc_start: 0.9248 (tp-100) cc_final: 0.8971 (tp-100) REVERT: C 268 ARG cc_start: 0.8516 (mtm180) cc_final: 0.8158 (ttp80) REVERT: C 311 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8559 (mt-10) REVERT: D 61 MET cc_start: 0.8910 (ttp) cc_final: 0.8670 (ttp) REVERT: D 170 ARG cc_start: 0.9084 (mtt180) cc_final: 0.8778 (mtt90) REVERT: D 171 TYR cc_start: 0.9168 (t80) cc_final: 0.8695 (t80) REVERT: D 172 LEU cc_start: 0.9069 (mt) cc_final: 0.8801 (mt) REVERT: D 232 GLN cc_start: 0.9234 (tp-100) cc_final: 0.9011 (tp-100) REVERT: D 311 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8579 (mt-10) outliers start: 47 outliers final: 15 residues processed: 385 average time/residue: 1.0876 time to fit residues: 452.5125 Evaluate side-chains 322 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 307 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 43 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 300 THR 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 33 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 13 optimal weight: 0.0980 chunk 115 optimal weight: 30.0000 chunk 54 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.101639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.079112 restraints weight = 26195.826| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 5.61 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9864 Z= 0.259 Angle : 0.803 9.462 13384 Z= 0.407 Chirality : 0.049 0.204 1632 Planarity : 0.004 0.037 1652 Dihedral : 5.177 17.225 1316 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.09 % Allowed : 28.91 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.23), residues: 1244 helix: 0.10 (0.22), residues: 524 sheet: -1.54 (0.41), residues: 132 loop : 0.27 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 249 HIS 0.004 0.001 HIS C 230 PHE 0.017 0.003 PHE B 169 TYR 0.018 0.002 TYR D 171 ARG 0.007 0.001 ARG D 168 *********************** 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: 56 poor density : 349 time to evaluate : 0.994 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 61 MET cc_start: 0.8911 (ttp) cc_final: 0.8708 (ttp) REVERT: A 170 ARG cc_start: 0.8961 (mtt180) cc_final: 0.8694 (mtt180) REVERT: A 171 TYR cc_start: 0.9195 (t80) cc_final: 0.8836 (t80) REVERT: A 217 MET cc_start: 0.6872 (ptm) cc_final: 0.6641 (ptm) REVERT: A 232 GLN cc_start: 0.9261 (tp-100) cc_final: 0.8982 (tp-100) REVERT: B 56 LYS cc_start: 0.9127 (tppt) cc_final: 0.8908 (tppp) REVERT: B 61 MET cc_start: 0.8928 (ttp) cc_final: 0.8689 (ttp) REVERT: B 65 GLN cc_start: 0.8948 (pt0) cc_final: 0.8626 (pt0) REVERT: B 170 ARG cc_start: 0.8977 (mtt180) cc_final: 0.8502 (mtt-85) REVERT: B 171 TYR cc_start: 0.9209 (t80) cc_final: 0.8906 (t80) REVERT: B 232 GLN cc_start: 0.9170 (tp-100) cc_final: 0.8965 (tp-100) REVERT: B 294 LEU cc_start: 0.9089 (mp) cc_final: 0.8765 (tm) REVERT: B 311 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8644 (mt-10) REVERT: C 61 MET cc_start: 0.8955 (ttp) cc_final: 0.8740 (ttp) REVERT: C 170 ARG cc_start: 0.9004 (mtt180) cc_final: 0.8671 (mtt90) REVERT: C 171 TYR cc_start: 0.9191 (t80) cc_final: 0.8814 (t80) REVERT: C 232 GLN cc_start: 0.9158 (tp-100) cc_final: 0.8769 (tp-100) REVERT: C 235 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8625 (pt0) REVERT: D 170 ARG cc_start: 0.9016 (mtt180) cc_final: 0.8689 (mtt90) REVERT: D 171 TYR cc_start: 0.9190 (t80) cc_final: 0.8896 (t80) REVERT: D 232 GLN cc_start: 0.9201 (tp-100) cc_final: 0.8829 (tp-100) REVERT: D 235 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8635 (pt0) outliers start: 56 outliers final: 19 residues processed: 385 average time/residue: 0.9719 time to fit residues: 406.1946 Evaluate side-chains 334 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 315 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 276 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 75 LYS 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 121 optimal weight: 7.9990 chunk 120 optimal weight: 40.0000 chunk 43 optimal weight: 20.0000 chunk 60 optimal weight: 30.0000 chunk 109 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 7 optimal weight: 30.0000 chunk 38 optimal weight: 30.0000 chunk 55 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 overall best weight: 6.5388 ------------------------------------------------------------------------------- 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 B 155 HIS C 155 HIS D 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.099927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.077769 restraints weight = 25923.413| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 5.58 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.6536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9864 Z= 0.295 Angle : 0.822 8.329 13384 Z= 0.417 Chirality : 0.049 0.260 1632 Planarity : 0.005 0.061 1652 Dihedral : 5.075 16.538 1316 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.64 % Allowed : 30.18 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1244 helix: 0.24 (0.22), residues: 528 sheet: -1.44 (0.42), residues: 132 loop : 0.47 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 249 HIS 0.004 0.001 HIS A 180 PHE 0.014 0.003 PHE C 169 TYR 0.016 0.002 TYR A 126 ARG 0.010 0.001 ARG C 268 *********************** 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 406 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 355 time to evaluate : 1.107 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 8 ILE cc_start: 0.8976 (mt) cc_final: 0.8698 (pt) REVERT: A 82 TYR cc_start: 0.8561 (m-80) cc_final: 0.8331 (m-10) REVERT: A 168 ARG cc_start: 0.8677 (tpp80) cc_final: 0.8460 (tpp80) REVERT: A 170 ARG cc_start: 0.8957 (mtt180) cc_final: 0.8707 (mtt180) REVERT: A 171 TYR cc_start: 0.9220 (t80) cc_final: 0.8853 (t80) REVERT: A 232 GLN cc_start: 0.9227 (tp-100) cc_final: 0.8982 (tp-100) REVERT: A 311 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8644 (mt-10) REVERT: B 61 MET cc_start: 0.8978 (ttp) cc_final: 0.8691 (ttp) REVERT: B 65 GLN cc_start: 0.8959 (pt0) cc_final: 0.8617 (pt0) REVERT: B 81 ASP cc_start: 0.9017 (p0) cc_final: 0.8811 (p0) REVERT: B 170 ARG cc_start: 0.8991 (mtt180) cc_final: 0.8775 (mtt180) REVERT: B 171 TYR cc_start: 0.9237 (t80) cc_final: 0.8957 (t80) REVERT: B 232 GLN cc_start: 0.9193 (tp-100) cc_final: 0.8905 (tp-100) REVERT: B 235 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8718 (pt0) REVERT: B 249 TRP cc_start: 0.7997 (m-90) cc_final: 0.7398 (m-90) REVERT: B 311 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8622 (mt-10) REVERT: C 81 ASP cc_start: 0.9041 (p0) cc_final: 0.8820 (p0) REVERT: C 170 ARG cc_start: 0.9022 (mtt180) cc_final: 0.8522 (mtt-85) REVERT: C 171 TYR cc_start: 0.9172 (t80) cc_final: 0.8829 (t80) REVERT: C 232 GLN cc_start: 0.9191 (tp-100) cc_final: 0.8963 (tp-100) REVERT: C 235 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8549 (pt0) REVERT: C 249 TRP cc_start: 0.8105 (m-90) cc_final: 0.7549 (m-90) REVERT: C 257 GLU cc_start: 0.8505 (tp30) cc_final: 0.7816 (tp30) REVERT: C 311 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8653 (mt-10) REVERT: D 81 ASP cc_start: 0.9014 (p0) cc_final: 0.8765 (p0) REVERT: D 170 ARG cc_start: 0.9043 (mtt180) cc_final: 0.8548 (mtt-85) REVERT: D 171 TYR cc_start: 0.9214 (t80) cc_final: 0.8904 (t80) REVERT: D 232 GLN cc_start: 0.9193 (tp-100) cc_final: 0.8875 (tp-100) REVERT: D 235 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8669 (pt0) REVERT: D 249 TRP cc_start: 0.8045 (m-90) cc_final: 0.7418 (m-90) REVERT: D 257 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7635 (tp30) REVERT: D 311 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8651 (mt-10) outliers start: 51 outliers final: 28 residues processed: 387 average time/residue: 1.0304 time to fit residues: 432.1148 Evaluate side-chains 312 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 284 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 182 THR Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 75 LYS 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 255 VAL 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 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 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 121 optimal weight: 40.0000 chunk 3 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 62 optimal weight: 30.0000 chunk 32 optimal weight: 30.0000 chunk 99 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 45 optimal weight: 30.0000 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 214 ASN D 20 ASN D 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.100061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.079717 restraints weight = 26828.209| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 5.23 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.6888 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= 0.296 Angle : 0.870 10.382 13384 Z= 0.440 Chirality : 0.050 0.224 1632 Planarity : 0.005 0.076 1652 Dihedral : 5.081 16.920 1316 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.09 % Allowed : 33.00 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1244 helix: 0.34 (0.23), residues: 524 sheet: -1.36 (0.43), residues: 132 loop : 0.66 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 249 HIS 0.005 0.001 HIS C 180 PHE 0.019 0.004 PHE C 70 TYR 0.021 0.002 TYR D 126 ARG 0.010 0.001 ARG D 168 *********************** 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 389 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 344 time to evaluate : 1.064 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: A 8 ILE cc_start: 0.9006 (mt) cc_final: 0.8721 (pt) REVERT: A 61 MET cc_start: 0.8871 (ttp) cc_final: 0.8507 (tpp) REVERT: A 170 ARG cc_start: 0.8974 (mtt180) cc_final: 0.8709 (mtt180) REVERT: A 171 TYR cc_start: 0.9208 (t80) cc_final: 0.8959 (t80) REVERT: A 232 GLN cc_start: 0.9233 (tp-100) cc_final: 0.8938 (tp-100) REVERT: A 235 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8740 (pt0) REVERT: A 311 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8630 (mt-10) REVERT: B 61 MET cc_start: 0.8934 (ttp) cc_final: 0.8658 (ttp) REVERT: B 65 GLN cc_start: 0.8970 (pt0) cc_final: 0.8634 (pt0) REVERT: B 170 ARG cc_start: 0.8974 (mtt180) cc_final: 0.8748 (mtt180) REVERT: B 171 TYR cc_start: 0.9219 (t80) cc_final: 0.8950 (t80) REVERT: B 232 GLN cc_start: 0.9257 (tp-100) cc_final: 0.8952 (tp-100) REVERT: B 235 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8769 (pt0) REVERT: B 249 TRP cc_start: 0.8072 (m-90) cc_final: 0.7580 (m-90) REVERT: B 264 LYS cc_start: 0.8909 (mmmm) cc_final: 0.8619 (mtpt) REVERT: B 311 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8628 (mt-10) REVERT: B 316 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8875 (mtpp) REVERT: C 61 MET cc_start: 0.8877 (ttp) cc_final: 0.8667 (ttp) REVERT: C 170 ARG cc_start: 0.9023 (mtt180) cc_final: 0.8525 (mtt-85) REVERT: C 171 TYR cc_start: 0.9182 (t80) cc_final: 0.8899 (t80) REVERT: C 232 GLN cc_start: 0.9300 (tp-100) cc_final: 0.8855 (tp-100) REVERT: C 249 TRP cc_start: 0.8106 (m-90) cc_final: 0.7627 (m-90) REVERT: C 262 MET cc_start: 0.8614 (mmm) cc_final: 0.7243 (mmm) REVERT: C 294 LEU cc_start: 0.9083 (mp) cc_final: 0.8423 (tp) REVERT: C 311 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8655 (mt-10) REVERT: D 170 ARG cc_start: 0.9074 (mtt180) cc_final: 0.8793 (mtt180) REVERT: D 171 TYR cc_start: 0.9233 (t80) cc_final: 0.8940 (t80) REVERT: D 232 GLN cc_start: 0.9248 (tp-100) cc_final: 0.8956 (tp-100) REVERT: D 235 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8728 (pt0) REVERT: D 249 TRP cc_start: 0.8114 (m-90) cc_final: 0.7589 (m-90) REVERT: D 264 LYS cc_start: 0.8833 (mmmm) cc_final: 0.8523 (mtpt) REVERT: D 294 LEU cc_start: 0.9114 (mp) cc_final: 0.8493 (tp) REVERT: D 311 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8675 (mt-10) outliers start: 45 outliers final: 30 residues processed: 369 average time/residue: 1.0155 time to fit residues: 407.4941 Evaluate side-chains 324 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 293 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET 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 293 VAL Chi-restraints excluded: chain A residue 300 THR 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 182 THR Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 276 VAL 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 32 MET Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 255 VAL 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 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 122 optimal weight: 40.0000 chunk 118 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 68 optimal weight: 30.0000 chunk 47 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 22 optimal weight: 40.0000 chunk 84 optimal weight: 50.0000 overall best weight: 7.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN C 232 GLN C 284 ASN D 20 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.099180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.076885 restraints weight = 26983.430| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 5.44 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.7051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9864 Z= 0.311 Angle : 0.885 11.873 13384 Z= 0.448 Chirality : 0.050 0.235 1632 Planarity : 0.005 0.055 1652 Dihedral : 5.090 18.149 1316 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.82 % Allowed : 32.91 % Favored : 61.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1244 helix: 0.51 (0.23), residues: 516 sheet: -1.31 (0.43), residues: 132 loop : 0.68 (0.29), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 249 HIS 0.005 0.002 HIS C 180 PHE 0.025 0.004 PHE C 70 TYR 0.038 0.002 TYR C 246 ARG 0.011 0.002 ARG A 168 *********************** 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 395 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 331 time to evaluate : 1.208 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: A 8 ILE cc_start: 0.9016 (mt) cc_final: 0.8727 (pt) REVERT: A 61 MET cc_start: 0.8938 (ttp) cc_final: 0.8488 (tpp) REVERT: A 170 ARG cc_start: 0.8972 (mtt180) cc_final: 0.8433 (mtt-85) REVERT: A 171 TYR cc_start: 0.9210 (t80) cc_final: 0.8993 (t80) REVERT: A 232 GLN cc_start: 0.9205 (tp-100) cc_final: 0.8950 (tp-100) REVERT: A 235 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8759 (pt0) REVERT: A 294 LEU cc_start: 0.9009 (mp) cc_final: 0.8508 (tp) REVERT: A 311 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8654 (mt-10) REVERT: B 61 MET cc_start: 0.9014 (ttp) cc_final: 0.8735 (ttp) REVERT: B 65 GLN cc_start: 0.8982 (pt0) cc_final: 0.8662 (pt0) REVERT: B 170 ARG cc_start: 0.8980 (mtt180) cc_final: 0.8681 (mtt180) REVERT: B 232 GLN cc_start: 0.9257 (tp-100) cc_final: 0.8936 (tp-100) REVERT: B 235 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8758 (pt0) REVERT: B 264 LYS cc_start: 0.8815 (mmmm) cc_final: 0.8529 (mtpt) REVERT: B 311 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8668 (mt-10) REVERT: B 316 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.8946 (mtpp) REVERT: C 8 ILE cc_start: 0.9027 (mt) cc_final: 0.8736 (pt) REVERT: C 56 LYS cc_start: 0.9327 (tppp) cc_final: 0.9115 (tppt) REVERT: C 61 MET cc_start: 0.8982 (ttp) cc_final: 0.8595 (tpp) REVERT: C 170 ARG cc_start: 0.9010 (mtt180) cc_final: 0.8510 (mtt-85) REVERT: C 171 TYR cc_start: 0.9174 (t80) cc_final: 0.8939 (t80) REVERT: C 232 GLN cc_start: 0.9233 (tp40) cc_final: 0.9000 (tp-100) REVERT: C 311 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8687 (mt-10) REVERT: C 328 ASP cc_start: 0.9059 (p0) cc_final: 0.8728 (p0) REVERT: D 170 ARG cc_start: 0.9077 (mtt180) cc_final: 0.8821 (mtt180) REVERT: D 171 TYR cc_start: 0.9211 (t80) cc_final: 0.8973 (t80) REVERT: D 232 GLN cc_start: 0.9283 (tp-100) cc_final: 0.8941 (tp-100) REVERT: D 235 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8775 (pt0) REVERT: D 249 TRP cc_start: 0.8011 (m-90) cc_final: 0.7686 (m-90) REVERT: D 264 LYS cc_start: 0.8803 (mmmm) cc_final: 0.8548 (mtpt) REVERT: D 294 LEU cc_start: 0.9086 (mp) cc_final: 0.8492 (tp) REVERT: D 311 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8665 (mt-10) outliers start: 64 outliers final: 30 residues processed: 370 average time/residue: 1.0100 time to fit residues: 405.7732 Evaluate side-chains 335 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 304 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 204 ASN 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 324 SER Chi-restraints excluded: chain B residue 30 VAL 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 276 VAL 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 173 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 255 VAL 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 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 324 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 80 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 109 optimal weight: 0.4980 chunk 38 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 47 optimal weight: 30.0000 chunk 74 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 overall best weight: 6.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.100930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.080283 restraints weight = 27330.732| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 5.24 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.7318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9864 Z= 0.309 Angle : 0.967 13.350 13384 Z= 0.481 Chirality : 0.052 0.280 1632 Planarity : 0.005 0.073 1652 Dihedral : 5.224 17.085 1316 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.73 % Allowed : 35.82 % Favored : 60.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1244 helix: 0.44 (0.23), residues: 516 sheet: -0.20 (0.55), residues: 92 loop : 0.33 (0.28), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 226 HIS 0.005 0.001 HIS C 180 PHE 0.024 0.004 PHE A 287 TYR 0.036 0.002 TYR B 171 ARG 0.011 0.002 ARG A 168 *********************** 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 378 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 337 time to evaluate : 1.001 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: A 8 ILE cc_start: 0.9002 (mt) cc_final: 0.8703 (pt) REVERT: A 46 GLU cc_start: 0.8594 (tp30) cc_final: 0.8086 (tp30) REVERT: A 61 MET cc_start: 0.8890 (ttp) cc_final: 0.8631 (tpp) REVERT: A 65 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8696 (pm20) REVERT: A 170 ARG cc_start: 0.9000 (mtt180) cc_final: 0.8461 (mtt-85) REVERT: A 171 TYR cc_start: 0.9194 (t80) cc_final: 0.8926 (t80) REVERT: A 232 GLN cc_start: 0.9191 (tp-100) cc_final: 0.8945 (tp-100) REVERT: A 235 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8756 (pt0) REVERT: A 294 LEU cc_start: 0.9022 (mp) cc_final: 0.8506 (tp) REVERT: A 311 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8644 (mt-10) REVERT: A 328 ASP cc_start: 0.8989 (p0) cc_final: 0.8630 (p0) REVERT: B 61 MET cc_start: 0.9039 (ttp) cc_final: 0.8754 (ttp) REVERT: B 65 GLN cc_start: 0.8996 (pt0) cc_final: 0.8642 (pt0) REVERT: B 170 ARG cc_start: 0.8844 (mtt180) cc_final: 0.8460 (mtt-85) REVERT: B 232 GLN cc_start: 0.9246 (tp-100) cc_final: 0.8881 (tp-100) REVERT: B 235 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8769 (pt0) REVERT: B 264 LYS cc_start: 0.8816 (mmmm) cc_final: 0.8550 (mtpt) REVERT: B 311 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8627 (mt-10) REVERT: B 316 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.8881 (mtpp) REVERT: B 317 LYS cc_start: 0.9407 (mtmm) cc_final: 0.9071 (pttm) REVERT: C 61 MET cc_start: 0.8971 (ttp) cc_final: 0.8617 (tpp) REVERT: C 79 ASP cc_start: 0.8185 (p0) cc_final: 0.7886 (p0) REVERT: C 170 ARG cc_start: 0.9011 (mtt180) cc_final: 0.8507 (mtt-85) REVERT: C 264 LYS cc_start: 0.8813 (mmmm) cc_final: 0.8439 (mtpt) REVERT: C 294 LEU cc_start: 0.9055 (mp) cc_final: 0.8485 (tp) REVERT: C 311 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8649 (mt-10) REVERT: D 170 ARG cc_start: 0.9060 (mtt180) cc_final: 0.8799 (mtt180) REVERT: D 171 TYR cc_start: 0.9204 (t80) cc_final: 0.8977 (t80) REVERT: D 217 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.5640 (pmt) REVERT: D 232 GLN cc_start: 0.9214 (tp-100) cc_final: 0.8989 (tp-100) REVERT: D 235 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8663 (pt0) REVERT: D 294 LEU cc_start: 0.9049 (mp) cc_final: 0.8486 (tp) REVERT: D 311 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8651 (mt-10) outliers start: 41 outliers final: 22 residues processed: 360 average time/residue: 1.0184 time to fit residues: 399.3223 Evaluate side-chains 334 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 309 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 276 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 30 VAL 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 276 VAL 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 182 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 276 VAL 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 217 MET Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 276 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 0.0770 chunk 62 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 93 optimal weight: 40.0000 chunk 52 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 110 optimal weight: 30.0000 chunk 102 optimal weight: 10.0000 chunk 45 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN B 204 ASN B 214 ASN B 232 GLN B 284 ASN C 232 GLN D 232 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.102093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.080901 restraints weight = 27622.890| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 5.37 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.7531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9864 Z= 0.302 Angle : 1.029 13.731 13384 Z= 0.512 Chirality : 0.054 0.322 1632 Planarity : 0.005 0.066 1652 Dihedral : 5.331 17.228 1316 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.27 % Allowed : 38.00 % Favored : 58.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1244 helix: 0.41 (0.24), residues: 508 sheet: -0.16 (0.55), residues: 92 loop : 0.22 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 226 HIS 0.005 0.001 HIS B 180 PHE 0.027 0.005 PHE A 287 TYR 0.044 0.002 TYR B 171 ARG 0.014 0.002 ARG B 168 *********************** 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 336 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 300 time to evaluate : 1.207 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 8 ILE cc_start: 0.8980 (mt) cc_final: 0.8677 (pt) REVERT: A 61 MET cc_start: 0.8825 (ttp) cc_final: 0.8602 (tpp) REVERT: A 65 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8376 (pm20) REVERT: A 79 ASP cc_start: 0.8486 (t70) cc_final: 0.7946 (t0) REVERT: A 170 ARG cc_start: 0.9027 (mtt180) cc_final: 0.8551 (mtt-85) REVERT: A 232 GLN cc_start: 0.9210 (tp-100) cc_final: 0.8974 (tp-100) REVERT: A 235 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8786 (pt0) REVERT: A 275 LEU cc_start: 0.8410 (mt) cc_final: 0.8003 (tm) REVERT: A 294 LEU cc_start: 0.8981 (mp) cc_final: 0.8478 (tp) REVERT: A 311 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8616 (mt-10) REVERT: A 328 ASP cc_start: 0.8937 (p0) cc_final: 0.8578 (p0) REVERT: B 61 MET cc_start: 0.8828 (ttp) cc_final: 0.8595 (ttp) REVERT: B 65 GLN cc_start: 0.8841 (pt0) cc_final: 0.8532 (pt0) REVERT: B 79 ASP cc_start: 0.8181 (p0) cc_final: 0.7810 (p0) REVERT: B 170 ARG cc_start: 0.8730 (mtt180) cc_final: 0.8277 (mtt90) REVERT: B 171 TYR cc_start: 0.9172 (t80) cc_final: 0.8956 (t80) REVERT: B 275 LEU cc_start: 0.8475 (mt) cc_final: 0.8026 (tm) REVERT: B 294 LEU cc_start: 0.9041 (mp) cc_final: 0.8512 (tp) REVERT: B 316 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8999 (mtpp) REVERT: B 317 LYS cc_start: 0.9324 (mtmm) cc_final: 0.8973 (pttm) REVERT: C 61 MET cc_start: 0.8814 (ttp) cc_final: 0.8543 (tpp) REVERT: C 168 ARG cc_start: 0.8839 (mmt90) cc_final: 0.8623 (mmt90) REVERT: C 170 ARG cc_start: 0.8901 (mtt180) cc_final: 0.8447 (mtt-85) REVERT: C 294 LEU cc_start: 0.8962 (mp) cc_final: 0.8449 (tp) REVERT: C 311 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8660 (mt-10) REVERT: D 170 ARG cc_start: 0.9019 (mtt180) cc_final: 0.8509 (mtt-85) REVERT: D 217 MET cc_start: 0.5525 (OUTLIER) cc_final: 0.5176 (pmt) REVERT: D 232 GLN cc_start: 0.9310 (tp40) cc_final: 0.9108 (tp-100) REVERT: D 275 LEU cc_start: 0.8451 (mt) cc_final: 0.7987 (mt) REVERT: D 294 LEU cc_start: 0.9046 (mp) cc_final: 0.8515 (tp) outliers start: 36 outliers final: 24 residues processed: 314 average time/residue: 0.9049 time to fit residues: 311.1149 Evaluate side-chains 295 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 268 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 204 ASN 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 B residue 30 VAL 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 276 VAL 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 182 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 6.9990 chunk 14 optimal weight: 30.0000 chunk 38 optimal weight: 30.0000 chunk 105 optimal weight: 8.9990 chunk 73 optimal weight: 30.0000 chunk 81 optimal weight: 40.0000 chunk 45 optimal weight: 30.0000 chunk 21 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 0.0980 chunk 18 optimal weight: 30.0000 overall best weight: 6.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.100344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.079476 restraints weight = 27404.502| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 5.29 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.7669 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= 0.325 Angle : 1.045 14.030 13384 Z= 0.520 Chirality : 0.054 0.318 1632 Planarity : 0.005 0.057 1652 Dihedral : 5.362 18.902 1316 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 24.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.82 % Allowed : 38.64 % Favored : 58.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1244 helix: 0.29 (0.24), residues: 508 sheet: -1.31 (0.44), residues: 144 loop : 0.44 (0.28), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 226 HIS 0.005 0.001 HIS C 180 PHE 0.031 0.006 PHE B 70 TYR 0.044 0.003 TYR C 171 ARG 0.010 0.002 ARG A 168 ********************** 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 326 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 295 time to evaluate : 1.088 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 8 ILE cc_start: 0.8983 (mt) cc_final: 0.8682 (pt) REVERT: A 65 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8421 (pm20) REVERT: A 170 ARG cc_start: 0.8967 (mtt180) cc_final: 0.8694 (mtt180) REVERT: A 232 GLN cc_start: 0.9197 (tp-100) cc_final: 0.8984 (tp-100) REVERT: A 275 LEU cc_start: 0.8434 (mt) cc_final: 0.7975 (tm) REVERT: A 294 LEU cc_start: 0.9051 (mp) cc_final: 0.8470 (tp) REVERT: A 311 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8629 (mt-10) REVERT: B 8 ILE cc_start: 0.8975 (mt) cc_final: 0.8665 (pt) REVERT: B 61 MET cc_start: 0.8852 (ttp) cc_final: 0.8635 (ttp) REVERT: B 65 GLN cc_start: 0.8910 (pt0) cc_final: 0.8596 (pt0) REVERT: B 170 ARG cc_start: 0.8776 (mtt180) cc_final: 0.8319 (mtt90) REVERT: B 171 TYR cc_start: 0.9204 (t80) cc_final: 0.8968 (t80) REVERT: B 294 LEU cc_start: 0.9069 (mp) cc_final: 0.8524 (tp) REVERT: B 316 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.9002 (mtpp) REVERT: B 317 LYS cc_start: 0.9341 (mtmm) cc_final: 0.9004 (pttm) REVERT: C 61 MET cc_start: 0.8792 (ttp) cc_final: 0.8509 (tpp) REVERT: C 170 ARG cc_start: 0.8761 (mtt180) cc_final: 0.8418 (mtt90) REVERT: C 264 LYS cc_start: 0.8718 (mmmm) cc_final: 0.8431 (mtpt) REVERT: C 294 LEU cc_start: 0.9025 (mp) cc_final: 0.8469 (tp) REVERT: C 311 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8670 (mt-10) REVERT: D 170 ARG cc_start: 0.8938 (mtt180) cc_final: 0.8530 (mtt-85) REVERT: D 232 GLN cc_start: 0.9278 (tp40) cc_final: 0.9065 (tp-100) REVERT: D 294 LEU cc_start: 0.9012 (mp) cc_final: 0.8441 (tp) outliers start: 31 outliers final: 27 residues processed: 306 average time/residue: 0.9646 time to fit residues: 322.1307 Evaluate side-chains 302 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 273 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 49 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 204 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 263 LEU 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 B residue 30 VAL 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 276 VAL 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 173 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 64 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 90 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 118 optimal weight: 30.0000 chunk 81 optimal weight: 9.9990 chunk 75 optimal weight: 0.0370 chunk 119 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 overall best weight: 6.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.101427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.080632 restraints weight = 27469.413| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 5.22 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.7786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9864 Z= 0.323 Angle : 1.061 14.072 13384 Z= 0.530 Chirality : 0.054 0.298 1632 Planarity : 0.005 0.055 1652 Dihedral : 5.437 19.676 1316 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 24.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.55 % Allowed : 39.82 % Favored : 57.64 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1244 helix: 0.24 (0.24), residues: 508 sheet: -0.14 (0.56), residues: 92 loop : 0.22 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 226 HIS 0.005 0.002 HIS A 66 PHE 0.029 0.005 PHE B 70 TYR 0.040 0.003 TYR C 171 ARG 0.009 0.001 ARG B 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7272.70 seconds wall clock time: 129 minutes 22.56 seconds (7762.56 seconds total)