Starting phenix.real_space_refine on Wed Feb 4 16:55:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dx4_47280/02_2026/9dx4_47280_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dx4_47280/02_2026/9dx4_47280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dx4_47280/02_2026/9dx4_47280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dx4_47280/02_2026/9dx4_47280.map" model { file = "/net/cci-nas-00/data/ceres_data/9dx4_47280/02_2026/9dx4_47280_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dx4_47280/02_2026/9dx4_47280_trim.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 44 5.16 5 C 7299 2.51 5 N 2065 2.21 5 O 2157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11575 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2174 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 15, 'TRANS': 260} Chain breaks: 3 Chain: "C" Number of atoms: 2304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2304 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 276} Chain breaks: 1 Chain: "D" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2328 Classifications: {'peptide': 297} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 279} Chain breaks: 1 Chain: "E" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2328 Classifications: {'peptide': 297} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 279} Chain breaks: 1 Chain: "B" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2306 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 277} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.71, per 1000 atoms: 0.23 Number of scatterers: 11575 At special positions: 0 Unit cell: (80.25, 123.05, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 10 15.00 O 2157 8.00 N 2065 7.00 C 7299 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: 1.08 Conformation dependent library (CDL) restraints added in 651.2 milliseconds 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2692 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 9 sheets defined 62.5% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.672A pdb=" N ARG A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 31 Processing helix chain 'A' and resid 34 through 52 Processing helix chain 'A' and resid 69 through 80 Processing helix chain 'A' and resid 93 through 103 removed outlier: 3.693A pdb=" N LEU A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 118 Processing helix chain 'A' and resid 119 through 133 removed outlier: 3.647A pdb=" N VAL A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.541A pdb=" N ARG A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 219 through 238 Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 262 through 275 Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.697A pdb=" N GLN A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 329 removed outlier: 3.592A pdb=" N PHE A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 31 Processing helix chain 'C' and resid 34 through 51 Processing helix chain 'C' and resid 67 through 80 Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.753A pdb=" N LEU C 97 " --> pdb=" O LYS C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 118 Processing helix chain 'C' and resid 119 through 132 removed outlier: 3.583A pdb=" N VAL C 125 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Proline residue: C 128 - end of helix Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 185 through 200 Processing helix chain 'C' and resid 205 through 215 Processing helix chain 'C' and resid 219 through 238 Processing helix chain 'C' and resid 243 through 254 Processing helix chain 'C' and resid 262 through 275 Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 293 through 300 removed outlier: 4.015A pdb=" N ILE C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 307 Processing helix chain 'C' and resid 321 through 329 Processing helix chain 'D' and resid 20 through 24 removed outlier: 3.937A pdb=" N ARG D 24 " --> pdb=" O ASP D 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 20 through 24' Processing helix chain 'D' and resid 34 through 52 Processing helix chain 'D' and resid 67 through 80 Processing helix chain 'D' and resid 93 through 103 removed outlier: 3.691A pdb=" N LEU D 97 " --> pdb=" O LYS D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 118 Processing helix chain 'D' and resid 119 through 133 removed outlier: 3.580A pdb=" N VAL D 125 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Proline residue: D 128 - end of helix Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 185 through 200 Processing helix chain 'D' and resid 205 through 215 Processing helix chain 'D' and resid 219 through 238 removed outlier: 3.860A pdb=" N VAL D 230 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 254 Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 282 through 290 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 301 through 308 Processing helix chain 'D' and resid 321 through 329 removed outlier: 3.517A pdb=" N PHE D 328 " --> pdb=" O ALA D 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 34 through 52 Processing helix chain 'E' and resid 69 through 80 removed outlier: 3.659A pdb=" N ASN E 73 " --> pdb=" O THR E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 103 removed outlier: 3.708A pdb=" N LEU E 97 " --> pdb=" O LYS E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 118 Processing helix chain 'E' and resid 119 through 133 removed outlier: 3.535A pdb=" N VAL E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR E 127 " --> pdb=" O GLU E 123 " (cutoff:3.500A) Proline residue: E 128 - end of helix Processing helix chain 'E' and resid 168 through 174 removed outlier: 3.752A pdb=" N ARG E 174 " --> pdb=" O PRO E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 200 Processing helix chain 'E' and resid 205 through 215 Processing helix chain 'E' and resid 219 through 238 Processing helix chain 'E' and resid 243 through 254 Processing helix chain 'E' and resid 262 through 275 Processing helix chain 'E' and resid 282 through 291 Processing helix chain 'E' and resid 293 through 301 removed outlier: 3.627A pdb=" N LEU E 301 " --> pdb=" O ILE E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 309 removed outlier: 4.455A pdb=" N LEU E 305 " --> pdb=" O LEU E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 329 removed outlier: 3.608A pdb=" N PHE E 328 " --> pdb=" O ALA E 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 24 Processing helix chain 'B' and resid 27 through 31 Processing helix chain 'B' and resid 34 through 52 Processing helix chain 'B' and resid 67 through 80 Processing helix chain 'B' and resid 93 through 103 removed outlier: 3.569A pdb=" N LEU B 97 " --> pdb=" O LYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 118 Processing helix chain 'B' and resid 119 through 133 removed outlier: 3.549A pdb=" N TYR B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Proline residue: B 128 - end of helix Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.652A pdb=" N ARG B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 200 Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 219 through 238 Processing helix chain 'B' and resid 243 through 254 Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 282 through 291 Processing helix chain 'B' and resid 293 through 301 Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.568A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 329 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 87 removed outlier: 6.267A pdb=" N ARG A 84 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASP A 113 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR A 86 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP A 108 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE A 158 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A 110 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ALA A 160 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A 112 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU A 59 " --> pdb=" O GLN A 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 87 removed outlier: 6.363A pdb=" N ARG C 84 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP C 113 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR C 86 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASP C 108 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ILE C 158 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU C 110 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ALA C 160 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE C 112 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU C 59 " --> pdb=" O GLN C 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AA4, first strand: chain 'D' and resid 83 through 87 removed outlier: 6.202A pdb=" N ARG D 84 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP D 113 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR D 86 " --> pdb=" O ASP D 113 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP D 108 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE D 158 " --> pdb=" O ASP D 108 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU D 110 " --> pdb=" O ILE D 158 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA D 160 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE D 112 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU D 59 " --> pdb=" O GLN D 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 311 through 313 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 87 removed outlier: 6.238A pdb=" N ARG E 84 " --> pdb=" O PHE E 111 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ASP E 113 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR E 86 " --> pdb=" O ASP E 113 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP E 108 " --> pdb=" O THR E 156 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE E 158 " --> pdb=" O ASP E 108 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU E 110 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA E 160 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE E 112 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU E 59 " --> pdb=" O GLN E 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 311 through 314 Processing sheet with id=AA8, first strand: chain 'B' and resid 83 through 87 removed outlier: 6.270A pdb=" N ARG B 84 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ASP B 113 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR B 86 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU B 59 " --> pdb=" O GLN B 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 311 through 314 583 hydrogen bonds defined for protein. 1680 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3795 1.34 - 1.45: 1228 1.45 - 1.57: 6657 1.57 - 1.69: 22 1.69 - 1.81: 88 Bond restraints: 11790 Sorted by residual: bond pdb=" C2' ADP A 401 " pdb=" C3' ADP A 401 " ideal model delta sigma weight residual 1.524 1.283 0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C2' ADP D 401 " pdb=" C3' ADP D 401 " ideal model delta sigma weight residual 1.524 1.283 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C2' ADP E 401 " pdb=" C3' ADP E 401 " ideal model delta sigma weight residual 1.524 1.288 0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C2' ADP B 401 " pdb=" C3' ADP B 401 " ideal model delta sigma weight residual 1.524 1.293 0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C2' ADP C 401 " pdb=" C3' ADP C 401 " ideal model delta sigma weight residual 1.524 1.297 0.227 2.00e-02 2.50e+03 1.29e+02 ... (remaining 11785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.07: 15930 6.07 - 12.13: 37 12.13 - 18.20: 6 18.20 - 24.27: 4 24.27 - 30.33: 5 Bond angle restraints: 15982 Sorted by residual: angle pdb=" C2' ADP B 401 " pdb=" C1' ADP B 401 " pdb=" N9 ADP B 401 " ideal model delta sigma weight residual 109.47 139.80 -30.33 3.00e+00 1.11e-01 1.02e+02 angle pdb=" C2' ADP C 401 " pdb=" C1' ADP C 401 " pdb=" N9 ADP C 401 " ideal model delta sigma weight residual 109.47 136.67 -27.20 3.00e+00 1.11e-01 8.22e+01 angle pdb=" C2' ADP D 401 " pdb=" C1' ADP D 401 " pdb=" N9 ADP D 401 " ideal model delta sigma weight residual 109.47 136.14 -26.67 3.00e+00 1.11e-01 7.90e+01 angle pdb=" N9 ADP C 401 " pdb=" C1' ADP C 401 " pdb=" O4' ADP C 401 " ideal model delta sigma weight residual 109.47 83.35 26.12 3.00e+00 1.11e-01 7.58e+01 angle pdb=" C2' ADP A 401 " pdb=" C1' ADP A 401 " pdb=" N9 ADP A 401 " ideal model delta sigma weight residual 109.47 133.89 -24.42 3.00e+00 1.11e-01 6.62e+01 ... (remaining 15977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 7094 35.97 - 71.95: 60 71.95 - 107.92: 6 107.92 - 143.90: 7 143.90 - 179.87: 1 Dihedral angle restraints: 7168 sinusoidal: 2995 harmonic: 4173 Sorted by residual: dihedral pdb=" CD ARG C 229 " pdb=" NE ARG C 229 " pdb=" CZ ARG C 229 " pdb=" NH1 ARG C 229 " ideal model delta sinusoidal sigma weight residual 0.00 -79.77 79.77 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 119.87 -179.87 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CD ARG D 313 " pdb=" NE ARG D 313 " pdb=" CZ ARG D 313 " pdb=" NH1 ARG D 313 " ideal model delta sinusoidal sigma weight residual 0.00 -56.89 56.89 1 1.00e+01 1.00e-02 4.36e+01 ... (remaining 7165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.984: 1785 0.984 - 1.967: 0 1.967 - 2.951: 0 2.951 - 3.934: 0 3.934 - 4.918: 14 Chirality restraints: 1799 Sorted by residual: chirality pdb=" C2' ADP A 401 " pdb=" C1' ADP A 401 " pdb=" C3' ADP A 401 " pdb=" O2' ADP A 401 " both_signs ideal model delta sigma weight residual False -2.51 2.41 -4.92 2.00e-01 2.50e+01 6.05e+02 chirality pdb=" C2' ADP B 401 " pdb=" C1' ADP B 401 " pdb=" C3' ADP B 401 " pdb=" O2' ADP B 401 " both_signs ideal model delta sigma weight residual False -2.51 2.35 -4.86 2.00e-01 2.50e+01 5.90e+02 chirality pdb=" C2' ADP D 401 " pdb=" C1' ADP D 401 " pdb=" C3' ADP D 401 " pdb=" O2' ADP D 401 " both_signs ideal model delta sigma weight residual False -2.51 2.34 -4.85 2.00e-01 2.50e+01 5.89e+02 ... (remaining 1796 not shown) Planarity restraints: 2088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 229 " 1.082 9.50e-02 1.11e+02 4.85e-01 1.42e+02 pdb=" NE ARG C 229 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG C 229 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG C 229 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 229 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 313 " 0.903 9.50e-02 1.11e+02 4.05e-01 9.95e+01 pdb=" NE ARG D 313 " -0.056 2.00e-02 2.50e+03 pdb=" CZ ARG D 313 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 313 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 313 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 228 " 0.273 9.50e-02 1.11e+02 1.23e-01 9.21e+00 pdb=" NE ARG C 228 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 228 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 228 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 228 " 0.010 2.00e-02 2.50e+03 ... (remaining 2085 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 109 2.60 - 3.18: 10170 3.18 - 3.75: 17882 3.75 - 4.33: 25295 4.33 - 4.90: 41635 Nonbonded interactions: 95091 Sorted by model distance: nonbonded pdb=" O LYS A 68 " pdb=" OG1 THR A 69 " model vdw 2.027 3.040 nonbonded pdb=" OD1 ASN E 255 " pdb=" NH2 ARG E 266 " model vdw 2.197 3.120 nonbonded pdb=" NH1 ARG E 217 " pdb=" OD2 ASP E 265 " model vdw 2.204 3.120 nonbonded pdb=" O GLY C 62 " pdb=" NZ LYS C 68 " model vdw 2.248 3.120 nonbonded pdb=" OE2 GLU E 123 " pdb=" OH TYR E 127 " model vdw 2.253 3.040 ... (remaining 95086 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 329 or resid 401)) selection = (chain 'B' and (resid 22 through 279 or resid 294 through 312 or resid 320 throu \ gh 401)) selection = (chain 'C' and (resid 22 through 279 or resid 294 through 312 or resid 320 throu \ gh 329 or resid 401)) selection = (chain 'D' and (resid 22 through 279 or resid 294 through 312 or resid 320 throu \ gh 329 or resid 401)) selection = (chain 'E' and (resid 22 through 279 or resid 294 through 312 or resid 320 throu \ gh 329 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.560 Find NCS groups from input model: 0.290 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5391 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 : 0.008 0.241 11790 Z= 0.399 Angle : 0.967 30.333 15982 Z= 0.379 Chirality : 0.419 4.918 1799 Planarity : 0.015 0.485 2088 Dihedral : 12.641 179.870 4476 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.17 % Allowed : 0.08 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.24), residues: 1434 helix: 1.64 (0.20), residues: 808 sheet: 2.35 (0.43), residues: 156 loop : 1.07 (0.32), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 318 TYR 0.032 0.001 TYR C 304 PHE 0.012 0.001 PHE D 310 TRP 0.007 0.001 TRP A 325 HIS 0.001 0.000 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00797 (11790) covalent geometry : angle 0.96733 (15982) hydrogen bonds : bond 0.15086 ( 583) hydrogen bonds : angle 7.04070 ( 1680) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 224 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 229 ARG cc_start: 0.5657 (OUTLIER) cc_final: 0.5329 (mmt-90) REVERT: D 318 ARG cc_start: 0.5489 (mpt180) cc_final: 0.4883 (mmt-90) REVERT: B 162 THR cc_start: 0.7514 (p) cc_final: 0.7256 (p) REVERT: B 237 LYS cc_start: 0.7158 (mmtt) cc_final: 0.6957 (tttm) outliers start: 2 outliers final: 1 residues processed: 225 average time/residue: 0.1313 time to fit residues: 39.7947 Evaluate side-chains 198 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain D residue 168 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS B 73 ASN B 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.222993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.195362 restraints weight = 15055.712| |-----------------------------------------------------------------------------| r_work (start): 0.4468 rms_B_bonded: 2.57 r_work: 0.4337 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5548 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11790 Z= 0.173 Angle : 0.780 10.490 15982 Z= 0.353 Chirality : 0.046 0.316 1799 Planarity : 0.006 0.057 2088 Dihedral : 10.545 152.636 1672 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.08 % Allowed : 6.67 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.23), residues: 1434 helix: 1.09 (0.18), residues: 836 sheet: 2.40 (0.42), residues: 150 loop : 1.17 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 313 TYR 0.029 0.002 TYR C 304 PHE 0.029 0.002 PHE D 233 TRP 0.011 0.002 TRP D 325 HIS 0.007 0.002 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00388 (11790) covalent geometry : angle 0.78044 (15982) hydrogen bonds : bond 0.04134 ( 583) hydrogen bonds : angle 5.69363 ( 1680) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 217 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 TYR cc_start: 0.5443 (t80) cc_final: 0.5172 (t80) REVERT: C 173 ASP cc_start: 0.6192 (m-30) cc_final: 0.5941 (m-30) REVERT: C 174 ARG cc_start: 0.6020 (mtt90) cc_final: 0.5792 (mtt90) REVERT: C 245 ASP cc_start: 0.6771 (m-30) cc_final: 0.6507 (m-30) REVERT: C 259 GLU cc_start: 0.6639 (mp0) cc_final: 0.6021 (mp0) REVERT: D 108 ASP cc_start: 0.6308 (m-30) cc_final: 0.5977 (m-30) REVERT: D 285 ASN cc_start: 0.7055 (t0) cc_final: 0.6815 (m-40) REVERT: E 319 MET cc_start: 0.4720 (tmm) cc_final: 0.4239 (ptp) REVERT: B 123 GLU cc_start: 0.6967 (tt0) cc_final: 0.6751 (tt0) REVERT: B 162 THR cc_start: 0.7767 (p) cc_final: 0.7458 (m) REVERT: B 198 ARG cc_start: 0.7397 (mtm180) cc_final: 0.7175 (mtm110) REVERT: B 281 VAL cc_start: 0.7632 (p) cc_final: 0.7390 (p) outliers start: 13 outliers final: 6 residues processed: 221 average time/residue: 0.1300 time to fit residues: 39.0078 Evaluate side-chains 212 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 206 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 269 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 112 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 50 optimal weight: 0.3980 chunk 20 optimal weight: 0.0060 chunk 21 optimal weight: 3.9990 chunk 89 optimal weight: 0.0030 chunk 98 optimal weight: 8.9990 overall best weight: 0.4408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 HIS D 308 GLN B 190 GLN B 224 ASN B 327 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.220895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.194170 restraints weight = 15130.065| |-----------------------------------------------------------------------------| r_work (start): 0.4460 rms_B_bonded: 2.54 r_work: 0.4333 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5563 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11790 Z= 0.128 Angle : 0.679 9.565 15982 Z= 0.308 Chirality : 0.042 0.152 1799 Planarity : 0.005 0.084 2088 Dihedral : 10.085 155.249 1667 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.42 % Allowed : 7.50 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.23), residues: 1434 helix: 1.19 (0.18), residues: 837 sheet: 2.42 (0.41), residues: 152 loop : 1.25 (0.33), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 318 TYR 0.015 0.001 TYR C 304 PHE 0.031 0.002 PHE D 233 TRP 0.008 0.001 TRP D 325 HIS 0.006 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00286 (11790) covalent geometry : angle 0.67945 (15982) hydrogen bonds : bond 0.03771 ( 583) hydrogen bonds : angle 5.44620 ( 1680) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 173 ASP cc_start: 0.6119 (m-30) cc_final: 0.5836 (m-30) REVERT: C 174 ARG cc_start: 0.5955 (mtt90) cc_final: 0.5656 (mtt90) REVERT: C 199 PHE cc_start: 0.5813 (OUTLIER) cc_final: 0.5532 (t80) REVERT: C 245 ASP cc_start: 0.6826 (m-30) cc_final: 0.6602 (m-30) REVERT: D 108 ASP cc_start: 0.6364 (m-30) cc_final: 0.5963 (m-30) REVERT: D 285 ASN cc_start: 0.7136 (t0) cc_final: 0.6883 (m110) REVERT: E 254 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6650 (mp) REVERT: E 319 MET cc_start: 0.4748 (tmm) cc_final: 0.4547 (ptp) REVERT: B 123 GLU cc_start: 0.6908 (tt0) cc_final: 0.6651 (tt0) outliers start: 17 outliers final: 6 residues processed: 204 average time/residue: 0.1206 time to fit residues: 33.8911 Evaluate side-chains 199 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 191 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain B residue 269 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 68 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 111 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 HIS E 185 GLN B 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.216083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.189410 restraints weight = 15006.476| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 2.47 r_work: 0.4264 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5654 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11790 Z= 0.157 Angle : 0.697 10.546 15982 Z= 0.323 Chirality : 0.044 0.203 1799 Planarity : 0.006 0.066 2088 Dihedral : 9.691 156.195 1667 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.75 % Allowed : 7.83 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.23), residues: 1434 helix: 1.15 (0.18), residues: 830 sheet: 2.40 (0.42), residues: 150 loop : 1.24 (0.33), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 217 TYR 0.014 0.002 TYR A 184 PHE 0.041 0.002 PHE D 233 TRP 0.007 0.001 TRP E 325 HIS 0.010 0.002 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00361 (11790) covalent geometry : angle 0.69698 (15982) hydrogen bonds : bond 0.03792 ( 583) hydrogen bonds : angle 5.24082 ( 1680) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 TYR cc_start: 0.5360 (t80) cc_final: 0.5120 (t80) REVERT: C 173 ASP cc_start: 0.6202 (m-30) cc_final: 0.5917 (m-30) REVERT: C 198 ARG cc_start: 0.7007 (mtm-85) cc_final: 0.6804 (mtm-85) REVERT: C 199 PHE cc_start: 0.5641 (OUTLIER) cc_final: 0.5376 (t80) REVERT: D 108 ASP cc_start: 0.6391 (m-30) cc_final: 0.5971 (m-30) REVERT: D 133 TYR cc_start: 0.5859 (m-80) cc_final: 0.5626 (m-80) REVERT: D 285 ASN cc_start: 0.7075 (t0) cc_final: 0.6845 (m110) REVERT: E 79 MET cc_start: 0.4828 (tpp) cc_final: 0.4591 (tpp) REVERT: E 254 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6674 (mp) REVERT: E 259 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6940 (mm-30) REVERT: E 319 MET cc_start: 0.4712 (tmm) cc_final: 0.4140 (ptp) REVERT: B 40 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.5392 (mp10) outliers start: 21 outliers final: 9 residues processed: 202 average time/residue: 0.1194 time to fit residues: 33.1854 Evaluate side-chains 201 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 189 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 269 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 63 optimal weight: 0.0000 chunk 129 optimal weight: 0.0070 chunk 138 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 28 optimal weight: 0.4980 chunk 109 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN E 185 GLN B 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.213741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.189448 restraints weight = 15080.142| |-----------------------------------------------------------------------------| r_work (start): 0.4409 rms_B_bonded: 2.33 r_work: 0.4287 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5629 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11790 Z= 0.121 Angle : 0.659 9.697 15982 Z= 0.297 Chirality : 0.041 0.149 1799 Planarity : 0.005 0.045 2088 Dihedral : 9.375 155.058 1667 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.75 % Allowed : 9.17 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.23), residues: 1434 helix: 1.32 (0.18), residues: 831 sheet: 2.46 (0.41), residues: 150 loop : 1.35 (0.33), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 195 TYR 0.013 0.001 TYR D 304 PHE 0.032 0.001 PHE D 233 TRP 0.006 0.001 TRP D 325 HIS 0.004 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00274 (11790) covalent geometry : angle 0.65863 (15982) hydrogen bonds : bond 0.03307 ( 583) hydrogen bonds : angle 5.14613 ( 1680) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.7453 (mtm180) cc_final: 0.6973 (mtm-85) REVERT: C 173 ASP cc_start: 0.6173 (m-30) cc_final: 0.5880 (m-30) REVERT: D 108 ASP cc_start: 0.6421 (m-30) cc_final: 0.6055 (m-30) REVERT: D 285 ASN cc_start: 0.7059 (t0) cc_final: 0.6848 (m110) REVERT: D 319 MET cc_start: 0.7682 (tmm) cc_final: 0.7226 (tmm) REVERT: E 259 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6828 (mm-30) REVERT: E 319 MET cc_start: 0.4736 (tmm) cc_final: 0.4165 (ptp) REVERT: B 40 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.5392 (mp10) outliers start: 21 outliers final: 11 residues processed: 199 average time/residue: 0.1144 time to fit residues: 31.6861 Evaluate side-chains 200 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 224 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 31 optimal weight: 0.0770 chunk 26 optimal weight: 0.0050 chunk 5 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 overall best weight: 0.3952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN C 327 HIS E 185 GLN B 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.215745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.190788 restraints weight = 15189.195| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 2.44 r_work: 0.4277 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5619 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11790 Z= 0.125 Angle : 0.666 9.637 15982 Z= 0.302 Chirality : 0.042 0.147 1799 Planarity : 0.005 0.055 2088 Dihedral : 9.204 154.041 1667 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.50 % Allowed : 9.92 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.23), residues: 1434 helix: 1.39 (0.18), residues: 831 sheet: 2.45 (0.41), residues: 150 loop : 1.35 (0.33), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 195 TYR 0.011 0.001 TYR D 133 PHE 0.035 0.001 PHE C 328 TRP 0.006 0.001 TRP D 325 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00284 (11790) covalent geometry : angle 0.66559 (15982) hydrogen bonds : bond 0.03316 ( 583) hydrogen bonds : angle 5.07249 ( 1680) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.7499 (mtm180) cc_final: 0.6981 (mtm-85) REVERT: C 173 ASP cc_start: 0.6182 (m-30) cc_final: 0.5882 (m-30) REVERT: D 108 ASP cc_start: 0.6388 (m-30) cc_final: 0.6129 (m-30) REVERT: D 285 ASN cc_start: 0.6982 (t0) cc_final: 0.6749 (m110) REVERT: D 319 MET cc_start: 0.7657 (tmm) cc_final: 0.7156 (tmm) REVERT: B 40 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.5288 (mp10) outliers start: 18 outliers final: 8 residues processed: 199 average time/residue: 0.1197 time to fit residues: 32.8189 Evaluate side-chains 194 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 185 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 40 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 140 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 98 optimal weight: 0.1980 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 185 GLN B 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.214651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.189904 restraints weight = 15024.542| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 2.44 r_work: 0.4251 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5683 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11790 Z= 0.148 Angle : 0.689 10.180 15982 Z= 0.317 Chirality : 0.043 0.226 1799 Planarity : 0.005 0.055 2088 Dihedral : 9.126 153.549 1667 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.42 % Allowed : 11.17 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.23), residues: 1434 helix: 1.32 (0.18), residues: 832 sheet: 2.42 (0.41), residues: 150 loop : 1.23 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 51 TYR 0.022 0.002 TYR D 304 PHE 0.022 0.001 PHE E 155 TRP 0.007 0.001 TRP D 325 HIS 0.005 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00341 (11790) covalent geometry : angle 0.68885 (15982) hydrogen bonds : bond 0.03533 ( 583) hydrogen bonds : angle 5.07962 ( 1680) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ARG cc_start: 0.6840 (mtt90) cc_final: 0.5237 (tpt170) REVERT: A 198 ARG cc_start: 0.7538 (mtm180) cc_final: 0.7011 (mtm-85) REVERT: C 253 MET cc_start: 0.5310 (ttp) cc_final: 0.4918 (ttp) REVERT: D 319 MET cc_start: 0.7682 (tmm) cc_final: 0.7195 (tmm) REVERT: E 108 ASP cc_start: 0.5831 (m-30) cc_final: 0.5350 (m-30) REVERT: E 131 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7089 (mt-10) REVERT: B 40 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.5304 (mp10) outliers start: 17 outliers final: 11 residues processed: 198 average time/residue: 0.1184 time to fit residues: 32.1944 Evaluate side-chains 199 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 269 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 92 optimal weight: 0.0870 chunk 129 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 114 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 185 GLN B 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.215806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.190871 restraints weight = 15392.657| |-----------------------------------------------------------------------------| r_work (start): 0.4459 rms_B_bonded: 2.09 r_work: 0.4343 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5673 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11790 Z= 0.125 Angle : 0.678 10.328 15982 Z= 0.309 Chirality : 0.042 0.236 1799 Planarity : 0.005 0.062 2088 Dihedral : 8.931 153.536 1667 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.58 % Allowed : 11.50 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.23), residues: 1434 helix: 1.40 (0.18), residues: 832 sheet: 2.39 (0.41), residues: 150 loop : 1.28 (0.33), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 51 TYR 0.017 0.001 TYR D 304 PHE 0.022 0.001 PHE E 155 TRP 0.007 0.001 TRP D 325 HIS 0.004 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00284 (11790) covalent geometry : angle 0.67775 (15982) hydrogen bonds : bond 0.03247 ( 583) hydrogen bonds : angle 4.95015 ( 1680) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ARG cc_start: 0.6766 (mtt90) cc_final: 0.5292 (tpt170) REVERT: A 198 ARG cc_start: 0.7442 (mtm180) cc_final: 0.7241 (mtm-85) REVERT: C 173 ASP cc_start: 0.6032 (m-30) cc_final: 0.5787 (m-30) REVERT: C 253 MET cc_start: 0.5229 (ttp) cc_final: 0.4847 (ttp) REVERT: D 51 ARG cc_start: 0.7328 (mtm-85) cc_final: 0.6967 (mtt180) REVERT: D 112 ILE cc_start: 0.6444 (mt) cc_final: 0.6122 (mm) REVERT: D 227 LEU cc_start: 0.5028 (OUTLIER) cc_final: 0.4115 (pp) REVERT: D 319 MET cc_start: 0.7625 (tmm) cc_final: 0.7329 (tmm) REVERT: E 28 LEU cc_start: 0.6639 (tt) cc_final: 0.6063 (tt) REVERT: E 108 ASP cc_start: 0.6011 (m-30) cc_final: 0.5513 (m-30) REVERT: E 131 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7113 (mt-10) REVERT: B 40 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.5364 (mp10) outliers start: 19 outliers final: 12 residues processed: 200 average time/residue: 0.1149 time to fit residues: 31.4849 Evaluate side-chains 202 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 263 TYR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 269 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 78 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 59 optimal weight: 0.0170 chunk 115 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN E 185 GLN B 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.214327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.188300 restraints weight = 15293.708| |-----------------------------------------------------------------------------| r_work (start): 0.4429 rms_B_bonded: 2.24 r_work: 0.4310 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5721 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11790 Z= 0.149 Angle : 0.711 10.808 15982 Z= 0.326 Chirality : 0.044 0.269 1799 Planarity : 0.005 0.072 2088 Dihedral : 8.925 152.957 1667 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.67 % Allowed : 11.75 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.23), residues: 1434 helix: 1.32 (0.18), residues: 833 sheet: 2.38 (0.41), residues: 150 loop : 1.18 (0.32), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 51 TYR 0.021 0.002 TYR C 184 PHE 0.024 0.001 PHE E 155 TRP 0.007 0.001 TRP D 325 HIS 0.007 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00347 (11790) covalent geometry : angle 0.71110 (15982) hydrogen bonds : bond 0.03494 ( 583) hydrogen bonds : angle 4.99205 ( 1680) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ARG cc_start: 0.6670 (mtt90) cc_final: 0.5197 (tpt170) REVERT: C 245 ASP cc_start: 0.7233 (m-30) cc_final: 0.6835 (m-30) REVERT: D 41 MET cc_start: 0.7035 (tpt) cc_final: 0.6803 (tpp) REVERT: D 112 ILE cc_start: 0.6555 (mt) cc_final: 0.6260 (mm) REVERT: D 227 LEU cc_start: 0.5166 (OUTLIER) cc_final: 0.4262 (pp) REVERT: D 319 MET cc_start: 0.7669 (tmm) cc_final: 0.7149 (tmm) REVERT: E 28 LEU cc_start: 0.6505 (tt) cc_final: 0.6299 (tt) REVERT: E 108 ASP cc_start: 0.5989 (m-30) cc_final: 0.5439 (m-30) REVERT: E 131 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7167 (mt-10) REVERT: E 235 GLU cc_start: 0.5987 (mt-10) cc_final: 0.5625 (mp0) REVERT: B 40 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.5304 (mp10) REVERT: B 228 ARG cc_start: 0.5579 (mtp-110) cc_final: 0.4968 (ttm-80) outliers start: 20 outliers final: 17 residues processed: 195 average time/residue: 0.1202 time to fit residues: 31.8789 Evaluate side-chains 203 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 263 TYR Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 121 optimal weight: 0.0270 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 129 optimal weight: 0.0980 chunk 112 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 56 optimal weight: 0.3980 chunk 94 optimal weight: 0.5980 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.215687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.189799 restraints weight = 15460.921| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 2.25 r_work: 0.4304 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5701 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11790 Z= 0.122 Angle : 0.692 10.629 15982 Z= 0.316 Chirality : 0.042 0.266 1799 Planarity : 0.005 0.073 2088 Dihedral : 8.777 152.977 1667 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.42 % Allowed : 12.17 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.23), residues: 1434 helix: 1.36 (0.18), residues: 833 sheet: 2.40 (0.41), residues: 150 loop : 1.25 (0.32), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 51 TYR 0.028 0.001 TYR D 304 PHE 0.023 0.001 PHE E 155 TRP 0.007 0.001 TRP D 325 HIS 0.006 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00278 (11790) covalent geometry : angle 0.69157 (15982) hydrogen bonds : bond 0.03241 ( 583) hydrogen bonds : angle 4.96855 ( 1680) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ARG cc_start: 0.6626 (mtt90) cc_final: 0.5278 (tpt170) REVERT: A 198 ARG cc_start: 0.7661 (mtm180) cc_final: 0.7112 (mtm-85) REVERT: C 245 ASP cc_start: 0.7167 (m-30) cc_final: 0.6810 (m-30) REVERT: D 112 ILE cc_start: 0.6444 (mt) cc_final: 0.6119 (mm) REVERT: D 174 ARG cc_start: 0.6313 (mmt-90) cc_final: 0.5812 (mtm-85) REVERT: D 227 LEU cc_start: 0.5052 (OUTLIER) cc_final: 0.4146 (pp) REVERT: D 319 MET cc_start: 0.7635 (tmm) cc_final: 0.7418 (tmm) REVERT: E 28 LEU cc_start: 0.6556 (tt) cc_final: 0.5952 (tt) REVERT: E 108 ASP cc_start: 0.6020 (m-30) cc_final: 0.5496 (m-30) REVERT: B 40 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.5346 (mp10) REVERT: B 228 ARG cc_start: 0.5382 (mtp-110) cc_final: 0.4919 (ttm-80) outliers start: 17 outliers final: 14 residues processed: 194 average time/residue: 0.1060 time to fit residues: 28.5788 Evaluate side-chains 199 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 263 TYR Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 84 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 82 optimal weight: 0.0570 chunk 16 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.215252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.189314 restraints weight = 15541.365| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 2.26 r_work: 0.4293 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5720 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 11790 Z= 0.136 Angle : 0.703 10.434 15982 Z= 0.324 Chirality : 0.043 0.260 1799 Planarity : 0.005 0.074 2088 Dihedral : 8.711 152.115 1667 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.42 % Allowed : 12.25 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.23), residues: 1434 helix: 1.31 (0.18), residues: 833 sheet: 2.41 (0.42), residues: 150 loop : 1.19 (0.32), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 51 TYR 0.021 0.002 TYR D 304 PHE 0.025 0.001 PHE E 155 TRP 0.007 0.001 TRP D 325 HIS 0.005 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00317 (11790) covalent geometry : angle 0.70272 (15982) hydrogen bonds : bond 0.03418 ( 583) hydrogen bonds : angle 4.98657 ( 1680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3518.93 seconds wall clock time: 60 minutes 40.16 seconds (3640.16 seconds total)