Starting phenix.real_space_refine on Fri Oct 10 14:56:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8j_36071/10_2025/8j8j_36071.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8j_36071/10_2025/8j8j_36071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j8j_36071/10_2025/8j8j_36071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8j_36071/10_2025/8j8j_36071.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j8j_36071/10_2025/8j8j_36071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8j_36071/10_2025/8j8j_36071.map" } resolution = 2.76 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= 0.002 sd= 0.101 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 3 5.21 5 S 30 5.16 5 C 4515 2.51 5 N 1104 2.21 5 O 1209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6873 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2217 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "A" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2217 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "B" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2217 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {' MG': 1, 'PGW': 1, 'PRP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {' MG': 1, 'PGW': 1, 'PRP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {' MG': 1, 'PGW': 1, 'PRP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.00, per 1000 atoms: 0.29 Number of scatterers: 6873 At special positions: 0 Unit cell: (107.52, 99.84, 73.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 12 15.00 Mg 3 11.99 O 1209 8.00 N 1104 7.00 C 4515 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 406.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1614 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 82.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'D' and resid 13 through 18 removed outlier: 3.667A pdb=" N VAL D 18 " --> pdb=" O VAL D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 32 removed outlier: 4.018A pdb=" N VAL D 27 " --> pdb=" O ARG D 24 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D 28 " --> pdb=" O GLN D 25 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 30 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU D 31 " --> pdb=" O LYS D 28 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 32 " --> pdb=" O ASN D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 39 removed outlier: 3.768A pdb=" N LEU D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 77 removed outlier: 3.888A pdb=" N SER D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET D 57 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 123 through 139 removed outlier: 3.575A pdb=" N VAL D 127 " --> pdb=" O ASN D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 removed outlier: 6.541A pdb=" N LYS D 143 " --> pdb=" O PHE D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 168 removed outlier: 3.524A pdb=" N CYS D 151 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 153 " --> pdb=" O GLU D 149 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR D 157 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA D 161 " --> pdb=" O TYR D 157 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 202 removed outlier: 3.667A pdb=" N LEU D 177 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG D 201 " --> pdb=" O HIS D 197 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 213 Processing helix chain 'D' and resid 214 through 242 removed outlier: 3.505A pdb=" N PHE D 238 " --> pdb=" O GLY D 234 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY D 242 " --> pdb=" O PHE D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 268 removed outlier: 3.777A pdb=" N SER D 251 " --> pdb=" O TRP D 247 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET D 252 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Proline residue: D 254 - end of helix removed outlier: 3.650A pdb=" N VAL D 264 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP D 265 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 281 removed outlier: 3.946A pdb=" N LEU D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP D 281 " --> pdb=" O ILE D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 302 removed outlier: 3.860A pdb=" N GLN D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.668A pdb=" N VAL A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 14 through 18' Processing helix chain 'A' and resid 22 through 32 removed outlier: 4.018A pdb=" N VAL A 27 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 28 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 30 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 31 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 32 " --> pdb=" O ASN A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 removed outlier: 3.768A pdb=" N LEU A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 77 removed outlier: 3.889A pdb=" N SER A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 121 Processing helix chain 'A' and resid 123 through 139 removed outlier: 3.575A pdb=" N VAL A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 removed outlier: 6.576A pdb=" N LYS A 143 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 168 removed outlier: 3.523A pdb=" N CYS A 151 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 157 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 161 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 202 removed outlier: 3.667A pdb=" N LEU A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A 201 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 214 through 242 removed outlier: 3.504A pdb=" N PHE A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 268 removed outlier: 3.777A pdb=" N SER A 251 " --> pdb=" O TRP A 247 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Proline residue: A 254 - end of helix removed outlier: 3.650A pdb=" N VAL A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 281 removed outlier: 3.807A pdb=" N LEU A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 281 " --> pdb=" O ILE A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 302 removed outlier: 3.861A pdb=" N GLN A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.668A pdb=" N VAL B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 14 through 18' Processing helix chain 'B' and resid 22 through 32 removed outlier: 4.017A pdb=" N VAL B 27 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 28 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 30 " --> pdb=" O VAL B 27 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU B 31 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 32 " --> pdb=" O ASN B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 39 removed outlier: 3.769A pdb=" N LEU B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 77 removed outlier: 3.889A pdb=" N SER B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 121 Processing helix chain 'B' and resid 123 through 139 removed outlier: 3.574A pdb=" N VAL B 127 " --> pdb=" O ASN B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 6.530A pdb=" N LYS B 143 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 168 removed outlier: 3.523A pdb=" N CYS B 151 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 161 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 202 removed outlier: 3.668A pdb=" N LEU B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 201 " --> pdb=" O HIS B 197 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 213 Processing helix chain 'B' and resid 214 through 242 removed outlier: 3.504A pdb=" N PHE B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY B 242 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 268 removed outlier: 3.777A pdb=" N SER B 251 " --> pdb=" O TRP B 247 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Proline residue: B 254 - end of helix removed outlier: 3.650A pdb=" N VAL B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.882A pdb=" N LEU B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B 281 " --> pdb=" O ILE B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 302 removed outlier: 3.860A pdb=" N GLN B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 removed outlier: 5.010A pdb=" N ARG D 82 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 removed outlier: 5.010A pdb=" N ARG A 82 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 83 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 removed outlier: 5.010A pdb=" N ARG B 82 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1191 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: 0.98 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1020 1.27 - 1.40: 1782 1.40 - 1.54: 4011 1.54 - 1.67: 157 1.67 - 1.81: 53 Bond restraints: 7023 Sorted by residual: bond pdb=" C1 PRP D 401 " pdb=" O4 PRP D 401 " ideal model delta sigma weight residual 1.656 1.418 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C1 PRP A 401 " pdb=" O4 PRP A 401 " ideal model delta sigma weight residual 1.656 1.419 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1 PRP B 401 " pdb=" O4 PRP B 401 " ideal model delta sigma weight residual 1.656 1.420 0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C1 PRP A 401 " pdb=" C2 PRP A 401 " ideal model delta sigma weight residual 1.327 1.509 -0.182 2.00e-02 2.50e+03 8.27e+01 bond pdb=" C1 PRP B 401 " pdb=" C2 PRP B 401 " ideal model delta sigma weight residual 1.327 1.508 -0.181 2.00e-02 2.50e+03 8.23e+01 ... (remaining 7018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 9239 2.73 - 5.46: 207 5.46 - 8.19: 81 8.19 - 10.92: 26 10.92 - 13.64: 14 Bond angle restraints: 9567 Sorted by residual: angle pdb=" N ILE D 206 " pdb=" CA ILE D 206 " pdb=" C ILE D 206 " ideal model delta sigma weight residual 112.12 98.48 13.64 8.40e-01 1.42e+00 2.64e+02 angle pdb=" N ILE A 206 " pdb=" CA ILE A 206 " pdb=" C ILE A 206 " ideal model delta sigma weight residual 112.12 100.15 11.97 8.40e-01 1.42e+00 2.03e+02 angle pdb=" N ILE B 206 " pdb=" CA ILE B 206 " pdb=" C ILE B 206 " ideal model delta sigma weight residual 112.12 100.25 11.87 8.40e-01 1.42e+00 2.00e+02 angle pdb=" N ARG D 207 " pdb=" CA ARG D 207 " pdb=" C ARG D 207 " ideal model delta sigma weight residual 111.30 121.24 -9.94 1.36e+00 5.41e-01 5.34e+01 angle pdb=" N ARG D 207 " pdb=" CA ARG D 207 " pdb=" CB ARG D 207 " ideal model delta sigma weight residual 111.62 102.91 8.71 1.43e+00 4.89e-01 3.71e+01 ... (remaining 9562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.58: 3971 31.58 - 63.15: 160 63.15 - 94.73: 18 94.73 - 126.31: 6 126.31 - 157.89: 9 Dihedral angle restraints: 4164 sinusoidal: 1644 harmonic: 2520 Sorted by residual: dihedral pdb=" C LYS B 143 " pdb=" N LYS B 143 " pdb=" CA LYS B 143 " pdb=" CB LYS B 143 " ideal model delta harmonic sigma weight residual -122.60 -110.15 -12.45 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" C03 PGW B 403 " pdb=" C01 PGW B 403 " pdb=" C02 PGW B 403 " pdb=" O03 PGW B 403 " ideal model delta sinusoidal sigma weight residual -64.65 93.24 -157.89 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C03 PGW A 403 " pdb=" C01 PGW A 403 " pdb=" C02 PGW A 403 " pdb=" O03 PGW A 403 " ideal model delta sinusoidal sigma weight residual -64.65 93.23 -157.88 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 4161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1084 0.111 - 0.223: 33 0.223 - 0.334: 2 0.334 - 0.446: 6 0.446 - 0.557: 3 Chirality restraints: 1128 Sorted by residual: chirality pdb=" C02 PGW B 403 " pdb=" C01 PGW B 403 " pdb=" C03 PGW B 403 " pdb=" O01 PGW B 403 " both_signs ideal model delta sigma weight residual False 2.36 2.91 -0.56 2.00e-01 2.50e+01 7.76e+00 chirality pdb=" C02 PGW D 403 " pdb=" C01 PGW D 403 " pdb=" C03 PGW D 403 " pdb=" O01 PGW D 403 " both_signs ideal model delta sigma weight residual False 2.36 2.91 -0.56 2.00e-01 2.50e+01 7.72e+00 chirality pdb=" C02 PGW A 403 " pdb=" C01 PGW A 403 " pdb=" C03 PGW A 403 " pdb=" O01 PGW A 403 " both_signs ideal model delta sigma weight residual False 2.36 2.91 -0.55 2.00e-01 2.50e+01 7.69e+00 ... (remaining 1125 not shown) Planarity restraints: 1143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 169 " 0.013 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" C LYS B 169 " -0.047 2.00e-02 2.50e+03 pdb=" O LYS B 169 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE B 170 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 169 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" C LYS A 169 " 0.046 2.00e-02 2.50e+03 pdb=" O LYS A 169 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE A 170 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 168 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.48e+00 pdb=" C THR D 168 " -0.044 2.00e-02 2.50e+03 pdb=" O THR D 168 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS D 169 " 0.015 2.00e-02 2.50e+03 ... (remaining 1140 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 10 2.35 - 2.99: 3405 2.99 - 3.63: 9498 3.63 - 4.26: 14914 4.26 - 4.90: 25546 Nonbonded interactions: 53373 Sorted by model distance: nonbonded pdb=" O3B PRP A 401 " pdb="MG MG A 402 " model vdw 1.717 2.170 nonbonded pdb=" O3B PRP B 401 " pdb="MG MG B 402 " model vdw 1.821 2.170 nonbonded pdb=" O3B PRP D 401 " pdb="MG MG D 402 " model vdw 1.836 2.170 nonbonded pdb=" O1A PRP A 401 " pdb="MG MG A 402 " model vdw 1.989 2.170 nonbonded pdb=" O1A PRP D 401 " pdb="MG MG D 402 " model vdw 2.000 2.170 ... (remaining 53368 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: 0.01 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'A' selection = chain 'B' } 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.260 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 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 0.238 7023 Z= 0.578 Angle : 1.193 13.645 9567 Z= 0.641 Chirality : 0.061 0.557 1128 Planarity : 0.005 0.034 1143 Dihedral : 19.317 157.885 2550 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.54 (0.24), residues: 864 helix: -1.07 (0.18), residues: 663 sheet: None (None), residues: 0 loop : -3.37 (0.29), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 201 TYR 0.016 0.002 TYR A 217 PHE 0.014 0.002 PHE D 182 TRP 0.031 0.002 TRP B 222 HIS 0.005 0.002 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.01098 ( 7023) covalent geometry : angle 1.19335 ( 9567) hydrogen bonds : bond 0.15943 ( 421) hydrogen bonds : angle 4.26645 ( 1191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.262 Fit side-chains REVERT: D 212 SER cc_start: 0.8357 (m) cc_final: 0.8044 (p) REVERT: B 187 MET cc_start: 0.8118 (mmt) cc_final: 0.7898 (mmt) REVERT: B 270 LEU cc_start: 0.7196 (mt) cc_final: 0.6994 (mt) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.5325 time to fit residues: 53.0114 Evaluate side-chains 75 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.159637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.096385 restraints weight = 7055.275| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.94 r_work: 0.2885 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7023 Z= 0.129 Angle : 0.580 7.412 9567 Z= 0.295 Chirality : 0.039 0.190 1128 Planarity : 0.004 0.025 1143 Dihedral : 18.119 148.874 1176 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.83 % Allowed : 13.24 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.27), residues: 864 helix: 0.22 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -2.34 (0.36), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 201 TYR 0.025 0.001 TYR D 213 PHE 0.011 0.002 PHE D 255 TRP 0.030 0.002 TRP B 222 HIS 0.003 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7023) covalent geometry : angle 0.57985 ( 9567) hydrogen bonds : bond 0.06400 ( 421) hydrogen bonds : angle 3.15361 ( 1191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.300 Fit side-chains REVERT: D 45 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6205 (ttt90) REVERT: A 142 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8261 (mp) REVERT: B 270 LEU cc_start: 0.7215 (mt) cc_final: 0.6976 (mt) outliers start: 19 outliers final: 6 residues processed: 85 average time/residue: 0.5201 time to fit residues: 46.9934 Evaluate side-chains 81 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 0.0870 chunk 77 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 0.0570 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.164153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.104687 restraints weight = 7144.556| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.84 r_work: 0.2938 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7023 Z= 0.110 Angle : 0.524 6.913 9567 Z= 0.267 Chirality : 0.038 0.182 1128 Planarity : 0.003 0.022 1143 Dihedral : 16.307 150.113 1176 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.98 % Allowed : 14.88 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.29), residues: 864 helix: 1.26 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -1.33 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 201 TYR 0.019 0.001 TYR D 213 PHE 0.009 0.001 PHE D 255 TRP 0.026 0.001 TRP D 222 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 7023) covalent geometry : angle 0.52439 ( 9567) hydrogen bonds : bond 0.05348 ( 421) hydrogen bonds : angle 2.91303 ( 1191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.241 Fit side-chains REVERT: D 45 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6181 (ttt90) REVERT: D 56 SER cc_start: 0.8224 (t) cc_final: 0.7933 (p) REVERT: D 62 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.7544 (t80) REVERT: A 45 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6834 (ttt90) REVERT: A 56 SER cc_start: 0.8257 (OUTLIER) cc_final: 0.8025 (p) REVERT: A 62 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8256 (t80) REVERT: A 142 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8202 (mp) REVERT: B 56 SER cc_start: 0.8404 (OUTLIER) cc_final: 0.8117 (p) outliers start: 20 outliers final: 4 residues processed: 90 average time/residue: 0.5737 time to fit residues: 54.5080 Evaluate side-chains 86 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 62 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.162171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.100921 restraints weight = 7141.849| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.90 r_work: 0.2727 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7023 Z= 0.145 Angle : 0.585 9.811 9567 Z= 0.295 Chirality : 0.040 0.199 1128 Planarity : 0.003 0.023 1143 Dihedral : 16.381 151.785 1176 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.27 % Allowed : 16.07 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.28), residues: 864 helix: 1.28 (0.21), residues: 633 sheet: None (None), residues: 0 loop : -1.21 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 240 TYR 0.022 0.002 TYR D 213 PHE 0.015 0.002 PHE D 182 TRP 0.031 0.002 TRP B 222 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7023) covalent geometry : angle 0.58505 ( 9567) hydrogen bonds : bond 0.07023 ( 421) hydrogen bonds : angle 3.06500 ( 1191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.250 Fit side-chains REVERT: D 45 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6114 (ttt90) REVERT: D 62 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.7488 (t80) REVERT: A 45 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6821 (ttt90) REVERT: A 62 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8286 (t80) REVERT: A 142 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8107 (mp) REVERT: B 208 LYS cc_start: 0.5150 (OUTLIER) cc_final: 0.4818 (pttp) outliers start: 22 outliers final: 7 residues processed: 84 average time/residue: 0.5404 time to fit residues: 48.0278 Evaluate side-chains 87 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.159115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.096980 restraints weight = 7048.659| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.08 r_work: 0.2871 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7023 Z= 0.134 Angle : 0.570 10.812 9567 Z= 0.286 Chirality : 0.039 0.195 1128 Planarity : 0.003 0.023 1143 Dihedral : 15.956 150.294 1176 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.83 % Allowed : 16.37 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.28), residues: 864 helix: 1.39 (0.21), residues: 633 sheet: None (None), residues: 0 loop : -1.05 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 24 TYR 0.018 0.001 TYR D 213 PHE 0.013 0.002 PHE D 182 TRP 0.028 0.002 TRP B 222 HIS 0.002 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7023) covalent geometry : angle 0.57031 ( 9567) hydrogen bonds : bond 0.06447 ( 421) hydrogen bonds : angle 2.99948 ( 1191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.256 Fit side-chains REVERT: D 45 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6084 (ttt90) REVERT: D 62 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.7582 (t80) REVERT: A 45 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6631 (ttt90) REVERT: A 62 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8379 (t80) REVERT: A 142 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8164 (mp) REVERT: B 208 LYS cc_start: 0.5221 (OUTLIER) cc_final: 0.4811 (pttp) outliers start: 19 outliers final: 7 residues processed: 82 average time/residue: 0.5032 time to fit residues: 43.7924 Evaluate side-chains 84 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.160993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.097787 restraints weight = 7060.422| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.97 r_work: 0.2922 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7023 Z= 0.113 Angle : 0.543 10.284 9567 Z= 0.269 Chirality : 0.038 0.187 1128 Planarity : 0.003 0.022 1143 Dihedral : 15.423 147.195 1176 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.68 % Allowed : 17.41 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.29), residues: 864 helix: 1.64 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -0.84 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 24 TYR 0.014 0.001 TYR D 213 PHE 0.009 0.001 PHE A 182 TRP 0.026 0.001 TRP B 222 HIS 0.002 0.000 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 7023) covalent geometry : angle 0.54274 ( 9567) hydrogen bonds : bond 0.05486 ( 421) hydrogen bonds : angle 2.86537 ( 1191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.278 Fit side-chains REVERT: D 45 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6075 (ttt90) REVERT: D 62 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.7533 (t80) REVERT: D 140 PHE cc_start: 0.8558 (m-80) cc_final: 0.8249 (m-80) REVERT: A 45 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6662 (ttt90) REVERT: A 56 SER cc_start: 0.8233 (OUTLIER) cc_final: 0.7970 (p) REVERT: A 62 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8424 (t80) REVERT: A 142 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8149 (mp) outliers start: 18 outliers final: 5 residues processed: 82 average time/residue: 0.5584 time to fit residues: 48.4110 Evaluate side-chains 80 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 44 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.159247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.095566 restraints weight = 6977.602| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.95 r_work: 0.2879 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7023 Z= 0.131 Angle : 0.563 11.033 9567 Z= 0.282 Chirality : 0.039 0.193 1128 Planarity : 0.003 0.023 1143 Dihedral : 15.513 145.712 1176 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.53 % Allowed : 17.86 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.28), residues: 864 helix: 1.53 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -0.69 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 24 TYR 0.015 0.001 TYR D 213 PHE 0.013 0.002 PHE D 182 TRP 0.030 0.002 TRP B 222 HIS 0.002 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7023) covalent geometry : angle 0.56300 ( 9567) hydrogen bonds : bond 0.06368 ( 421) hydrogen bonds : angle 2.92851 ( 1191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.259 Fit side-chains REVERT: D 45 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6397 (ttt90) REVERT: D 62 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.7550 (t80) REVERT: A 45 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6649 (ttt90) REVERT: A 56 SER cc_start: 0.8289 (OUTLIER) cc_final: 0.7990 (p) REVERT: A 62 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8348 (t80) REVERT: A 142 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8157 (mp) REVERT: B 208 LYS cc_start: 0.5152 (OUTLIER) cc_final: 0.4729 (pttp) outliers start: 17 outliers final: 7 residues processed: 82 average time/residue: 0.5360 time to fit residues: 46.5056 Evaluate side-chains 86 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 22 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.159557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.097615 restraints weight = 7036.011| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.27 r_work: 0.2873 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7023 Z= 0.128 Angle : 0.571 10.914 9567 Z= 0.281 Chirality : 0.039 0.191 1128 Planarity : 0.003 0.023 1143 Dihedral : 15.374 144.420 1176 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.53 % Allowed : 18.30 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.28), residues: 864 helix: 1.61 (0.21), residues: 633 sheet: None (None), residues: 0 loop : -0.56 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 24 TYR 0.014 0.001 TYR D 213 PHE 0.013 0.002 PHE A 182 TRP 0.028 0.002 TRP B 222 HIS 0.002 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7023) covalent geometry : angle 0.57054 ( 9567) hydrogen bonds : bond 0.06168 ( 421) hydrogen bonds : angle 2.90185 ( 1191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.251 Fit side-chains REVERT: D 45 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6146 (ttt90) REVERT: D 62 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.7491 (t80) REVERT: D 270 LEU cc_start: 0.7092 (mt) cc_final: 0.6785 (mt) REVERT: A 45 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6630 (ttt90) REVERT: A 62 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8315 (t80) REVERT: A 142 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8081 (mp) REVERT: B 208 LYS cc_start: 0.5079 (OUTLIER) cc_final: 0.4669 (pttp) outliers start: 17 outliers final: 8 residues processed: 84 average time/residue: 0.5268 time to fit residues: 46.8005 Evaluate side-chains 85 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 60 optimal weight: 0.0270 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.160754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.098363 restraints weight = 7035.870| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.92 r_work: 0.2919 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7023 Z= 0.117 Angle : 0.547 10.672 9567 Z= 0.271 Chirality : 0.038 0.188 1128 Planarity : 0.003 0.022 1143 Dihedral : 15.069 142.216 1176 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.38 % Allowed : 18.75 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.28), residues: 864 helix: 1.77 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -0.50 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 24 TYR 0.012 0.001 TYR D 213 PHE 0.010 0.002 PHE D 182 TRP 0.026 0.001 TRP B 222 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 7023) covalent geometry : angle 0.54740 ( 9567) hydrogen bonds : bond 0.05639 ( 421) hydrogen bonds : angle 2.81778 ( 1191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.247 Fit side-chains REVERT: D 45 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6407 (ttt90) REVERT: D 62 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.7576 (t80) REVERT: D 270 LEU cc_start: 0.7164 (mt) cc_final: 0.6869 (mt) REVERT: A 45 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6642 (ttt90) REVERT: A 62 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8396 (t80) REVERT: A 142 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8164 (mp) REVERT: B 208 LYS cc_start: 0.5124 (OUTLIER) cc_final: 0.4739 (pttp) outliers start: 16 outliers final: 7 residues processed: 81 average time/residue: 0.4794 time to fit residues: 41.1485 Evaluate side-chains 82 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.160600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.097421 restraints weight = 7020.345| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.96 r_work: 0.2897 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7023 Z= 0.117 Angle : 0.556 10.654 9567 Z= 0.274 Chirality : 0.038 0.187 1128 Planarity : 0.003 0.023 1143 Dihedral : 14.873 140.874 1176 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.23 % Allowed : 19.05 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.29), residues: 864 helix: 1.73 (0.21), residues: 639 sheet: None (None), residues: 0 loop : -0.32 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 201 TYR 0.012 0.001 TYR D 213 PHE 0.011 0.002 PHE D 182 TRP 0.028 0.001 TRP B 222 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 7023) covalent geometry : angle 0.55626 ( 9567) hydrogen bonds : bond 0.05683 ( 421) hydrogen bonds : angle 2.80893 ( 1191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.179 Fit side-chains REVERT: D 45 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6399 (ttt90) REVERT: D 62 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.7531 (t80) REVERT: D 270 LEU cc_start: 0.7134 (mt) cc_final: 0.6831 (mt) REVERT: A 25 GLN cc_start: 0.8502 (mm110) cc_final: 0.8287 (mm110) REVERT: A 45 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6623 (ttt90) REVERT: A 62 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8362 (t80) REVERT: A 142 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8116 (mp) REVERT: B 208 LYS cc_start: 0.5059 (OUTLIER) cc_final: 0.4666 (pttp) outliers start: 15 outliers final: 8 residues processed: 80 average time/residue: 0.5275 time to fit residues: 44.6607 Evaluate side-chains 86 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 29 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 4 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.161355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.098352 restraints weight = 7046.515| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.96 r_work: 0.2926 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7023 Z= 0.112 Angle : 0.540 10.494 9567 Z= 0.267 Chirality : 0.038 0.183 1128 Planarity : 0.003 0.022 1143 Dihedral : 14.604 138.426 1176 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.08 % Allowed : 19.05 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.29), residues: 864 helix: 1.86 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -0.34 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 201 TYR 0.012 0.001 TYR D 213 PHE 0.010 0.001 PHE B 182 TRP 0.026 0.001 TRP A 222 HIS 0.001 0.000 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 7023) covalent geometry : angle 0.54023 ( 9567) hydrogen bonds : bond 0.05364 ( 421) hydrogen bonds : angle 2.75889 ( 1191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2856.00 seconds wall clock time: 49 minutes 15.71 seconds (2955.71 seconds total)