Starting phenix.real_space_refine on Tue Mar 11 23:33:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8j_36071/03_2025/8j8j_36071.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8j_36071/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j8j_36071/03_2025/8j8j_36071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8j_36071/03_2025/8j8j_36071.map" model { file = "/net/cci-nas-00/data/ceres_data/8j8j_36071/03_2025/8j8j_36071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8j_36071/03_2025/8j8j_36071.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.13, per 1000 atoms: 0.75 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: 1.98 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.59 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: 1.78 Time building geometry restraints manager: 2.26 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.720 Find NCS groups from input model: 0.130 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:17.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.570 ------------------------------------------------------------------------------- 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= 0.703 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.002 TRP B 222 HIS 0.005 0.002 HIS D 197 PHE 0.014 0.002 PHE D 182 TYR 0.016 0.002 TYR A 217 ARG 0.005 0.000 ARG D 201 *********************** 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 : 0.683 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: 0.9949 time to fit residues: 99.5080 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 : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.159743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.100564 restraints weight = 7132.459| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.14 r_work: 0.2858 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1310 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= 0.193 Angle : 0.594 7.991 9567 Z= 0.302 Chirality : 0.040 0.196 1128 Planarity : 0.004 0.026 1143 Dihedral : 18.166 148.886 1176 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.83 % Allowed : 13.39 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.27), residues: 864 helix: 0.18 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -2.35 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 222 HIS 0.004 0.001 HIS D 197 PHE 0.012 0.002 PHE D 182 TYR 0.030 0.002 TYR D 213 ARG 0.002 0.000 ARG B 201 *********************** 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 93 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.678 Fit side-chains REVERT: D 45 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6180 (ttt90) REVERT: A 142 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8181 (mp) REVERT: B 270 LEU cc_start: 0.7101 (mt) cc_final: 0.6881 (mt) outliers start: 19 outliers final: 6 residues processed: 84 average time/residue: 1.0410 time to fit residues: 93.1409 Evaluate side-chains 80 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 8 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.160149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.097286 restraints weight = 7026.655| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.90 r_work: 0.2894 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7023 Z= 0.172 Angle : 0.557 7.664 9567 Z= 0.284 Chirality : 0.039 0.189 1128 Planarity : 0.003 0.023 1143 Dihedral : 17.011 150.702 1176 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.98 % Allowed : 15.48 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.28), residues: 864 helix: 1.08 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -1.40 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 222 HIS 0.003 0.001 HIS D 197 PHE 0.012 0.002 PHE D 182 TYR 0.021 0.001 TYR D 213 ARG 0.002 0.000 ARG B 201 *********************** 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 : 0.675 Fit side-chains REVERT: D 45 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6144 (ttt90) REVERT: D 62 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.7623 (t80) REVERT: A 45 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6855 (ttt90) REVERT: A 62 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8316 (t80) REVERT: A 142 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8196 (mp) outliers start: 20 outliers final: 6 residues processed: 89 average time/residue: 1.0522 time to fit residues: 99.5162 Evaluate side-chains 87 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 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 295 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 83 optimal weight: 0.0980 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.159953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.096907 restraints weight = 7073.129| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.92 r_work: 0.2890 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1849 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= 0.171 Angle : 0.556 9.823 9567 Z= 0.281 Chirality : 0.039 0.189 1128 Planarity : 0.003 0.023 1143 Dihedral : 16.220 151.325 1176 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.42 % Allowed : 15.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.28), residues: 864 helix: 1.36 (0.21), residues: 633 sheet: None (None), residues: 0 loop : -1.16 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 222 HIS 0.003 0.001 HIS A 197 PHE 0.012 0.002 PHE D 182 TYR 0.019 0.001 TYR D 213 ARG 0.001 0.000 ARG B 201 *********************** 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: 23 poor density : 73 time to evaluate : 0.685 Fit side-chains REVERT: D 45 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6112 (ttt90) REVERT: D 62 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.7595 (t80) REVERT: A 45 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6798 (ttt90) REVERT: A 62 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8404 (t80) REVERT: A 142 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8170 (mp) REVERT: B 208 LYS cc_start: 0.5214 (OUTLIER) cc_final: 0.4832 (pttp) outliers start: 23 outliers final: 9 residues processed: 86 average time/residue: 1.1337 time to fit residues: 103.2310 Evaluate side-chains 87 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 21 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 23 optimal weight: 0.0670 chunk 7 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.160351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.097160 restraints weight = 6906.313| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.95 r_work: 0.2771 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7023 Z= 0.163 Angle : 0.544 10.091 9567 Z= 0.274 Chirality : 0.038 0.191 1128 Planarity : 0.003 0.022 1143 Dihedral : 15.720 150.149 1176 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.27 % Allowed : 15.62 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.29), residues: 864 helix: 1.51 (0.21), residues: 633 sheet: None (None), residues: 0 loop : -1.00 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 222 HIS 0.002 0.001 HIS D 197 PHE 0.011 0.002 PHE A 182 TYR 0.015 0.001 TYR D 213 ARG 0.001 0.000 ARG B 201 *********************** 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 94 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.702 Fit side-chains REVERT: D 45 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6148 (ttt90) REVERT: D 62 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.7537 (t80) REVERT: A 45 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6633 (ttt90) REVERT: A 52 LEU cc_start: 0.8468 (mp) cc_final: 0.8213 (mt) REVERT: A 56 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7936 (p) REVERT: A 62 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8372 (t80) REVERT: A 142 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8086 (mp) REVERT: B 208 LYS cc_start: 0.5108 (OUTLIER) cc_final: 0.4742 (pttp) outliers start: 22 outliers final: 7 residues processed: 85 average time/residue: 1.1162 time to fit residues: 100.5842 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 : 0.674 ------------------------------------------------------------------------------- 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 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 41 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 8 optimal weight: 0.0060 chunk 33 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.5000 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.156122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.092703 restraints weight = 6945.154| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.91 r_work: 0.2819 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7023 Z= 0.285 Angle : 0.654 12.570 9567 Z= 0.326 Chirality : 0.043 0.219 1128 Planarity : 0.004 0.026 1143 Dihedral : 16.238 149.499 1176 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.68 % Allowed : 16.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.28), residues: 864 helix: 1.19 (0.20), residues: 633 sheet: None (None), residues: 0 loop : -0.97 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 222 HIS 0.002 0.001 HIS A 197 PHE 0.018 0.002 PHE D 182 TYR 0.021 0.002 TYR D 213 ARG 0.002 0.000 ARG B 240 *********************** 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 90 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.690 Fit side-chains REVERT: D 45 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6178 (ttt90) REVERT: D 62 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.7527 (t80) REVERT: D 212 SER cc_start: 0.8388 (m) cc_final: 0.7881 (p) REVERT: A 45 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6758 (ttt90) REVERT: A 62 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8390 (t80) REVERT: A 142 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8166 (mp) REVERT: B 208 LYS cc_start: 0.5046 (OUTLIER) cc_final: 0.4641 (pttp) outliers start: 18 outliers final: 8 residues processed: 82 average time/residue: 1.1058 time to fit residues: 96.2649 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 : 0.762 ------------------------------------------------------------------------------- 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 134 MET 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 292 ILE 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 67 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 54 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.159511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.100258 restraints weight = 6927.593| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.14 r_work: 0.2872 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7023 Z= 0.170 Angle : 0.563 11.006 9567 Z= 0.281 Chirality : 0.039 0.191 1128 Planarity : 0.003 0.024 1143 Dihedral : 15.644 146.433 1176 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.28), residues: 864 helix: 1.46 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -0.77 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 222 HIS 0.002 0.001 HIS D 197 PHE 0.011 0.002 PHE B 182 TYR 0.014 0.001 TYR D 213 ARG 0.001 0.000 ARG B 201 *********************** 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 90 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.698 Fit side-chains REVERT: D 45 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6153 (ttt90) REVERT: D 62 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.7577 (t80) REVERT: A 45 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6721 (ttt90) REVERT: A 62 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8453 (t80) REVERT: A 142 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8188 (mp) REVERT: B 208 LYS cc_start: 0.5178 (OUTLIER) cc_final: 0.4782 (pttp) outliers start: 17 outliers final: 7 residues processed: 83 average time/residue: 1.0878 time to fit residues: 95.9087 Evaluate side-chains 85 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.158766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.096511 restraints weight = 6978.102| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.21 r_work: 0.2870 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2031 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= 0.182 Angle : 0.583 11.216 9567 Z= 0.288 Chirality : 0.039 0.191 1128 Planarity : 0.003 0.024 1143 Dihedral : 15.539 144.972 1176 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.38 % Allowed : 19.05 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.28), residues: 864 helix: 1.51 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -0.65 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 222 HIS 0.003 0.001 HIS A 197 PHE 0.013 0.002 PHE D 182 TYR 0.014 0.001 TYR D 213 ARG 0.001 0.000 ARG B 201 *********************** 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 90 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.749 Fit side-chains REVERT: D 45 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6122 (ttt90) REVERT: D 62 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.7512 (t80) REVERT: D 270 LEU cc_start: 0.7097 (mt) cc_final: 0.6782 (mt) REVERT: A 45 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6636 (ttt90) REVERT: A 56 SER cc_start: 0.8238 (OUTLIER) cc_final: 0.7923 (p) REVERT: A 62 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8339 (t80) REVERT: A 142 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8096 (mp) outliers start: 16 outliers final: 9 residues processed: 84 average time/residue: 1.0761 time to fit residues: 96.2417 Evaluate side-chains 88 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 A residue 289 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 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 63 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 61 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.160497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.098320 restraints weight = 7062.547| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.91 r_work: 0.2911 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7023 Z= 0.154 Angle : 0.552 10.671 9567 Z= 0.274 Chirality : 0.038 0.187 1128 Planarity : 0.003 0.023 1143 Dihedral : 15.183 142.981 1176 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.08 % Allowed : 19.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.28), residues: 864 helix: 1.75 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -0.55 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 222 HIS 0.002 0.000 HIS D 197 PHE 0.010 0.002 PHE D 182 TYR 0.012 0.001 TYR D 213 ARG 0.002 0.000 ARG B 201 *********************** 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 84 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.674 Fit side-chains REVERT: D 45 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6102 (ttt90) REVERT: D 62 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.7556 (t80) REVERT: D 270 LEU cc_start: 0.7133 (mt) cc_final: 0.6829 (mt) REVERT: A 45 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6600 (ttt90) REVERT: A 56 SER cc_start: 0.8212 (OUTLIER) cc_final: 0.7965 (p) REVERT: A 62 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8386 (t80) REVERT: A 142 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8159 (mp) outliers start: 14 outliers final: 6 residues processed: 78 average time/residue: 1.1069 time to fit residues: 91.6167 Evaluate side-chains 82 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 A residue 292 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 62 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 0 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.161384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.100280 restraints weight = 7311.620| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.92 r_work: 0.2914 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7023 Z= 0.159 Angle : 0.566 10.794 9567 Z= 0.278 Chirality : 0.038 0.187 1128 Planarity : 0.003 0.023 1143 Dihedral : 14.994 141.703 1176 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.93 % Allowed : 19.49 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.28), residues: 864 helix: 1.76 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 222 HIS 0.003 0.001 HIS A 197 PHE 0.010 0.002 PHE D 182 TYR 0.012 0.001 TYR D 213 ARG 0.002 0.000 ARG A 201 ********************** 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 84 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.752 Fit side-chains REVERT: D 45 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6419 (ttt90) REVERT: D 62 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.7567 (t80) REVERT: D 270 LEU cc_start: 0.7154 (mt) cc_final: 0.6854 (mt) REVERT: A 45 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6525 (ttt90) REVERT: A 56 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7980 (p) REVERT: A 62 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8391 (t80) REVERT: A 142 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8142 (mp) REVERT: B 208 LYS cc_start: 0.4872 (OUTLIER) cc_final: 0.4478 (pttp) outliers start: 13 outliers final: 5 residues processed: 79 average time/residue: 1.2223 time to fit residues: 102.1483 Evaluate side-chains 83 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 A residue 292 ILE Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 208 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 45 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.157898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.094708 restraints weight = 7059.641| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.92 r_work: 0.2849 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7023 Z= 0.217 Angle : 0.604 11.787 9567 Z= 0.300 Chirality : 0.040 0.203 1128 Planarity : 0.003 0.025 1143 Dihedral : 15.313 142.377 1176 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.08 % Allowed : 19.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.28), residues: 864 helix: 1.54 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -0.42 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 222 HIS 0.002 0.001 HIS B 197 PHE 0.015 0.002 PHE D 182 TYR 0.016 0.002 TYR D 213 ARG 0.001 0.000 ARG D 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5491.05 seconds wall clock time: 94 minutes 0.01 seconds (5640.01 seconds total)