Starting phenix.real_space_refine on Mon Apr 6 09:50:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qhk_53172/04_2026/9qhk_53172_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qhk_53172/04_2026/9qhk_53172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qhk_53172/04_2026/9qhk_53172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qhk_53172/04_2026/9qhk_53172.map" model { file = "/net/cci-nas-00/data/ceres_data/9qhk_53172/04_2026/9qhk_53172_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qhk_53172/04_2026/9qhk_53172_trim.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.038 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 2 5.49 5 S 32 5.16 5 C 5524 2.51 5 N 1448 2.21 5 O 1470 1.98 5 H 8566 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17042 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4441 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 252} Chain: "B" Number of atoms: 4441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4441 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 252} Chain: "C" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4030 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 255} Chain: "D" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4030 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 255} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.19, per 1000 atoms: 0.19 Number of scatterers: 17042 At special positions: 0 Unit cell: (102.24, 79.2, 108, 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 32 16.00 P 2 15.00 O 1470 8.00 N 1448 7.00 C 5524 6.00 H 8566 1.00 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: 1.27 Conformation dependent library (CDL) restraints added in 611.8 milliseconds 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 69.8% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 46 through 65 removed outlier: 3.519A pdb=" N ARG A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 87 removed outlier: 4.291A pdb=" N ILE A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 94 through 121 Proline residue: A 100 - end of helix removed outlier: 3.540A pdb=" N LEU A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.892A pdb=" N LYS A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 166 removed outlier: 3.646A pdb=" N VAL A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 144 " --> pdb=" O HIS A 140 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE A 158 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.601A pdb=" N LEU A 175 " --> pdb=" O PHE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 202 removed outlier: 3.547A pdb=" N TRP A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 218 removed outlier: 4.202A pdb=" N LEU A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.927A pdb=" N MET A 228 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.644A pdb=" N VAL A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 258 removed outlier: 4.130A pdb=" N HIS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 262 through 288 removed outlier: 3.841A pdb=" N TRP A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 46 through 65 removed outlier: 3.519A pdb=" N ARG B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 87 removed outlier: 4.291A pdb=" N ILE B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 94 through 121 Proline residue: B 100 - end of helix removed outlier: 3.539A pdb=" N LEU B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.892A pdb=" N LYS B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 166 removed outlier: 3.647A pdb=" N VAL B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 144 " --> pdb=" O HIS B 140 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE B 158 " --> pdb=" O HIS B 154 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.601A pdb=" N LEU B 175 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 202 removed outlier: 3.547A pdb=" N TRP B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 218 removed outlier: 4.201A pdb=" N LEU B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.927A pdb=" N MET B 228 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.645A pdb=" N VAL B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 258 removed outlier: 4.130A pdb=" N HIS B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 262 through 288 removed outlier: 3.842A pdb=" N TRP B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'C' and resid 22 through 31 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 70 through 80 Processing helix chain 'C' and resid 110 through 122 removed outlier: 3.802A pdb=" N ILE C 116 " --> pdb=" O TYR C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 137 removed outlier: 3.593A pdb=" N ALA C 131 " --> pdb=" O LYS C 127 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASP C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 145 through 148 removed outlier: 3.559A pdb=" N MET C 148 " --> pdb=" O TYR C 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 145 through 148' Processing helix chain 'C' and resid 156 through 167 removed outlier: 3.589A pdb=" N ARG C 160 " --> pdb=" O GLY C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 Processing helix chain 'C' and resid 184 through 191 Processing helix chain 'C' and resid 191 through 202 Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.674A pdb=" N ARG C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 244 removed outlier: 3.847A pdb=" N VAL C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 241 " --> pdb=" O GLU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 263 removed outlier: 3.832A pdb=" N ALA C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 31 Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 70 through 80 Processing helix chain 'D' and resid 110 through 122 removed outlier: 3.803A pdb=" N ILE D 116 " --> pdb=" O TYR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 137 removed outlier: 3.593A pdb=" N ALA D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASP D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 145 through 148 removed outlier: 3.558A pdb=" N MET D 148 " --> pdb=" O TYR D 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 145 through 148' Processing helix chain 'D' and resid 156 through 167 removed outlier: 3.589A pdb=" N ARG D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 183 Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 191 through 202 Processing helix chain 'D' and resid 211 through 219 removed outlier: 3.674A pdb=" N ARG D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 244 removed outlier: 3.847A pdb=" N VAL D 240 " --> pdb=" O ILE D 236 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG D 241 " --> pdb=" O GLU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 263 removed outlier: 3.832A pdb=" N ALA D 248 " --> pdb=" O GLU D 244 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 44 through 55 removed outlier: 6.404A pdb=" N VAL C 11 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG C 49 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA C 9 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE C 51 " --> pdb=" O HIS C 7 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N HIS C 7 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU C 53 " --> pdb=" O GLN C 5 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN C 5 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA C 9 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG C 86 " --> pdb=" O ALA C 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.672A pdb=" N LEU C 175 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU C 174 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ALA C 208 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU C 176 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG C 60 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N MET C 223 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY C 62 " --> pdb=" O MET C 223 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ILE C 225 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL C 64 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ALA C 222 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER C 233 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP C 224 " --> pdb=" O LYS C 231 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 44 through 55 removed outlier: 6.404A pdb=" N VAL D 11 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG D 49 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA D 9 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE D 51 " --> pdb=" O HIS D 7 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N HIS D 7 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU D 53 " --> pdb=" O GLN D 5 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN D 5 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA D 9 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG D 86 " --> pdb=" O ALA D 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 95 through 96 removed outlier: 3.672A pdb=" N LEU D 175 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU D 174 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ALA D 208 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU D 176 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG D 60 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N MET D 223 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY D 62 " --> pdb=" O MET D 223 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE D 225 " --> pdb=" O GLY D 62 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL D 64 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ALA D 222 " --> pdb=" O SER D 233 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER D 233 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP D 224 " --> pdb=" O LYS D 231 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8562 1.03 - 1.23: 15 1.23 - 1.42: 3585 1.42 - 1.62: 5008 1.62 - 1.82: 64 Bond restraints: 17234 Sorted by residual: bond pdb=" CB PHE C 187 " pdb=" CG PHE C 187 " ideal model delta sigma weight residual 1.502 1.534 -0.032 2.30e-02 1.89e+03 1.95e+00 bond pdb=" CB PHE D 187 " pdb=" CG PHE D 187 " ideal model delta sigma weight residual 1.502 1.534 -0.032 2.30e-02 1.89e+03 1.89e+00 bond pdb=" C THR A 167 " pdb=" N PRO A 168 " ideal model delta sigma weight residual 1.334 1.364 -0.031 2.34e-02 1.83e+03 1.70e+00 bond pdb=" C THR B 167 " pdb=" N PRO B 168 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.67e+00 bond pdb=" CB ASN C 114 " pdb=" CG ASN C 114 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.20e+00 ... (remaining 17229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.40: 31105 5.40 - 10.80: 29 10.80 - 16.20: 0 16.20 - 21.61: 0 21.61 - 27.01: 2 Bond angle restraints: 31136 Sorted by residual: angle pdb=" C40 PTY B2301 " pdb=" C41 PTY B2301 " pdb=" C42 PTY B2301 " ideal model delta sigma weight residual 113.20 140.21 -27.01 3.00e+00 1.11e-01 8.10e+01 angle pdb=" C40 PTY A2301 " pdb=" C41 PTY A2301 " pdb=" C42 PTY A2301 " ideal model delta sigma weight residual 113.20 140.18 -26.98 3.00e+00 1.11e-01 8.09e+01 angle pdb=" CB MET C 188 " pdb=" CG MET C 188 " pdb=" SD MET C 188 " ideal model delta sigma weight residual 112.70 123.03 -10.33 3.00e+00 1.11e-01 1.19e+01 angle pdb=" CB MET D 188 " pdb=" CG MET D 188 " pdb=" SD MET D 188 " ideal model delta sigma weight residual 112.70 122.98 -10.28 3.00e+00 1.11e-01 1.17e+01 angle pdb="HD21 LEU D 161 " pdb=" CD2 LEU D 161 " pdb="HD22 LEU D 161 " ideal model delta sigma weight residual 110.00 119.50 -9.50 3.00e+00 1.11e-01 1.00e+01 ... (remaining 31131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.91: 7211 19.91 - 39.82: 583 39.82 - 59.73: 200 59.73 - 79.64: 24 79.64 - 99.55: 12 Dihedral angle restraints: 8030 sinusoidal: 4400 harmonic: 3630 Sorted by residual: dihedral pdb=" CA PHE D 13 " pdb=" C PHE D 13 " pdb=" N PRO D 14 " pdb=" CA PRO D 14 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE C 13 " pdb=" C PHE C 13 " pdb=" N PRO C 14 " pdb=" CA PRO C 14 " ideal model delta harmonic sigma weight residual 180.00 161.40 18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" C3 PTY B2301 " pdb=" O11 PTY B2301 " pdb=" P1 PTY B2301 " pdb=" O12 PTY B2301 " ideal model delta sinusoidal sigma weight residual -59.77 39.78 -99.55 1 3.00e+01 1.11e-03 1.24e+01 ... (remaining 8027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 978 0.041 - 0.083: 284 0.083 - 0.124: 62 0.124 - 0.165: 12 0.165 - 0.206: 2 Chirality restraints: 1338 Sorted by residual: chirality pdb=" CG LEU C 215 " pdb=" CB LEU C 215 " pdb=" CD1 LEU C 215 " pdb=" CD2 LEU C 215 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CG LEU D 215 " pdb=" CB LEU D 215 " pdb=" CD1 LEU D 215 " pdb=" CD2 LEU D 215 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE D 45 " pdb=" N ILE D 45 " pdb=" C ILE D 45 " pdb=" CB ILE D 45 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 1335 not shown) Planarity restraints: 2476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 166 " 0.016 2.00e-02 2.50e+03 1.26e-02 4.74e+00 pdb=" CG TYR A 166 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 166 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 166 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 166 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 166 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 166 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 166 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR A 166 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR A 166 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR A 166 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR A 166 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 166 " -0.016 2.00e-02 2.50e+03 1.25e-02 4.66e+00 pdb=" CG TYR B 166 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR B 166 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 166 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 166 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 166 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 166 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 166 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR B 166 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR B 166 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR B 166 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR B 166 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 68 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 69 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 69 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 69 " 0.029 5.00e-02 4.00e+02 ... (remaining 2473 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 6157 2.37 - 2.93: 39142 2.93 - 3.49: 44770 3.49 - 4.04: 57692 4.04 - 4.60: 88025 Nonbonded interactions: 235786 Sorted by model distance: nonbonded pdb="HD11 ILE D 115 " pdb="HD21 LEU D 161 " model vdw 1.814 2.440 nonbonded pdb="HD11 ILE C 115 " pdb="HD21 LEU C 161 " model vdw 1.815 2.440 nonbonded pdb="HE22 GLN A 214 " pdb="HE22 GLN B 214 " model vdw 1.907 2.100 nonbonded pdb=" H SER C 154 " pdb=" HG SER C 154 " model vdw 1.917 2.100 nonbonded pdb=" H SER D 154 " pdb=" HG SER D 154 " model vdw 1.919 2.100 ... (remaining 235781 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 0.110 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.570 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 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 : 0.004 0.033 8668 Z= 0.190 Angle : 0.872 27.006 11750 Z= 0.426 Chirality : 0.041 0.206 1338 Planarity : 0.006 0.052 1462 Dihedral : 16.851 99.554 3170 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % 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 are not related in a simple way. whole: -2.06 (0.24), residues: 1046 helix: -1.25 (0.19), residues: 628 sheet: -1.43 (0.61), residues: 68 loop : -1.22 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 63 TYR 0.038 0.003 TYR A 166 PHE 0.018 0.002 PHE A 152 TRP 0.017 0.002 TRP A 50 HIS 0.002 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 8668) covalent geometry : angle 0.87225 (11750) hydrogen bonds : bond 0.17167 ( 464) hydrogen bonds : angle 7.66508 ( 1356) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6612 (tp40) cc_final: 0.6285 (tp40) REVERT: A 230 ASN cc_start: 0.7970 (t0) cc_final: 0.7634 (t0) REVERT: B 35 ARG cc_start: 0.7648 (mtt90) cc_final: 0.7327 (ttm110) REVERT: B 52 GLN cc_start: 0.6607 (tp40) cc_final: 0.6290 (tp40) REVERT: B 230 ASN cc_start: 0.7981 (t0) cc_final: 0.7644 (t0) REVERT: C 8 GLN cc_start: 0.6526 (tm-30) cc_final: 0.6291 (tm-30) REVERT: C 145 TYR cc_start: 0.7359 (m-10) cc_final: 0.6905 (m-10) REVERT: C 148 MET cc_start: 0.6527 (ptp) cc_final: 0.6210 (ptm) REVERT: C 194 ARG cc_start: 0.7361 (mtp180) cc_final: 0.7061 (ttm110) REVERT: D 8 GLN cc_start: 0.6627 (tm-30) cc_final: 0.6397 (tm-30) REVERT: D 145 TYR cc_start: 0.7342 (m-10) cc_final: 0.6890 (m-10) REVERT: D 148 MET cc_start: 0.6525 (ptp) cc_final: 0.6199 (ptm) REVERT: D 194 ARG cc_start: 0.7368 (mtp180) cc_final: 0.7051 (ttm110) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1952 time to fit residues: 44.5999 Evaluate side-chains 138 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 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 = 0.4507 r_free = 0.4507 target = 0.217869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.166640 restraints weight = 31240.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.173866 restraints weight = 14622.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.178411 restraints weight = 9593.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.181139 restraints weight = 7541.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.182235 restraints weight = 6569.634| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8668 Z= 0.133 Angle : 0.566 6.780 11750 Z= 0.301 Chirality : 0.037 0.140 1338 Planarity : 0.004 0.033 1462 Dihedral : 10.421 95.007 1232 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.90 % Allowed : 15.13 % Favored : 83.97 % 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 are not related in a simple way. whole: -0.84 (0.25), residues: 1046 helix: -0.07 (0.21), residues: 618 sheet: -1.28 (0.57), residues: 68 loop : -1.07 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 160 TYR 0.023 0.001 TYR D 153 PHE 0.015 0.001 PHE D 27 TRP 0.018 0.001 TRP A 50 HIS 0.003 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8668) covalent geometry : angle 0.56644 (11750) hydrogen bonds : bond 0.04722 ( 464) hydrogen bonds : angle 5.29763 ( 1356) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6855 (tp40) cc_final: 0.6447 (tp40) REVERT: A 81 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8005 (tt) REVERT: A 99 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7778 (tp) REVERT: A 112 PHE cc_start: 0.8106 (m-80) cc_final: 0.7889 (m-10) REVERT: A 230 ASN cc_start: 0.7946 (t0) cc_final: 0.7682 (t0) REVERT: B 52 GLN cc_start: 0.6854 (tp40) cc_final: 0.6450 (tp40) REVERT: B 81 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.7987 (tt) REVERT: B 230 ASN cc_start: 0.7952 (t0) cc_final: 0.7684 (t0) REVERT: C 8 GLN cc_start: 0.6436 (tm-30) cc_final: 0.6194 (tm-30) REVERT: C 194 ARG cc_start: 0.7403 (mtp180) cc_final: 0.7169 (ttm110) REVERT: D 8 GLN cc_start: 0.6377 (tm-30) cc_final: 0.6109 (tm-30) REVERT: D 194 ARG cc_start: 0.7377 (mtp180) cc_final: 0.7096 (ttm110) outliers start: 8 outliers final: 5 residues processed: 155 average time/residue: 0.2003 time to fit residues: 43.1671 Evaluate side-chains 146 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain D residue 202 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 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 = 0.4449 r_free = 0.4449 target = 0.207542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.158168 restraints weight = 31183.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.165441 restraints weight = 14772.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.169863 restraints weight = 9676.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.172488 restraints weight = 7616.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.173602 restraints weight = 6636.050| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8668 Z= 0.133 Angle : 0.533 6.096 11750 Z= 0.278 Chirality : 0.036 0.136 1338 Planarity : 0.003 0.029 1462 Dihedral : 9.731 86.447 1232 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.68 % Allowed : 14.80 % Favored : 83.52 % 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 are not related in a simple way. whole: -0.47 (0.26), residues: 1046 helix: 0.24 (0.21), residues: 624 sheet: -1.02 (0.56), residues: 68 loop : -0.96 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 194 TYR 0.019 0.001 TYR D 153 PHE 0.008 0.001 PHE A 159 TRP 0.018 0.001 TRP B 50 HIS 0.009 0.001 HIS C 210 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8668) covalent geometry : angle 0.53334 (11750) hydrogen bonds : bond 0.03883 ( 464) hydrogen bonds : angle 4.84845 ( 1356) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7008 (tp40) cc_final: 0.6533 (tp40) REVERT: A 81 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8247 (tt) REVERT: A 230 ASN cc_start: 0.7903 (t0) cc_final: 0.7662 (t0) REVERT: B 52 GLN cc_start: 0.7005 (tp40) cc_final: 0.6536 (tp40) REVERT: B 81 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8238 (tt) REVERT: B 230 ASN cc_start: 0.7911 (t0) cc_final: 0.7662 (t0) REVERT: C 8 GLN cc_start: 0.6507 (tm-30) cc_final: 0.6185 (tm-30) REVERT: C 194 ARG cc_start: 0.7310 (mtp180) cc_final: 0.6996 (ttm110) REVERT: D 8 GLN cc_start: 0.6432 (tm-30) cc_final: 0.6184 (tm-30) REVERT: D 194 ARG cc_start: 0.7247 (mtp180) cc_final: 0.6996 (ttm110) outliers start: 15 outliers final: 11 residues processed: 153 average time/residue: 0.1885 time to fit residues: 40.4645 Evaluate side-chains 150 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 202 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 95 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN C 128 GLN D 124 GLN D 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.212370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.159616 restraints weight = 31611.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.166628 restraints weight = 15139.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.170991 restraints weight = 10044.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.173519 restraints weight = 7970.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.174789 restraints weight = 6987.693| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8668 Z= 0.154 Angle : 0.528 6.099 11750 Z= 0.279 Chirality : 0.036 0.140 1338 Planarity : 0.004 0.028 1462 Dihedral : 9.589 85.732 1232 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.35 % Allowed : 15.92 % Favored : 82.74 % 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 are not related in a simple way. whole: -0.17 (0.26), residues: 1046 helix: 0.64 (0.21), residues: 592 sheet: -1.00 (0.53), residues: 70 loop : -1.03 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 160 TYR 0.016 0.001 TYR C 153 PHE 0.010 0.001 PHE B 159 TRP 0.019 0.001 TRP A 50 HIS 0.004 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8668) covalent geometry : angle 0.52822 (11750) hydrogen bonds : bond 0.03721 ( 464) hydrogen bonds : angle 4.71429 ( 1356) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ASN cc_start: 0.7914 (t0) cc_final: 0.7668 (t0) REVERT: B 230 ASN cc_start: 0.7939 (t0) cc_final: 0.7686 (t0) REVERT: C 8 GLN cc_start: 0.6592 (tm-30) cc_final: 0.6165 (tm-30) REVERT: D 8 GLN cc_start: 0.6553 (tm-30) cc_final: 0.6196 (tm-30) outliers start: 12 outliers final: 9 residues processed: 145 average time/residue: 0.1968 time to fit residues: 39.9930 Evaluate side-chains 144 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 202 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 GLN D 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.210881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.158830 restraints weight = 31454.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.165724 restraints weight = 15330.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.169974 restraints weight = 10244.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.172353 restraints weight = 8144.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.173950 restraints weight = 7167.270| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8668 Z= 0.123 Angle : 0.500 6.125 11750 Z= 0.263 Chirality : 0.036 0.132 1338 Planarity : 0.003 0.028 1462 Dihedral : 9.284 86.154 1232 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.23 % Allowed : 16.14 % Favored : 82.62 % 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 are not related in a simple way. whole: -0.04 (0.26), residues: 1046 helix: 0.73 (0.21), residues: 606 sheet: -0.92 (0.53), residues: 70 loop : -0.99 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 63 TYR 0.016 0.001 TYR C 153 PHE 0.009 0.001 PHE A 159 TRP 0.018 0.001 TRP A 50 HIS 0.003 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8668) covalent geometry : angle 0.49963 (11750) hydrogen bonds : bond 0.03453 ( 464) hydrogen bonds : angle 4.48597 ( 1356) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8504 (tt) REVERT: A 230 ASN cc_start: 0.7881 (t0) cc_final: 0.7653 (t0) REVERT: B 214 GLN cc_start: 0.7661 (tp40) cc_final: 0.7427 (tp40) REVERT: B 230 ASN cc_start: 0.7890 (t0) cc_final: 0.7655 (t0) REVERT: C 8 GLN cc_start: 0.6578 (tm-30) cc_final: 0.6141 (tm-30) REVERT: C 202 SER cc_start: 0.8262 (OUTLIER) cc_final: 0.7771 (p) REVERT: D 8 GLN cc_start: 0.6542 (tm-30) cc_final: 0.6111 (tm-30) outliers start: 11 outliers final: 8 residues processed: 152 average time/residue: 0.1965 time to fit residues: 41.9785 Evaluate side-chains 149 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 202 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 GLN D 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.210189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.157093 restraints weight = 31508.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.163969 restraints weight = 15410.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.168205 restraints weight = 10350.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.170777 restraints weight = 8257.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.172097 restraints weight = 7227.744| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8668 Z= 0.176 Angle : 0.539 6.139 11750 Z= 0.286 Chirality : 0.037 0.145 1338 Planarity : 0.004 0.028 1462 Dihedral : 9.350 85.229 1232 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.02 % Allowed : 15.92 % Favored : 82.06 % 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 are not related in a simple way. whole: 0.01 (0.26), residues: 1046 helix: 0.77 (0.21), residues: 586 sheet: -0.97 (0.52), residues: 70 loop : -0.87 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 201 TYR 0.014 0.001 TYR D 153 PHE 0.012 0.001 PHE A 159 TRP 0.019 0.002 TRP B 50 HIS 0.004 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 8668) covalent geometry : angle 0.53911 (11750) hydrogen bonds : bond 0.03624 ( 464) hydrogen bonds : angle 4.60454 ( 1356) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8558 (tt) REVERT: A 132 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7866 (mp10) REVERT: A 230 ASN cc_start: 0.7937 (t0) cc_final: 0.7714 (t0) REVERT: B 81 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8562 (tt) REVERT: B 132 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7960 (mp10) REVERT: B 230 ASN cc_start: 0.7946 (t0) cc_final: 0.7719 (t0) REVERT: C 202 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.7817 (p) outliers start: 18 outliers final: 11 residues processed: 147 average time/residue: 0.2291 time to fit residues: 45.1915 Evaluate side-chains 145 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 202 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 99 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.4461 r_free = 0.4461 target = 0.212046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.159015 restraints weight = 31539.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.165850 restraints weight = 15306.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.170268 restraints weight = 10240.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.172837 restraints weight = 8137.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.174137 restraints weight = 7131.433| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8668 Z= 0.128 Angle : 0.503 6.172 11750 Z= 0.265 Chirality : 0.036 0.134 1338 Planarity : 0.003 0.028 1462 Dihedral : 9.195 86.306 1232 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.47 % Allowed : 15.92 % Favored : 81.61 % 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 are not related in a simple way. whole: 0.10 (0.26), residues: 1046 helix: 0.86 (0.21), residues: 586 sheet: -0.94 (0.53), residues: 70 loop : -0.87 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 63 TYR 0.014 0.001 TYR D 153 PHE 0.008 0.001 PHE B 159 TRP 0.018 0.001 TRP A 50 HIS 0.002 0.000 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8668) covalent geometry : angle 0.50256 (11750) hydrogen bonds : bond 0.03426 ( 464) hydrogen bonds : angle 4.45519 ( 1356) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8601 (tt) REVERT: A 132 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7779 (mp10) REVERT: A 230 ASN cc_start: 0.7975 (t0) cc_final: 0.7751 (t0) REVERT: B 81 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8605 (tt) REVERT: B 132 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: B 230 ASN cc_start: 0.7979 (t0) cc_final: 0.7748 (t0) REVERT: C 175 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7175 (mp) REVERT: C 202 SER cc_start: 0.8155 (OUTLIER) cc_final: 0.7686 (p) outliers start: 22 outliers final: 12 residues processed: 157 average time/residue: 0.1855 time to fit residues: 41.3008 Evaluate side-chains 156 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain C residue 16 PHE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 202 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN D 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.213488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.160374 restraints weight = 31463.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.167365 restraints weight = 15290.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.171775 restraints weight = 10190.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.174441 restraints weight = 8074.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.175805 restraints weight = 7048.431| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8668 Z= 0.107 Angle : 0.489 6.262 11750 Z= 0.255 Chirality : 0.036 0.130 1338 Planarity : 0.003 0.025 1462 Dihedral : 9.068 89.170 1232 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.79 % Allowed : 16.48 % Favored : 81.73 % 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 are not related in a simple way. whole: 0.25 (0.26), residues: 1046 helix: 1.00 (0.21), residues: 586 sheet: -0.82 (0.54), residues: 70 loop : -0.85 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 63 TYR 0.014 0.001 TYR D 153 PHE 0.007 0.001 PHE C 187 TRP 0.017 0.001 TRP B 50 HIS 0.003 0.000 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8668) covalent geometry : angle 0.48887 (11750) hydrogen bonds : bond 0.03289 ( 464) hydrogen bonds : angle 4.33155 ( 1356) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: A 187 ASN cc_start: 0.7924 (m-40) cc_final: 0.7658 (m-40) REVERT: B 81 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8667 (tt) REVERT: B 132 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7890 (mp10) REVERT: B 187 ASN cc_start: 0.7920 (m-40) cc_final: 0.7646 (m-40) REVERT: B 230 ASN cc_start: 0.7977 (t0) cc_final: 0.7753 (t0) REVERT: C 175 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7155 (mp) REVERT: C 202 SER cc_start: 0.8150 (OUTLIER) cc_final: 0.7686 (p) REVERT: D 175 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7194 (mp) outliers start: 16 outliers final: 8 residues processed: 154 average time/residue: 0.1891 time to fit residues: 41.3135 Evaluate side-chains 160 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain C residue 16 PHE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 175 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 102 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 14 optimal weight: 0.0270 chunk 26 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.213405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.160518 restraints weight = 31486.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.167375 restraints weight = 15268.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.171755 restraints weight = 10209.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.174399 restraints weight = 8100.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.175721 restraints weight = 7080.518| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8668 Z= 0.109 Angle : 0.492 6.277 11750 Z= 0.258 Chirality : 0.036 0.132 1338 Planarity : 0.003 0.027 1462 Dihedral : 9.022 88.414 1232 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.02 % Allowed : 16.37 % Favored : 81.61 % 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 are not related in a simple way. whole: 0.34 (0.26), residues: 1046 helix: 1.08 (0.21), residues: 586 sheet: -0.74 (0.55), residues: 70 loop : -0.84 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 63 TYR 0.014 0.001 TYR D 153 PHE 0.007 0.001 PHE C 187 TRP 0.024 0.001 TRP B 294 HIS 0.003 0.000 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8668) covalent geometry : angle 0.49175 (11750) hydrogen bonds : bond 0.03265 ( 464) hydrogen bonds : angle 4.28664 ( 1356) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8143 (tm-30) REVERT: A 132 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7748 (mp10) REVERT: A 187 ASN cc_start: 0.7920 (m-40) cc_final: 0.7654 (m-40) REVERT: B 81 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8686 (tt) REVERT: B 132 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7945 (mp10) REVERT: B 187 ASN cc_start: 0.7925 (m-40) cc_final: 0.7651 (m-40) REVERT: B 230 ASN cc_start: 0.7977 (t0) cc_final: 0.7750 (t0) REVERT: C 175 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7145 (mp) REVERT: C 202 SER cc_start: 0.8137 (OUTLIER) cc_final: 0.7675 (p) REVERT: D 175 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7190 (mp) outliers start: 18 outliers final: 11 residues processed: 157 average time/residue: 0.1918 time to fit residues: 42.8411 Evaluate side-chains 162 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain C residue 16 PHE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.211202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.158282 restraints weight = 31437.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.164949 restraints weight = 15399.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.169146 restraints weight = 10395.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.171815 restraints weight = 8303.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.173036 restraints weight = 7262.191| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8668 Z= 0.155 Angle : 0.522 6.076 11750 Z= 0.276 Chirality : 0.037 0.176 1338 Planarity : 0.004 0.027 1462 Dihedral : 9.080 89.511 1232 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.24 % Allowed : 16.70 % Favored : 81.05 % 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 are not related in a simple way. whole: 0.32 (0.26), residues: 1046 helix: 1.04 (0.21), residues: 586 sheet: -0.70 (0.56), residues: 70 loop : -0.80 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 63 TYR 0.013 0.001 TYR D 153 PHE 0.008 0.001 PHE D 13 TRP 0.021 0.002 TRP B 294 HIS 0.003 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8668) covalent geometry : angle 0.52245 (11750) hydrogen bonds : bond 0.03405 ( 464) hydrogen bonds : angle 4.43186 ( 1356) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8151 (tm-30) REVERT: A 132 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7881 (mp10) REVERT: B 132 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8029 (mp10) REVERT: B 230 ASN cc_start: 0.8067 (t0) cc_final: 0.7858 (t0) REVERT: C 129 MET cc_start: 0.8287 (tpp) cc_final: 0.7849 (tpp) REVERT: C 175 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7151 (mp) REVERT: C 202 SER cc_start: 0.8163 (OUTLIER) cc_final: 0.7804 (p) REVERT: D 175 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7176 (mp) outliers start: 20 outliers final: 13 residues processed: 156 average time/residue: 0.1948 time to fit residues: 42.9283 Evaluate side-chains 158 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain C residue 16 PHE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 202 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 62 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.212690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.159775 restraints weight = 31694.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.166666 restraints weight = 15427.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.171002 restraints weight = 10337.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.173537 restraints weight = 8204.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.175118 restraints weight = 7167.258| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8668 Z= 0.119 Angle : 0.508 6.113 11750 Z= 0.268 Chirality : 0.036 0.139 1338 Planarity : 0.003 0.027 1462 Dihedral : 8.895 87.416 1232 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.91 % Allowed : 17.49 % Favored : 80.61 % 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 are not related in a simple way. whole: 0.35 (0.26), residues: 1046 helix: 1.07 (0.21), residues: 594 sheet: -0.61 (0.57), residues: 70 loop : -0.87 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 63 TYR 0.014 0.001 TYR A 166 PHE 0.007 0.001 PHE B 195 TRP 0.018 0.001 TRP A 50 HIS 0.002 0.000 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8668) covalent geometry : angle 0.50754 (11750) hydrogen bonds : bond 0.03304 ( 464) hydrogen bonds : angle 4.36099 ( 1356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2903.95 seconds wall clock time: 49 minutes 54.59 seconds (2994.59 seconds total)