Starting phenix.real_space_refine on Fri Aug 7 23:23:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q23_72148/08_2026/9q23_72148_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q23_72148/08_2026/9q23_72148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q23_72148/08_2026/9q23_72148_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q23_72148/08_2026/9q23_72148_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q23_72148/08_2026/9q23_72148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q23_72148/08_2026/9q23_72148.map" } resolution = 2.84 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= -0.000 sd= 0.016 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: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 4 5.21 5 S 79 5.16 5 C 8854 2.51 5 N 2476 2.21 5 O 2683 1.98 5 H 9499 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23611 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 5164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 5164 Classifications: {'peptide': 325} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 312} Chain breaks: 1 Chain: "D" Number of atoms: 4685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 4685 Classifications: {'peptide': 305} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 296} Chain breaks: 1 Chain: "G" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2431 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 307} Chain: "H" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "I" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2153 Classifications: {'peptide': 279} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 272} Chain breaks: 3 Chain: "R" Number of atoms: 5044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 5044 Classifications: {'peptide': 321} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 300} Chain breaks: 2 Chain: "X" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3894 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 235} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.07, per 1000 atoms: 0.17 Number of scatterers: 23611 At special positions: 0 Unit cell: (137.344, 134.56, 121.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 79 16.00 P 16 15.00 Mg 4 11.99 O 2683 8.00 N 2476 7.00 C 8854 6.00 H 9499 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: 2.36 Conformation dependent library (CDL) restraints added in 759.9 milliseconds 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3330 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 13 sheets defined 53.2% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'C' and resid 13 through 17 Processing helix chain 'C' and resid 20 through 31 Processing helix chain 'C' and resid 35 through 40 removed outlier: 4.668A pdb=" N GLU C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 143 through 144 No H-bonds generated for 'chain 'C' and resid 143 through 144' Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 165 through 188 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 215 through 233 Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 245 through 249 Processing helix chain 'C' and resid 254 through 277 Processing helix chain 'C' and resid 303 through 308 Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 46 through 62 Processing helix chain 'D' and resid 68 through 79 Processing helix chain 'D' and resid 86 through 93 Processing helix chain 'D' and resid 112 through 128 Processing helix chain 'D' and resid 142 through 152 Processing helix chain 'D' and resid 156 through 166 Processing helix chain 'D' and resid 174 through 193 Processing helix chain 'D' and resid 207 through 213 removed outlier: 3.878A pdb=" N VAL D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 216 No H-bonds generated for 'chain 'D' and resid 214 through 216' Processing helix chain 'D' and resid 220 through 240 removed outlier: 4.225A pdb=" N LEU D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 270 removed outlier: 4.241A pdb=" N TRP D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 32 Processing helix chain 'G' and resid 34 through 44 Processing helix chain 'G' and resid 48 through 54 Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'G' and resid 67 through 82 Processing helix chain 'G' and resid 89 through 96 Processing helix chain 'G' and resid 106 through 113 Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 145 through 146 No H-bonds generated for 'chain 'G' and resid 145 through 146' Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 167 through 178 removed outlier: 3.641A pdb=" N LEU G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 188 Processing helix chain 'G' and resid 196 through 214 Processing helix chain 'G' and resid 227 through 232 Processing helix chain 'G' and resid 237 through 260 Processing helix chain 'G' and resid 275 through 280 Processing helix chain 'G' and resid 288 through 296 removed outlier: 3.801A pdb=" N ILE G 292 " --> pdb=" O GLY G 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 31 Processing helix chain 'I' and resid 34 through 44 Processing helix chain 'I' and resid 48 through 54 Processing helix chain 'I' and resid 56 through 63 removed outlier: 3.649A pdb=" N ILE I 63 " --> pdb=" O GLU I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.585A pdb=" N LEU I 81 " --> pdb=" O GLU I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 95 removed outlier: 3.731A pdb=" N ARG I 95 " --> pdb=" O GLU I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 113 Processing helix chain 'I' and resid 132 through 144 removed outlier: 3.665A pdb=" N VAL I 142 " --> pdb=" O HIS I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.915A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 187 Processing helix chain 'I' and resid 196 through 214 Processing helix chain 'I' and resid 239 through 260 Processing helix chain 'I' and resid 292 through 296 Processing helix chain 'R' and resid 1 through 6 removed outlier: 3.505A pdb=" N LEU R 6 " --> pdb=" O LEU R 3 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 20 Processing helix chain 'R' and resid 23 through 30 removed outlier: 3.749A pdb=" N PHE R 30 " --> pdb=" O GLU R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 40 Processing helix chain 'R' and resid 42 through 59 Processing helix chain 'R' and resid 64 through 71 Processing helix chain 'R' and resid 75 through 80 removed outlier: 3.782A pdb=" N HIS R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 93 Processing helix chain 'R' and resid 112 through 124 Processing helix chain 'R' and resid 125 through 126 No H-bonds generated for 'chain 'R' and resid 125 through 126' Processing helix chain 'R' and resid 127 through 131 Processing helix chain 'R' and resid 147 through 162 Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 166 through 173 Processing helix chain 'R' and resid 174 through 178 removed outlier: 3.576A pdb=" N GLN R 178 " --> pdb=" O ARG R 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 174 through 178' Processing helix chain 'R' and resid 186 through 204 removed outlier: 4.570A pdb=" N VAL R 198 " --> pdb=" O VAL R 194 " (cutoff:3.500A) Proline residue: R 199 - end of helix Processing helix chain 'R' and resid 215 through 223 removed outlier: 4.051A pdb=" N PHE R 219 " --> pdb=" O VAL R 215 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU R 222 " --> pdb=" O PRO R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 250 Processing helix chain 'R' and resid 284 through 290 removed outlier: 3.705A pdb=" N TRP R 288 " --> pdb=" O LEU R 284 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 67 Processing helix chain 'X' and resid 68 through 72 Processing helix chain 'X' and resid 88 through 99 Processing helix chain 'X' and resid 104 through 113 Processing helix chain 'X' and resid 122 through 140 removed outlier: 4.017A pdb=" N GLU X 134 " --> pdb=" O LEU X 130 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N SER X 135 " --> pdb=" O TYR X 131 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N MET X 136 " --> pdb=" O SER X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 153 Processing helix chain 'X' and resid 154 through 162 Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 170 through 188 Processing helix chain 'X' and resid 228 through 233 Processing sheet with id=AA1, first strand: chain 'C' and resid 85 through 86 removed outlier: 6.364A pdb=" N VAL D 132 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL D 170 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR D 134 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN D 131 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL D 202 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LYS D 201 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL D 246 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL D 203 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N THR D 248 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL D 205 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR D 103 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ASN D 249 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ILE D 105 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ARG D 275 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AA3, first strand: chain 'C' and resid 208 through 212 removed outlier: 5.698A pdb=" N GLU C 154 " --> pdb=" O VAL C 236 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 208 through 212 removed outlier: 5.698A pdb=" N GLU C 154 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR C 121 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ASN C 284 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE C 123 " --> pdb=" O ASN C 284 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N MET C 286 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLY C 125 " --> pdb=" O MET C 286 " (cutoff:3.500A) removed outlier: 9.770A pdb=" N THR C 288 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR C 120 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LEU C 313 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU C 122 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE C 315 " --> pdb=" O GLU C 122 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N CYS C 124 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N TRP C 317 " --> pdb=" O CYS C 124 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG C 312 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG C 322 " --> pdb=" O PHE C 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 66 through 67 removed outlier: 6.410A pdb=" N GLU X 77 " --> pdb=" O LEU X 143 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU X 145 " --> pdb=" O GLU X 77 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU X 44 " --> pdb=" O ALA X 193 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N THR X 195 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE X 46 " --> pdb=" O THR X 195 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE X 43 " --> pdb=" O HIS X 237 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N MET X 239 " --> pdb=" O ILE X 43 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU X 45 " --> pdb=" O MET X 239 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE X 241 " --> pdb=" O GLU X 45 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N HIS X 47 " --> pdb=" O PHE X 241 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N LYS X 243 " --> pdb=" O HIS X 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 81 through 82 Processing sheet with id=AA7, first strand: chain 'D' and resid 251 through 253 Processing sheet with id=AA8, first strand: chain 'G' and resid 87 through 88 removed outlier: 4.504A pdb=" N THR G 87 " --> pdb=" O ILE R 181 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLY R 136 " --> pdb=" O ALA R 207 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY R 107 " --> pdb=" O ASN R 257 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE R 102 " --> pdb=" O VAL R 294 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LEU R 296 " --> pdb=" O ILE R 102 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU R 104 " --> pdb=" O LEU R 296 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ALA R 298 " --> pdb=" O GLU R 104 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA R 106 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG R 295 " --> pdb=" O LEU R 318 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG R 313 " --> pdb=" O TYR R 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 284 through 286 removed outlier: 6.456A pdb=" N ILE G 122 " --> pdb=" O THR G 298 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU G 300 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLU G 124 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU G 302 " --> pdb=" O GLU G 124 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE G 126 " --> pdb=" O LEU G 302 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N LYS G 304 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG G 299 " --> pdb=" O TYR G 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 284 through 286 removed outlier: 6.864A pdb=" N ALA G 217 " --> pdb=" O ALA G 262 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL G 264 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU G 219 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N THR G 266 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL G 221 " --> pdb=" O THR G 266 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N GLN G 268 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LYS G 156 " --> pdb=" O TYR G 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 190 through 193 removed outlier: 3.922A pdb=" N ALA I 190 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS I 156 " --> pdb=" O ALA I 217 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU I 219 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N MET I 158 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL I 221 " --> pdb=" O MET I 158 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE I 160 " --> pdb=" O VAL I 221 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 81 through 82 Processing sheet with id=AB4, first strand: chain 'R' and resid 259 through 261 removed outlier: 3.614A pdb=" N SER R 281 " --> pdb=" O THR R 260 " (cutoff:3.500A) 776 hydrogen bonds defined for protein. 2184 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: 5.44 Time building geometry restraints manager: 3.15 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: 9468 1.03 - 1.23: 40 1.23 - 1.42: 5754 1.42 - 1.61: 8458 1.61 - 1.81: 118 Bond restraints: 23838 Sorted by residual: bond pdb=" C3' DT H 12 " pdb=" C2' DT H 12 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.46e+00 bond pdb=" N LYS I 313 " pdb=" CA LYS I 313 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.21e-02 6.83e+03 5.39e+00 bond pdb=" C1' DT H 8 " pdb=" N1 DT H 8 " ideal model delta sigma weight residual 1.468 1.499 -0.031 1.40e-02 5.10e+03 4.94e+00 bond pdb=" N ASP R 2 " pdb=" H ASP R 2 " ideal model delta sigma weight residual 0.860 0.902 -0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" N LEU R 3 " pdb=" H LEU R 3 " ideal model delta sigma weight residual 0.860 0.902 -0.042 2.00e-02 2.50e+03 4.36e+00 ... (remaining 23833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 40837 2.73 - 5.45: 113 5.45 - 8.18: 15 8.18 - 10.90: 2 10.90 - 13.63: 2 Bond angle restraints: 40969 Sorted by residual: angle pdb=" CA ASP R 2 " pdb=" CB ASP R 2 " pdb=" CG ASP R 2 " ideal model delta sigma weight residual 112.60 118.12 -5.52 1.00e+00 1.00e+00 3.05e+01 angle pdb=" N ASP R 2 " pdb=" CA ASP R 2 " pdb=" C ASP R 2 " ideal model delta sigma weight residual 113.01 107.05 5.96 1.20e+00 6.94e-01 2.47e+01 angle pdb=" C ASP X 149 " pdb=" N SER X 150 " pdb=" CA SER X 150 " ideal model delta sigma weight residual 121.70 130.16 -8.46 1.80e+00 3.09e-01 2.21e+01 angle pdb=" C2' ADP R 402 " pdb=" C1' ADP R 402 " pdb=" N9 ADP R 402 " ideal model delta sigma weight residual 109.47 123.10 -13.63 3.00e+00 1.11e-01 2.06e+01 angle pdb=" N3 DT H 10 " pdb=" C4 DT H 10 " pdb=" O4 DT H 10 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 40964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.40: 11430 25.40 - 50.80: 257 50.80 - 76.21: 93 76.21 - 101.61: 9 101.61 - 127.01: 1 Dihedral angle restraints: 11790 sinusoidal: 6190 harmonic: 5600 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -142.78 82.79 1 2.00e+01 2.50e-03 2.10e+01 dihedral pdb=" C4' DT H 8 " pdb=" C3' DT H 8 " pdb=" O3' DT H 8 " pdb=" P DT H 9 " ideal model delta sinusoidal sigma weight residual 220.00 92.99 127.01 1 3.50e+01 8.16e-04 1.26e+01 dihedral pdb=" CA LEU D 277 " pdb=" CB LEU D 277 " pdb=" CG LEU D 277 " pdb=" CD1 LEU D 277 " ideal model delta sinusoidal sigma weight residual 60.00 119.09 -59.09 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 11787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.341: 2266 0.341 - 0.681: 0 0.681 - 1.022: 0 1.022 - 1.363: 0 1.363 - 1.703: 1 Chirality restraints: 2267 Sorted by residual: chirality pdb=" C1' ADP R 402 " pdb=" C2' ADP R 402 " pdb=" N9 ADP R 402 " pdb=" O4' ADP R 402 " both_signs ideal model delta sigma weight residual False 2.48 0.78 1.70 2.00e-01 2.50e+01 7.25e+01 chirality pdb=" C2' ATP X 301 " pdb=" C1' ATP X 301 " pdb=" C3' ATP X 301 " pdb=" O2' ATP X 301 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C2' ATP D 402 " pdb=" C1' ATP D 402 " pdb=" C3' ATP D 402 " pdb=" O2' ATP D 402 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 2264 not shown) Planarity restraints: 3594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER X 37 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO X 38 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO X 38 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO X 38 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 3 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" N ASP R 4 " -0.028 2.00e-02 2.50e+03 pdb=" CA ASP R 4 " 0.007 2.00e-02 2.50e+03 pdb=" H ASP R 4 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 32 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO R 33 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 33 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 33 " -0.017 5.00e-02 4.00e+02 ... (remaining 3591 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1049 2.20 - 2.80: 42084 2.80 - 3.40: 57811 3.40 - 4.00: 79559 4.00 - 4.60: 124821 Nonbonded interactions: 305324 Sorted by model distance: nonbonded pdb=" HG SER C 47 " pdb=" O ILE C 52 " model vdw 1.604 2.450 nonbonded pdb=" OD1 ASP R 224 " pdb=" H ASP R 224 " model vdw 1.607 2.450 nonbonded pdb=" HG1 THR D 84 " pdb=" OD1 ASP D 90 " model vdw 1.620 2.450 nonbonded pdb="HH11 ARG R 11 " pdb=" OE2 GLU R 45 " model vdw 1.627 2.450 nonbonded pdb=" OE1 GLU D 104 " pdb=" HE ARG D 275 " model vdw 1.629 2.450 ... (remaining 305319 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 22 through 229 or resid 238 through 269 or resid 291 throu \ gh 315 or resid 325 through 338)) selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.430 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: 0.160 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.720 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 0.002 0.031 14339 Z= 0.127 Angle : 0.503 13.625 19414 Z= 0.275 Chirality : 0.054 1.703 2267 Planarity : 0.002 0.041 2452 Dihedral : 10.062 127.010 5404 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.38 % Favored : 97.45 % Rotamer: Outliers : 0.86 % Allowed : 2.06 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.22), residues: 1763 helix: 2.50 (0.19), residues: 806 sheet: 0.31 (0.31), residues: 311 loop : 0.25 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 24 TYR 0.007 0.001 TYR C 216 PHE 0.006 0.001 PHE G 195 TRP 0.004 0.001 TRP X 231 HIS 0.002 0.000 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (14339) covalent geometry : angle 0.50288 / 0.28 (19414) hydrogen bonds : bond 0.17423 / 11.56 ( 760) hydrogen bonds : angle 6.65339 / 4.72 ( 2184) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 384 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 ARG cc_start: 0.8178 (mtt180) cc_final: 0.7966 (mtm110) REVERT: C 84 LYS cc_start: 0.7543 (mtpt) cc_final: 0.6577 (ptmm) REVERT: C 101 ILE cc_start: 0.8088 (mt) cc_final: 0.7866 (pt) REVERT: C 198 ASP cc_start: 0.8798 (m-30) cc_final: 0.8567 (p0) REVERT: C 235 LYS cc_start: 0.8483 (mttt) cc_final: 0.8226 (mtpt) REVERT: C 277 ARG cc_start: 0.8407 (mtt180) cc_final: 0.7821 (mtm110) REVERT: C 342 LYS cc_start: 0.8764 (mttt) cc_final: 0.8524 (mtmt) REVERT: D 71 LEU cc_start: 0.9012 (tp) cc_final: 0.8812 (tp) REVERT: D 201 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8376 (mptt) REVERT: D 301 GLN cc_start: 0.8928 (mt0) cc_final: 0.8646 (mt0) REVERT: G 42 GLU cc_start: 0.8457 (tt0) cc_final: 0.7812 (mm-30) REVERT: G 81 LEU cc_start: 0.9101 (mt) cc_final: 0.8817 (mp) REVERT: I 58 LYS cc_start: 0.9263 (ttpt) cc_final: 0.8715 (ttpp) REVERT: I 72 ASP cc_start: 0.8722 (t70) cc_final: 0.8512 (t70) REVERT: I 137 CYS cc_start: 0.9017 (m) cc_final: 0.8694 (m) REVERT: I 159 TYR cc_start: 0.7706 (t80) cc_final: 0.6981 (t80) REVERT: I 203 LEU cc_start: 0.9056 (mt) cc_final: 0.8710 (mp) REVERT: I 243 MET cc_start: 0.8728 (mtt) cc_final: 0.8469 (mmp) REVERT: R 172 LYS cc_start: 0.8984 (mttt) cc_final: 0.8688 (mtpp) REVERT: R 192 GLU cc_start: 0.8508 (tt0) cc_final: 0.8215 (tt0) REVERT: X 90 LEU cc_start: 0.8456 (mt) cc_final: 0.8189 (tt) REVERT: X 111 CYS cc_start: 0.8973 (m) cc_final: 0.8729 (m) REVERT: X 165 SER cc_start: 0.8221 (t) cc_final: 0.7967 (p) REVERT: X 236 LYS cc_start: 0.8456 (mttt) cc_final: 0.8140 (mmtm) REVERT: X 258 ARG cc_start: 0.7791 (ttt180) cc_final: 0.7348 (ttt90) REVERT: X 261 LYS cc_start: 0.8909 (mttt) cc_final: 0.8362 (ttpp) REVERT: X 278 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7821 (mm-30) outliers start: 13 outliers final: 4 residues processed: 394 average time/residue: 1.3785 time to fit residues: 586.6994 Evaluate side-chains 201 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 197 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain R residue 2 ASP Chi-restraints excluded: chain R residue 224 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 GLN C 187 HIS C 267 GLN D 60 GLN D 183 GLN ** D 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN G 34 ASN G 62 ASN G 290 ASN G 294 HIS I 30 GLN I 94 GLN ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 GLN ** I 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 233 GLN X 244 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.113365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.078563 restraints weight = 60230.105| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.12 r_work: 0.2964 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14339 Z= 0.151 Angle : 0.541 6.387 19414 Z= 0.282 Chirality : 0.040 0.167 2267 Planarity : 0.004 0.076 2452 Dihedral : 9.779 128.231 2087 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.44 % Favored : 97.45 % Rotamer: Outliers : 2.06 % Allowed : 13.81 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.21), residues: 1763 helix: 2.21 (0.19), residues: 822 sheet: 0.10 (0.30), residues: 315 loop : 0.06 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 21 TYR 0.013 0.001 TYR I 301 PHE 0.019 0.001 PHE I 129 TRP 0.007 0.001 TRP X 231 HIS 0.003 0.001 HIS C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (14339) covalent geometry : angle 0.54111 / 0.28 (19414) hydrogen bonds : bond 0.04017 / 2.64 ( 760) hydrogen bonds : angle 5.28437 / 3.78 ( 2184) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.773 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: C 65 ARG cc_start: 0.8239 (mtt180) cc_final: 0.8000 (mtm110) REVERT: C 235 LYS cc_start: 0.8641 (mttt) cc_final: 0.8417 (mtpt) REVERT: C 277 ARG cc_start: 0.8673 (mtt180) cc_final: 0.8045 (mtm110) REVERT: D 201 LYS cc_start: 0.8752 (mmtt) cc_final: 0.8443 (mptt) REVERT: D 301 GLN cc_start: 0.9019 (mt0) cc_final: 0.8720 (mt0) REVERT: G 42 GLU cc_start: 0.8585 (tt0) cc_final: 0.7933 (tm-30) REVERT: G 107 LYS cc_start: 0.8545 (mttp) cc_final: 0.8323 (mmmm) REVERT: I 62 ASN cc_start: 0.8362 (m110) cc_final: 0.8021 (m110) REVERT: I 136 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8974 (pp) REVERT: I 137 CYS cc_start: 0.8984 (m) cc_final: 0.8419 (m) REVERT: I 203 LEU cc_start: 0.8958 (mt) cc_final: 0.8607 (mp) REVERT: I 243 MET cc_start: 0.8782 (mtt) cc_final: 0.8555 (mmp) REVERT: I 268 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6563 (tt0) REVERT: R 143 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7822 (pt0) REVERT: R 192 GLU cc_start: 0.8476 (tt0) cc_final: 0.8223 (tt0) REVERT: X 64 ARG cc_start: 0.8332 (mtp85) cc_final: 0.8085 (mmm160) REVERT: X 90 LEU cc_start: 0.8530 (mt) cc_final: 0.8262 (tt) REVERT: X 111 CYS cc_start: 0.9008 (m) cc_final: 0.8742 (m) REVERT: X 136 MET cc_start: 0.9064 (ttt) cc_final: 0.8836 (ttt) REVERT: X 236 LYS cc_start: 0.8492 (mttt) cc_final: 0.8160 (mmtm) REVERT: X 239 MET cc_start: 0.9105 (mtt) cc_final: 0.8627 (mtt) REVERT: X 258 ARG cc_start: 0.7490 (ttt180) cc_final: 0.7128 (ttt90) REVERT: X 278 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8084 (mm-30) outliers start: 31 outliers final: 14 residues processed: 225 average time/residue: 1.1605 time to fit residues: 286.6241 Evaluate side-chains 185 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 268 GLN Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain I residue 330 ASN Chi-restraints excluded: chain R residue 2 ASP Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 345 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 139 optimal weight: 0.3980 chunk 110 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 175 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 187 HIS D 60 GLN G 34 ASN ** I 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 GLN I 206 GLN ** I 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 233 GLN X 244 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.111788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.077123 restraints weight = 59544.611| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.09 r_work: 0.2935 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14339 Z= 0.173 Angle : 0.522 6.264 19414 Z= 0.269 Chirality : 0.040 0.163 2267 Planarity : 0.004 0.066 2452 Dihedral : 9.280 127.646 2082 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.72 % Favored : 97.16 % Rotamer: Outliers : 2.52 % Allowed : 13.88 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.21), residues: 1763 helix: 2.10 (0.19), residues: 829 sheet: -0.15 (0.30), residues: 318 loop : -0.01 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 160 TYR 0.011 0.001 TYR I 301 PHE 0.012 0.001 PHE G 92 TRP 0.006 0.001 TRP X 231 HIS 0.003 0.001 HIS C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (14339) covalent geometry : angle 0.52184 / 0.27 (19414) hydrogen bonds : bond 0.03692 / 2.44 ( 760) hydrogen bonds : angle 4.97773 / 3.55 ( 2184) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.741 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: C 65 ARG cc_start: 0.8267 (mtt180) cc_final: 0.8001 (mtm110) REVERT: C 235 LYS cc_start: 0.8719 (mttt) cc_final: 0.8467 (mtpt) REVERT: C 277 ARG cc_start: 0.8818 (mtt180) cc_final: 0.8137 (mtm110) REVERT: D 201 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8409 (mmtt) REVERT: G 42 GLU cc_start: 0.8621 (tt0) cc_final: 0.7970 (mm-30) REVERT: G 107 LYS cc_start: 0.8631 (mttp) cc_final: 0.8407 (mmmm) REVERT: I 46 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.7231 (t80) REVERT: I 136 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9056 (pt) REVERT: I 137 CYS cc_start: 0.9096 (m) cc_final: 0.8535 (m) REVERT: I 203 LEU cc_start: 0.8985 (mt) cc_final: 0.8663 (mp) REVERT: I 210 MET cc_start: 0.7857 (mtt) cc_final: 0.7437 (ptp) REVERT: I 243 MET cc_start: 0.8794 (mtt) cc_final: 0.8560 (OUTLIER) REVERT: I 250 ARG cc_start: 0.8626 (tpt-90) cc_final: 0.8248 (mmm160) REVERT: I 268 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6678 (tt0) REVERT: R 1 MET cc_start: 0.6809 (mmt) cc_final: 0.6560 (mmt) REVERT: R 2 ASP cc_start: 0.8312 (m-30) cc_final: 0.7315 (t0) REVERT: R 129 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8662 (mp10) REVERT: R 143 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7997 (pt0) REVERT: R 192 GLU cc_start: 0.8649 (tt0) cc_final: 0.8400 (tt0) REVERT: X 40 HIS cc_start: 0.5708 (OUTLIER) cc_final: 0.5502 (t-90) REVERT: X 64 ARG cc_start: 0.8364 (mtp85) cc_final: 0.8147 (mmm160) REVERT: X 90 LEU cc_start: 0.8679 (mt) cc_final: 0.8415 (tt) REVERT: X 111 CYS cc_start: 0.9089 (m) cc_final: 0.8815 (m) REVERT: X 236 LYS cc_start: 0.8585 (mttt) cc_final: 0.8218 (mmtm) REVERT: X 258 ARG cc_start: 0.7627 (ttt180) cc_final: 0.7239 (ttt90) outliers start: 38 outliers final: 20 residues processed: 198 average time/residue: 1.0459 time to fit residues: 229.6582 Evaluate side-chains 191 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 268 GLN Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain R residue 129 GLN Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 345 SER Chi-restraints excluded: chain X residue 40 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 31 optimal weight: 0.0050 chunk 44 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 GLN ** I 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 233 GLN X 244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.111826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.077287 restraints weight = 59578.478| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.09 r_work: 0.2937 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14339 Z= 0.147 Angle : 0.497 6.048 19414 Z= 0.254 Chirality : 0.040 0.162 2267 Planarity : 0.003 0.059 2452 Dihedral : 9.202 127.083 2080 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.61 % Favored : 97.28 % Rotamer: Outliers : 2.46 % Allowed : 14.54 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.21), residues: 1763 helix: 2.18 (0.19), residues: 826 sheet: -0.28 (0.29), residues: 318 loop : -0.01 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 11 TYR 0.010 0.001 TYR I 301 PHE 0.011 0.001 PHE G 92 TRP 0.006 0.001 TRP X 231 HIS 0.002 0.001 HIS D 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (14339) covalent geometry : angle 0.49679 / 0.25 (19414) hydrogen bonds : bond 0.03281 / 2.19 ( 760) hydrogen bonds : angle 4.73304 / 3.38 ( 2184) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.734 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: C 65 ARG cc_start: 0.8285 (mtt180) cc_final: 0.8031 (mtm110) REVERT: C 171 ASP cc_start: 0.8291 (m-30) cc_final: 0.8077 (m-30) REVERT: C 193 ARG cc_start: 0.8466 (tpp80) cc_final: 0.8024 (mpp80) REVERT: C 235 LYS cc_start: 0.8702 (mttt) cc_final: 0.8449 (mtpt) REVERT: C 277 ARG cc_start: 0.8816 (mtt180) cc_final: 0.8136 (mtm110) REVERT: D 201 LYS cc_start: 0.8795 (mmtt) cc_final: 0.8368 (mmtt) REVERT: D 308 MET cc_start: 0.8590 (tmm) cc_final: 0.8372 (tmm) REVERT: G 42 GLU cc_start: 0.8651 (tt0) cc_final: 0.7997 (tm-30) REVERT: G 107 LYS cc_start: 0.8644 (mttp) cc_final: 0.8405 (mmmm) REVERT: I 46 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7217 (t80) REVERT: I 136 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9088 (pt) REVERT: I 137 CYS cc_start: 0.9184 (m) cc_final: 0.8637 (m) REVERT: I 203 LEU cc_start: 0.9003 (mt) cc_final: 0.8692 (mp) REVERT: I 210 MET cc_start: 0.8007 (mtt) cc_final: 0.7553 (ptp) REVERT: I 243 MET cc_start: 0.8803 (mtt) cc_final: 0.8564 (OUTLIER) REVERT: I 250 ARG cc_start: 0.8609 (tpt-90) cc_final: 0.8351 (mmm160) REVERT: R 1 MET cc_start: 0.6860 (mmt) cc_final: 0.6629 (mmt) REVERT: R 2 ASP cc_start: 0.8248 (m-30) cc_final: 0.7319 (t0) REVERT: R 129 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8736 (mp10) REVERT: R 143 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7981 (pt0) REVERT: R 192 GLU cc_start: 0.8642 (tt0) cc_final: 0.8395 (tt0) REVERT: R 224 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7422 (p0) REVERT: X 64 ARG cc_start: 0.8334 (mtp85) cc_final: 0.8133 (mmm160) REVERT: X 90 LEU cc_start: 0.8664 (mt) cc_final: 0.8400 (tt) REVERT: X 111 CYS cc_start: 0.9138 (m) cc_final: 0.8856 (m) REVERT: X 136 MET cc_start: 0.9077 (ttt) cc_final: 0.8868 (ttt) REVERT: X 165 SER cc_start: 0.7945 (t) cc_final: 0.7626 (p) REVERT: X 236 LYS cc_start: 0.8603 (mttt) cc_final: 0.8205 (mmtm) REVERT: X 239 MET cc_start: 0.9218 (mtt) cc_final: 0.8819 (mtt) REVERT: X 258 ARG cc_start: 0.7634 (ttt180) cc_final: 0.7249 (ttt90) outliers start: 37 outliers final: 14 residues processed: 201 average time/residue: 1.0442 time to fit residues: 233.0726 Evaluate side-chains 181 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 129 GLN Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain R residue 345 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 88 optimal weight: 0.0670 chunk 99 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 268 GLN ** I 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.112219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.077684 restraints weight = 59445.804| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.09 r_work: 0.2944 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14339 Z= 0.121 Angle : 0.480 6.003 19414 Z= 0.245 Chirality : 0.039 0.166 2267 Planarity : 0.003 0.079 2452 Dihedral : 8.970 127.032 2080 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.61 % Favored : 97.33 % Rotamer: Outliers : 2.26 % Allowed : 14.81 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.21), residues: 1763 helix: 2.22 (0.19), residues: 828 sheet: -0.33 (0.29), residues: 318 loop : 0.02 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 24 TYR 0.010 0.001 TYR C 327 PHE 0.009 0.001 PHE G 92 TRP 0.005 0.001 TRP X 231 HIS 0.002 0.000 HIS D 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (14339) covalent geometry : angle 0.48004 / 0.24 (19414) hydrogen bonds : bond 0.03066 / 2.06 ( 760) hydrogen bonds : angle 4.55981 / 3.26 ( 2184) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.729 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: C 65 ARG cc_start: 0.8360 (mtt180) cc_final: 0.8083 (mtm110) REVERT: C 235 LYS cc_start: 0.8734 (mttt) cc_final: 0.8484 (mtpt) REVERT: C 277 ARG cc_start: 0.8793 (mtt180) cc_final: 0.8100 (mtm110) REVERT: D 201 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8369 (mmtt) REVERT: G 42 GLU cc_start: 0.8650 (tt0) cc_final: 0.7970 (tm-30) REVERT: G 58 LYS cc_start: 0.8259 (tptp) cc_final: 0.7924 (tptp) REVERT: G 107 LYS cc_start: 0.8660 (mttp) cc_final: 0.8430 (mmmm) REVERT: G 291 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7936 (mp) REVERT: I 54 TYR cc_start: 0.8404 (m-10) cc_final: 0.8093 (m-10) REVERT: I 84 MET cc_start: 0.7795 (ptp) cc_final: 0.7209 (mtm) REVERT: I 136 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.9106 (pp) REVERT: I 137 CYS cc_start: 0.9201 (m) cc_final: 0.8653 (m) REVERT: I 243 MET cc_start: 0.8791 (mtt) cc_final: 0.8546 (mmp) REVERT: R 1 MET cc_start: 0.6866 (mmt) cc_final: 0.6635 (mmt) REVERT: R 2 ASP cc_start: 0.8200 (m-30) cc_final: 0.7303 (t0) REVERT: R 9 ASN cc_start: 0.8295 (t0) cc_final: 0.7965 (t0) REVERT: R 129 GLN cc_start: 0.8970 (mt0) cc_final: 0.8757 (mp10) REVERT: R 143 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8015 (pt0) REVERT: R 192 GLU cc_start: 0.8621 (tt0) cc_final: 0.8382 (tt0) REVERT: X 40 HIS cc_start: 0.6023 (OUTLIER) cc_final: 0.5719 (t-90) REVERT: X 90 LEU cc_start: 0.8670 (mt) cc_final: 0.8401 (tt) REVERT: X 111 CYS cc_start: 0.9168 (m) cc_final: 0.8883 (m) REVERT: X 165 SER cc_start: 0.7909 (t) cc_final: 0.7602 (p) REVERT: X 236 LYS cc_start: 0.8622 (mttt) cc_final: 0.8229 (mmtm) REVERT: X 239 MET cc_start: 0.9220 (mtt) cc_final: 0.8837 (mtt) REVERT: X 258 ARG cc_start: 0.7635 (ttt180) cc_final: 0.7254 (ttt90) REVERT: X 261 LYS cc_start: 0.8988 (mttt) cc_final: 0.8371 (ttpp) outliers start: 34 outliers final: 18 residues processed: 200 average time/residue: 1.0426 time to fit residues: 231.6619 Evaluate side-chains 183 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 345 SER Chi-restraints excluded: chain X residue 40 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 144 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 96 optimal weight: 0.0570 chunk 122 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 98 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.0304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 GLN G 34 ASN ** I 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 HIS ** I 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.111210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.076787 restraints weight = 59794.742| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.06 r_work: 0.2935 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14339 Z= 0.157 Angle : 0.495 6.059 19414 Z= 0.251 Chirality : 0.039 0.165 2267 Planarity : 0.003 0.069 2452 Dihedral : 8.871 125.923 2078 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.28 % Rotamer: Outliers : 2.52 % Allowed : 15.67 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.21), residues: 1763 helix: 2.21 (0.19), residues: 828 sheet: -0.39 (0.29), residues: 316 loop : 0.03 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 250 TYR 0.012 0.001 TYR I 301 PHE 0.016 0.001 PHE I 46 TRP 0.005 0.001 TRP X 231 HIS 0.002 0.001 HIS D 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (14339) covalent geometry : angle 0.49510 / 0.25 (19414) hydrogen bonds : bond 0.03105 / 2.09 ( 760) hydrogen bonds : angle 4.54999 / 3.25 ( 2184) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.715 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: C 65 ARG cc_start: 0.8353 (mtt180) cc_final: 0.8065 (mtm110) REVERT: C 235 LYS cc_start: 0.8713 (mttt) cc_final: 0.8460 (mtpt) REVERT: C 277 ARG cc_start: 0.8776 (mtt180) cc_final: 0.8054 (mtm110) REVERT: D 201 LYS cc_start: 0.8795 (mmtt) cc_final: 0.8366 (mmtt) REVERT: G 42 GLU cc_start: 0.8650 (tt0) cc_final: 0.7960 (tm-30) REVERT: G 107 LYS cc_start: 0.8678 (mttp) cc_final: 0.8443 (mmmm) REVERT: G 291 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8017 (mp) REVERT: I 46 PHE cc_start: 0.7895 (t80) cc_final: 0.7507 (t80) REVERT: I 136 ILE cc_start: 0.9465 (OUTLIER) cc_final: 0.9185 (pp) REVERT: I 137 CYS cc_start: 0.9248 (m) cc_final: 0.8614 (m) REVERT: I 195 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7395 (p90) REVERT: I 210 MET cc_start: 0.8078 (mtt) cc_final: 0.7777 (ptp) REVERT: I 243 MET cc_start: 0.8801 (mtt) cc_final: 0.8543 (mmp) REVERT: R 129 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8759 (mp10) REVERT: R 143 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8023 (pt0) REVERT: R 192 GLU cc_start: 0.8594 (tt0) cc_final: 0.8355 (tt0) REVERT: X 24 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7743 (mt) REVERT: X 90 LEU cc_start: 0.8630 (mt) cc_final: 0.8363 (tt) REVERT: X 111 CYS cc_start: 0.9164 (m) cc_final: 0.8867 (m) REVERT: X 165 SER cc_start: 0.7978 (t) cc_final: 0.7665 (p) REVERT: X 236 LYS cc_start: 0.8607 (mttt) cc_final: 0.8189 (mmtm) REVERT: X 239 MET cc_start: 0.9208 (mtt) cc_final: 0.8818 (mtt) REVERT: X 258 ARG cc_start: 0.7606 (ttt180) cc_final: 0.7217 (ttt90) outliers start: 38 outliers final: 19 residues processed: 192 average time/residue: 1.0452 time to fit residues: 223.1385 Evaluate side-chains 179 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 195 PHE Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 129 GLN Chi-restraints excluded: chain R residue 144 ASP Chi-restraints excluded: chain R residue 345 SER Chi-restraints excluded: chain X residue 24 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 138 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 GLN ** I 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.109428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.075196 restraints weight = 59811.735| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.03 r_work: 0.2900 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14339 Z= 0.227 Angle : 0.539 6.854 19414 Z= 0.275 Chirality : 0.041 0.155 2267 Planarity : 0.004 0.077 2452 Dihedral : 8.974 122.338 2078 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 2.59 % Allowed : 16.14 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.21), residues: 1763 helix: 2.05 (0.19), residues: 826 sheet: -0.56 (0.29), residues: 318 loop : -0.09 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 250 TYR 0.013 0.001 TYR C 327 PHE 0.016 0.001 PHE G 92 TRP 0.005 0.001 TRP C 317 HIS 0.003 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (14339) covalent geometry : angle 0.53891 / 0.27 (19414) hydrogen bonds : bond 0.03446 / 2.32 ( 760) hydrogen bonds : angle 4.68055 / 3.34 ( 2184) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.755 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: C 65 ARG cc_start: 0.8315 (mtt180) cc_final: 0.8013 (mtm110) REVERT: C 235 LYS cc_start: 0.8762 (mttt) cc_final: 0.8498 (mtpt) REVERT: C 277 ARG cc_start: 0.8804 (mtt180) cc_final: 0.8101 (mtm110) REVERT: D 94 ASP cc_start: 0.8490 (t0) cc_final: 0.8176 (OUTLIER) REVERT: D 201 LYS cc_start: 0.8810 (mmtt) cc_final: 0.8374 (mmtt) REVERT: D 254 ASP cc_start: 0.7212 (t0) cc_final: 0.7007 (t0) REVERT: G 42 GLU cc_start: 0.8670 (tt0) cc_final: 0.7984 (tm-30) REVERT: G 107 LYS cc_start: 0.8707 (mttp) cc_final: 0.8460 (mmmm) REVERT: G 158 MET cc_start: 0.8956 (ttm) cc_final: 0.8604 (mtp) REVERT: I 46 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7058 (t80) REVERT: I 136 ILE cc_start: 0.9517 (OUTLIER) cc_final: 0.9216 (pp) REVERT: I 137 CYS cc_start: 0.9274 (m) cc_final: 0.8660 (m) REVERT: I 180 LEU cc_start: 0.8892 (mm) cc_final: 0.8176 (tp) REVERT: I 195 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7422 (p90) REVERT: I 210 MET cc_start: 0.8018 (mtt) cc_final: 0.7651 (ptp) REVERT: I 243 MET cc_start: 0.8819 (mtt) cc_final: 0.8601 (mmp) REVERT: R 143 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8017 (pt0) REVERT: R 192 GLU cc_start: 0.8626 (tt0) cc_final: 0.8393 (tt0) REVERT: X 24 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7719 (mt) REVERT: X 90 LEU cc_start: 0.8657 (mt) cc_final: 0.8389 (tt) REVERT: X 111 CYS cc_start: 0.9196 (m) cc_final: 0.8900 (m) REVERT: X 136 MET cc_start: 0.9143 (ttt) cc_final: 0.8932 (ttt) REVERT: X 165 SER cc_start: 0.8148 (t) cc_final: 0.7853 (p) REVERT: X 236 LYS cc_start: 0.8616 (mttt) cc_final: 0.8199 (mmtm) REVERT: X 258 ARG cc_start: 0.7684 (ttt180) cc_final: 0.7271 (ttt90) outliers start: 39 outliers final: 19 residues processed: 185 average time/residue: 1.0647 time to fit residues: 218.8825 Evaluate side-chains 176 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 195 PHE Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 345 SER Chi-restraints excluded: chain X residue 24 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.109480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.075060 restraints weight = 60035.127| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.06 r_work: 0.2905 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14339 Z= 0.210 Angle : 0.523 6.607 19414 Z= 0.266 Chirality : 0.041 0.150 2267 Planarity : 0.004 0.075 2452 Dihedral : 8.937 120.537 2078 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 2.26 % Allowed : 16.53 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.21), residues: 1763 helix: 2.08 (0.19), residues: 828 sheet: -0.77 (0.28), residues: 318 loop : -0.10 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 250 TYR 0.017 0.001 TYR I 301 PHE 0.015 0.001 PHE I 46 TRP 0.005 0.001 TRP C 317 HIS 0.004 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (14339) covalent geometry : angle 0.52265 / 0.27 (19414) hydrogen bonds : bond 0.03318 / 2.24 ( 760) hydrogen bonds : angle 4.63199 / 3.31 ( 2184) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.711 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: C 65 ARG cc_start: 0.8256 (mtt180) cc_final: 0.7973 (mtm110) REVERT: C 146 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7888 (tm-30) REVERT: C 235 LYS cc_start: 0.8729 (mttt) cc_final: 0.8456 (mtpt) REVERT: C 277 ARG cc_start: 0.8836 (mtt180) cc_final: 0.8116 (mtm110) REVERT: D 201 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8392 (mmtt) REVERT: D 254 ASP cc_start: 0.7267 (t0) cc_final: 0.7062 (t0) REVERT: G 42 GLU cc_start: 0.8669 (tt0) cc_final: 0.7988 (tm-30) REVERT: G 107 LYS cc_start: 0.8720 (mttp) cc_final: 0.8466 (mmmm) REVERT: G 243 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8106 (ttt) REVERT: I 46 PHE cc_start: 0.8017 (t80) cc_final: 0.7270 (t80) REVERT: I 136 ILE cc_start: 0.9522 (OUTLIER) cc_final: 0.9242 (pp) REVERT: I 137 CYS cc_start: 0.9281 (m) cc_final: 0.8694 (m) REVERT: I 180 LEU cc_start: 0.8955 (mm) cc_final: 0.8318 (tp) REVERT: I 195 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7421 (p90) REVERT: I 210 MET cc_start: 0.7989 (mtt) cc_final: 0.7589 (ptp) REVERT: I 243 MET cc_start: 0.8808 (mtt) cc_final: 0.8603 (mmp) REVERT: R 143 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8025 (pt0) REVERT: R 192 GLU cc_start: 0.8604 (tt0) cc_final: 0.8376 (tt0) REVERT: X 24 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7721 (mt) REVERT: X 90 LEU cc_start: 0.8626 (mt) cc_final: 0.8351 (tt) REVERT: X 111 CYS cc_start: 0.9194 (m) cc_final: 0.8891 (m) REVERT: X 165 SER cc_start: 0.8099 (t) cc_final: 0.7796 (p) REVERT: X 236 LYS cc_start: 0.8595 (mttt) cc_final: 0.8178 (mmtm) REVERT: X 258 ARG cc_start: 0.7636 (ttt180) cc_final: 0.7243 (ttt90) REVERT: X 261 LYS cc_start: 0.9121 (mttt) cc_final: 0.8577 (ttpt) outliers start: 34 outliers final: 18 residues processed: 184 average time/residue: 1.0284 time to fit residues: 210.4728 Evaluate side-chains 175 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 195 PHE Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 345 SER Chi-restraints excluded: chain X residue 24 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 136 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 167 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 GLN ** I 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.110420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.075989 restraints weight = 59875.722| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.08 r_work: 0.2926 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14339 Z= 0.146 Angle : 0.505 6.075 19414 Z= 0.255 Chirality : 0.039 0.152 2267 Planarity : 0.003 0.077 2452 Dihedral : 8.830 119.768 2078 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.28 % Rotamer: Outliers : 2.06 % Allowed : 17.00 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.21), residues: 1763 helix: 2.20 (0.19), residues: 828 sheet: -0.72 (0.29), residues: 315 loop : -0.05 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 250 TYR 0.010 0.001 TYR C 327 PHE 0.010 0.001 PHE G 92 TRP 0.005 0.001 TRP X 231 HIS 0.003 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (14339) covalent geometry : angle 0.50542 / 0.25 (19414) hydrogen bonds : bond 0.03098 / 2.09 ( 760) hydrogen bonds : angle 4.50445 / 3.23 ( 2184) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.722 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: C 65 ARG cc_start: 0.8282 (mtt180) cc_final: 0.7997 (mtm110) REVERT: C 235 LYS cc_start: 0.8712 (mttt) cc_final: 0.8445 (mtpt) REVERT: C 277 ARG cc_start: 0.8821 (mtt180) cc_final: 0.8114 (mtm110) REVERT: D 201 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8382 (mmtt) REVERT: D 254 ASP cc_start: 0.7266 (t0) cc_final: 0.7052 (t0) REVERT: G 42 GLU cc_start: 0.8666 (tt0) cc_final: 0.7993 (tm-30) REVERT: G 107 LYS cc_start: 0.8714 (mttp) cc_final: 0.8468 (mmmm) REVERT: I 46 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7239 (t80) REVERT: I 136 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9254 (pp) REVERT: I 137 CYS cc_start: 0.9294 (m) cc_final: 0.8747 (m) REVERT: I 180 LEU cc_start: 0.8917 (mm) cc_final: 0.8334 (tp) REVERT: I 210 MET cc_start: 0.8182 (mtt) cc_final: 0.7780 (ptp) REVERT: I 243 MET cc_start: 0.8807 (mtt) cc_final: 0.8590 (mmp) REVERT: R 143 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8019 (pt0) REVERT: R 192 GLU cc_start: 0.8604 (tt0) cc_final: 0.8376 (tt0) REVERT: X 24 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7660 (mt) REVERT: X 90 LEU cc_start: 0.8590 (mt) cc_final: 0.8321 (tt) REVERT: X 111 CYS cc_start: 0.9210 (m) cc_final: 0.8884 (m) REVERT: X 136 MET cc_start: 0.9117 (ttt) cc_final: 0.8915 (ttt) REVERT: X 165 SER cc_start: 0.8102 (t) cc_final: 0.7810 (p) REVERT: X 236 LYS cc_start: 0.8604 (mttt) cc_final: 0.8185 (mmtm) REVERT: X 258 ARG cc_start: 0.7672 (ttt180) cc_final: 0.7277 (ttt90) REVERT: X 261 LYS cc_start: 0.9100 (mttt) cc_final: 0.8537 (tmmt) outliers start: 31 outliers final: 18 residues processed: 179 average time/residue: 1.0671 time to fit residues: 211.4181 Evaluate side-chains 176 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 345 SER Chi-restraints excluded: chain X residue 24 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 108 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 GLN ** I 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.109371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.074745 restraints weight = 59620.934| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.06 r_work: 0.2905 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14339 Z= 0.197 Angle : 0.526 6.612 19414 Z= 0.267 Chirality : 0.040 0.172 2267 Planarity : 0.004 0.084 2452 Dihedral : 8.860 117.811 2078 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.82 % Rotamer: Outliers : 1.66 % Allowed : 17.13 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.21), residues: 1763 helix: 2.15 (0.19), residues: 828 sheet: -0.68 (0.29), residues: 313 loop : -0.08 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 250 TYR 0.017 0.001 TYR I 301 PHE 0.013 0.001 PHE G 92 TRP 0.005 0.001 TRP C 317 HIS 0.007 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (14339) covalent geometry : angle 0.52648 / 0.27 (19414) hydrogen bonds : bond 0.03275 / 2.21 ( 760) hydrogen bonds : angle 4.55579 / 3.26 ( 2184) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.500 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: C 11 GLN cc_start: 0.8136 (mt0) cc_final: 0.7795 (mm-40) REVERT: C 65 ARG cc_start: 0.8290 (mtt180) cc_final: 0.8012 (mtm110) REVERT: C 235 LYS cc_start: 0.8723 (mttt) cc_final: 0.8473 (mtpt) REVERT: C 277 ARG cc_start: 0.8854 (mtt180) cc_final: 0.8144 (mtm110) REVERT: D 24 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8281 (mpp-170) REVERT: D 201 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8406 (mmtt) REVERT: G 42 GLU cc_start: 0.8682 (tt0) cc_final: 0.8026 (tm-30) REVERT: G 107 LYS cc_start: 0.8732 (mttp) cc_final: 0.8486 (mmmm) REVERT: G 158 MET cc_start: 0.8961 (ttm) cc_final: 0.8620 (mtp) REVERT: I 46 PHE cc_start: 0.8012 (t80) cc_final: 0.7311 (t80) REVERT: I 136 ILE cc_start: 0.9547 (OUTLIER) cc_final: 0.9244 (pp) REVERT: I 137 CYS cc_start: 0.9293 (m) cc_final: 0.8782 (m) REVERT: I 180 LEU cc_start: 0.8885 (mm) cc_final: 0.8269 (tp) REVERT: I 195 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7465 (p90) REVERT: I 210 MET cc_start: 0.8019 (mtt) cc_final: 0.7634 (ptp) REVERT: I 243 MET cc_start: 0.8812 (mtt) cc_final: 0.8586 (mmp) REVERT: R 143 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8046 (pt0) REVERT: R 192 GLU cc_start: 0.8624 (tt0) cc_final: 0.8397 (tt0) REVERT: X 24 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7570 (mt) REVERT: X 90 LEU cc_start: 0.8592 (mt) cc_final: 0.8321 (tt) REVERT: X 111 CYS cc_start: 0.9221 (m) cc_final: 0.8890 (m) REVERT: X 136 MET cc_start: 0.9147 (ttt) cc_final: 0.8945 (ttt) REVERT: X 165 SER cc_start: 0.8182 (t) cc_final: 0.7869 (p) REVERT: X 236 LYS cc_start: 0.8616 (mttt) cc_final: 0.8201 (mmtm) REVERT: X 258 ARG cc_start: 0.7641 (ttt180) cc_final: 0.7238 (ttt90) REVERT: X 261 LYS cc_start: 0.9125 (mttt) cc_final: 0.8560 (tmmt) outliers start: 25 outliers final: 18 residues processed: 176 average time/residue: 1.0451 time to fit residues: 204.1794 Evaluate side-chains 174 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 195 PHE Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 345 SER Chi-restraints excluded: chain X residue 24 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 14 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 150 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 GLN ** I 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.110492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.076095 restraints weight = 59441.748| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.08 r_work: 0.2924 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14339 Z= 0.140 Angle : 0.507 8.638 19414 Z= 0.256 Chirality : 0.039 0.144 2267 Planarity : 0.003 0.074 2452 Dihedral : 8.753 116.784 2078 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.28 % Rotamer: Outliers : 1.59 % Allowed : 17.13 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.21), residues: 1763 helix: 2.24 (0.19), residues: 833 sheet: -0.66 (0.29), residues: 313 loop : -0.06 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 250 TYR 0.010 0.001 TYR C 327 PHE 0.015 0.001 PHE I 129 TRP 0.005 0.001 TRP X 231 HIS 0.002 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (14339) covalent geometry : angle 0.50724 / 0.26 (19414) hydrogen bonds : bond 0.03048 / 2.07 ( 760) hydrogen bonds : angle 4.42533 / 3.17 ( 2184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8667.72 seconds wall clock time: 147 minutes 43.88 seconds (8863.88 seconds total)