Starting phenix.real_space_refine on Tue Apr 7 09:41:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q28_72152/04_2026/9q28_72152_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q28_72152/04_2026/9q28_72152.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9q28_72152/04_2026/9q28_72152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q28_72152/04_2026/9q28_72152.map" model { file = "/net/cci-nas-00/data/ceres_data/9q28_72152/04_2026/9q28_72152_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q28_72152/04_2026/9q28_72152_trim.cif" } 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= 0.019 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 24 5.49 5 Mg 5 5.21 5 S 80 5.16 5 C 8860 2.51 5 N 2471 2.21 5 O 2714 1.98 5 H 11680 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25834 Number of models: 1 Model: "" Number of chains: 12 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: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 4704 Classifications: {'peptide': 306} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 297} Chain breaks: 1 Chain: "G" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2335 Classifications: {'peptide': 304} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 294} Chain breaks: 1 Chain: "H" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "I" Number of atoms: 4366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4366 Classifications: {'peptide': 282} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3833 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 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: "G" 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: "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: 4.94, per 1000 atoms: 0.19 Number of scatterers: 25834 At special positions: 0 Unit cell: (137.344, 123.424, 133.632, 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 80 16.00 P 24 15.00 Mg 5 11.99 O 2714 8.00 N 2471 7.00 C 8860 6.00 H 11680 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: 2.69 Conformation dependent library (CDL) restraints added in 804.8 milliseconds 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3302 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 14 sheets defined 53.4% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'C' and resid 13 through 17 Processing helix chain 'C' and resid 20 through 30 Processing helix chain 'C' and resid 35 through 40 removed outlier: 4.641A 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 removed outlier: 3.505A pdb=" N ILE C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) 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 removed outlier: 3.563A pdb=" N ASP C 171 " --> pdb=" O ASP C 167 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 199 removed outlier: 3.637A pdb=" N ARG C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU C 197 " --> pdb=" O ARG C 193 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP C 198 " --> pdb=" O LYS C 194 " (cutoff:3.500A) 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 removed outlier: 3.585A pdb=" N GLU C 232 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 249 Processing helix chain 'C' and resid 254 through 277 removed outlier: 3.517A pdb=" N ARG C 260 " --> pdb=" O SER C 256 " (cutoff:3.500A) 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 61 Processing helix chain 'D' and resid 68 through 79 Processing helix chain 'D' and resid 86 through 94 Processing helix chain 'D' and resid 112 through 127 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: 3.958A 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: 4.357A pdb=" N LEU D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 270 removed outlier: 3.829A 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 removed outlier: 3.546A pdb=" N TYR G 54 " --> pdb=" O GLU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'G' and resid 67 through 81 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: 3.537A 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 225 through 232 removed outlier: 3.660A pdb=" N ARG G 229 " --> pdb=" O THR G 225 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR G 230 " --> pdb=" O ALA G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 260 Processing helix chain 'G' and resid 288 through 296 removed outlier: 3.830A pdb=" N ILE G 292 " --> pdb=" O GLY G 288 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA G 293 " --> pdb=" O GLY G 289 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA G 295 " --> pdb=" O ILE G 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 31 Processing helix chain 'I' and resid 34 through 44 Processing helix chain 'I' and resid 48 through 55 Processing helix chain 'I' and resid 56 through 63 Processing helix chain 'I' and resid 67 through 82 Processing helix chain 'I' and resid 89 through 98 Processing helix chain 'I' and resid 106 through 113 Processing helix chain 'I' and resid 132 through 144 Processing helix chain 'I' and resid 145 through 146 No H-bonds generated for 'chain 'I' and resid 145 through 146' Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.779A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 188 Processing helix chain 'I' and resid 196 through 214 Processing helix chain 'I' and resid 239 through 260 Processing helix chain 'I' and resid 288 through 296 removed outlier: 3.620A pdb=" N ILE I 292 " --> pdb=" O GLY I 288 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA I 293 " --> pdb=" O GLY I 289 " (cutoff:3.500A) Processing helix chain 'R' and resid 1 through 6 Processing helix chain 'R' and resid 9 through 19 Processing helix chain 'R' and resid 23 through 30 removed outlier: 3.622A 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: 3.693A pdb=" N HIS R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 94 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 removed outlier: 3.522A pdb=" N GLY R 131 " --> pdb=" O ARG R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 162 Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 166 through 172 Processing helix chain 'R' and resid 175 through 177 No H-bonds generated for 'chain 'R' and resid 175 through 177' Processing helix chain 'R' and resid 186 through 204 removed outlier: 4.581A 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 221 removed outlier: 3.972A pdb=" N PHE R 219 " --> pdb=" O VAL R 215 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS R 221 " --> pdb=" O ALA R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 250 Processing helix chain 'R' and resid 284 through 290 removed outlier: 3.598A 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: 4.013A pdb=" N GLU X 134 " --> pdb=" O LEU X 130 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SER X 135 " --> pdb=" O TYR X 131 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET X 136 " --> pdb=" O SER X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 154 through 162 Processing helix chain 'X' and resid 165 through 188 removed outlier: 5.008A pdb=" N THR X 172 " --> pdb=" O LEU X 168 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU X 173 " --> pdb=" O GLN X 169 " (cutoff:3.500A) Processing helix chain 'X' and resid 228 through 235 removed outlier: 3.832A pdb=" N LEU X 234 " --> pdb=" O ALA X 230 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 85 through 86 removed outlier: 6.247A pdb=" N VAL D 132 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL D 170 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N TYR D 134 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN D 131 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL D 202 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL D 102 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE D 276 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU D 104 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU D 278 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL D 106 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 6.204A 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: 5.523A pdb=" N GLU C 154 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 296 " --> pdb=" O LYS C 289 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 208 through 212 removed outlier: 5.523A pdb=" N GLU C 154 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR C 121 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ASN C 284 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE C 123 " --> pdb=" O ASN C 284 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N MET C 286 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLY C 125 " --> pdb=" O MET C 286 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N THR C 288 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR C 120 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU C 313 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU C 122 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE C 315 " --> pdb=" O GLU C 122 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N CYS C 124 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N TRP C 317 " --> pdb=" O CYS C 124 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG C 312 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.996A 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: 6.497A pdb=" N GLU X 77 " --> pdb=" O LEU X 143 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU X 145 " --> pdb=" O GLU X 77 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE X 43 " --> pdb=" O HIS X 237 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N MET X 239 " --> pdb=" O ILE X 43 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU X 45 " --> pdb=" O MET X 239 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE X 241 " --> pdb=" O GLU X 45 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N HIS X 47 " --> pdb=" O PHE X 241 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N LYS X 243 " --> pdb=" O HIS X 47 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN X 252 " --> pdb=" O GLN X 244 " (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: 4.299A pdb=" N THR G 87 " --> pdb=" O ILE R 181 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA R 137 " --> pdb=" O PHE R 180 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLU R 182 " --> pdb=" O ALA R 137 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR R 139 " --> pdb=" O GLU R 182 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLY R 136 " --> pdb=" O ALA R 207 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LEU R 254 " --> pdb=" O ARG R 208 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL R 210 " --> pdb=" O LEU R 254 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE R 256 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE R 212 " --> pdb=" O ILE R 256 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY R 107 " --> pdb=" O ASN R 257 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE R 102 " --> pdb=" O VAL R 294 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N LEU R 296 " --> pdb=" O ILE R 102 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLU R 104 " --> pdb=" O LEU R 296 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA R 298 " --> pdb=" O GLU R 104 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA R 106 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG R 295 " --> pdb=" O LEU R 318 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG R 313 " --> pdb=" O TYR R 330 " (cutoff:3.500A) removed outlier: 10.456A pdb=" N SER R 327 " --> pdb=" O GLY R 342 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N GLY R 342 " --> pdb=" O SER R 327 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N SER R 329 " --> pdb=" O THR R 340 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 333 through 336 removed outlier: 6.378A pdb=" N ARG G 299 " --> pdb=" O TYR G 315 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS G 156 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU G 219 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET G 158 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL G 221 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE G 160 " --> pdb=" O VAL G 221 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AB2, first strand: chain 'I' and resid 189 through 193 removed outlier: 6.690A pdb=" N ALA I 157 " --> pdb=" O ALA I 190 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ALA I 192 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR I 159 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS I 156 " --> pdb=" O LEU I 218 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ILE I 220 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N MET I 158 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP I 222 " --> pdb=" O MET I 158 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE I 160 " --> pdb=" O ASP I 222 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA I 217 " --> pdb=" O ALA I 262 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL I 264 " --> pdb=" O ALA I 217 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU I 219 " --> pdb=" O VAL I 264 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR I 266 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL I 221 " --> pdb=" O THR I 266 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N THR I 123 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASN I 267 " --> pdb=" O THR I 123 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N MET I 125 " --> pdb=" O ASN I 267 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG I 299 " --> pdb=" O TYR I 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 328 through 330 Processing sheet with id=AB4, first strand: chain 'R' and resid 81 through 82 Processing sheet with id=AB5, first strand: chain 'R' and resid 259 through 261 removed outlier: 3.828A pdb=" N SER R 281 " --> pdb=" O THR R 260 " (cutoff:3.500A) 757 hydrogen bonds defined for protein. 2133 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: 5.85 Time building geometry restraints manager: 3.83 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: 11644 1.03 - 1.23: 52 1.23 - 1.42: 5757 1.42 - 1.61: 8499 1.61 - 1.81: 119 Bond restraints: 26071 Sorted by residual: bond pdb=" N MET D 1 " pdb=" H3 MET D 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N MET D 1 " pdb=" H2 MET D 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N MET R 1 " pdb=" H3 MET R 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N MET R 1 " pdb=" H2 MET R 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N MET R 1 " pdb=" CA MET R 1 " ideal model delta sigma weight residual 1.491 1.457 0.034 2.10e-02 2.27e+03 2.60e+00 ... (remaining 26066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 20.51: 46010 20.51 - 41.02: 0 41.02 - 61.53: 0 61.53 - 82.04: 0 82.04 - 102.55: 1 Bond angle restraints: 46011 Sorted by residual: angle pdb=" H1 MET R 1 " pdb=" N MET R 1 " pdb=" H2 MET R 1 " ideal model delta sigma weight residual 109.47 6.92 102.55 3.00e+00 1.11e-01 1.17e+03 angle pdb=" C ASP X 149 " pdb=" N SER X 150 " pdb=" CA SER X 150 " ideal model delta sigma weight residual 121.70 130.05 -8.35 1.80e+00 3.09e-01 2.15e+01 angle pdb=" C2' ADP R 401 " pdb=" C1' ADP R 401 " pdb=" N9 ADP R 401 " ideal model delta sigma weight residual 109.47 123.12 -13.65 3.00e+00 1.11e-01 2.07e+01 angle pdb=" C ASP I 222 " pdb=" N SER I 223 " pdb=" CA SER I 223 " ideal model delta sigma weight residual 121.70 129.12 -7.42 1.80e+00 3.09e-01 1.70e+01 angle pdb=" C ASP C 242 " pdb=" N GLY C 243 " pdb=" CA GLY C 243 " ideal model delta sigma weight residual 121.70 128.95 -7.25 1.80e+00 3.09e-01 1.62e+01 ... (remaining 46006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.06: 12032 25.06 - 50.12: 340 50.12 - 75.18: 108 75.18 - 100.24: 13 100.24 - 125.29: 1 Dihedral angle restraints: 12494 sinusoidal: 6834 harmonic: 5660 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 -147.65 87.65 1 2.00e+01 2.50e-03 2.30e+01 dihedral pdb=" CA PRO G 83 " pdb=" C PRO G 83 " pdb=" N MET G 84 " pdb=" CA MET G 84 " ideal model delta harmonic sigma weight residual -180.00 -161.74 -18.26 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" C4' DT H 14 " pdb=" C3' DT H 14 " pdb=" O3' DT H 14 " pdb=" P DT H 15 " ideal model delta sinusoidal sigma weight residual 220.00 94.71 125.29 1 3.50e+01 8.16e-04 1.24e+01 ... (remaining 12491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 2279 0.338 - 0.676: 0 0.676 - 1.014: 0 1.014 - 1.352: 0 1.352 - 1.690: 1 Chirality restraints: 2280 Sorted by residual: chirality pdb=" C1' ADP R 401 " pdb=" C2' ADP R 401 " pdb=" N9 ADP R 401 " pdb=" O4' ADP R 401 " both_signs ideal model delta sigma weight residual False 2.48 0.79 1.69 2.00e-01 2.50e+01 7.14e+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 2.14e+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 2277 not shown) Planarity restraints: 3847 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 82 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO G 83 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO G 83 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 83 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER X 37 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO X 38 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO X 38 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO X 38 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 32 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO R 33 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO R 33 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 33 " -0.019 5.00e-02 4.00e+02 ... (remaining 3844 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1149 2.20 - 2.80: 50569 2.80 - 3.40: 66567 3.40 - 4.00: 90449 4.00 - 4.60: 142548 Nonbonded interactions: 351282 Sorted by model distance: nonbonded pdb=" HG SER C 47 " pdb=" O ILE C 52 " model vdw 1.602 2.450 nonbonded pdb=" HG1 THR D 84 " pdb=" OD1 ASP D 90 " model vdw 1.605 2.450 nonbonded pdb=" OE1 GLU D 104 " pdb=" HE ARG D 275 " model vdw 1.612 2.450 nonbonded pdb=" HG1 THR I 103 " pdb=" OD2 ASP I 110 " model vdw 1.627 2.450 nonbonded pdb="HH22 ARG C 12 " pdb=" OD1 ASP D 180 " model vdw 1.629 2.450 ... (remaining 351277 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 23 through 229 or resid 238 through 268 or resid 287 throu \ gh 303 or resid 310 through 336)) selection = (chain 'I' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2)) or (resid 24 and (name N or name \ CA or name C or name O or name CB or name CG or name CD )) or (resid 25 and (na \ me N or name CA or name C or name O or name CB or name CG1 or name CG2 or name C \ D1)) or (resid 26 and (name N or name CA or name C or name O or name CB or name \ OG )) or (resid 27 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 28 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or name \ CD2)) or (resid 29 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name OE1 or name OE2)) or (resid 30 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or \ (resid 31 and (name N or name CA or name C or name O or name CB or name SG )) or \ (resid 32 and (name N or name CA or name C or name O )) or (resid 33 and (name \ N or name CA or name C or name O or name CB or name CG1 or name CG2 or name CD1) \ ) or (resid 34 and (name N or name CA or name C or name O or name CB or name CG \ or name OD1 or name ND2)) or (resid 35 and (name N or name CA or name C or name \ O or name CB )) or (resid 36 and (name N or name CA or name C or name O or name \ CB or name CG or name OD1 or name ND2)) or (resid 37 and (name N or name CA or n \ ame C or name O or name CB or name CG or name OD1 or name OD2)) or (resid 38 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2)) or \ (resid 39 through 40 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name CE or name NZ )) or (resid 41 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 42 t \ hrough 43 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name OE1 or name OE2)) or (resid 44 and (name N or name CA or name C or \ name O or name CB )) or (resid 45 and (name N or name CA or name C or name O )) \ or (resid 46 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 47 and (n \ ame N or name CA or name C or name O or name CB or name CG or name ND1 or name C \ D2 or name CE1 or name NE2)) or (resid 48 and (name N or name CA or name C or na \ me O or name CB or name OG1 or name CG2)) or (resid 49 and (name N or name CA or \ name C or name O or name CB or name CG1 or name CG2)) or (resid 50 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name OE1 or n \ ame OE2)) or (resid 51 and (name N or name CA or name C or name O or name CB )) \ or (resid 52 and (name N or name CA or name C or name O or name CB or name CG1 o \ r name CG2)) or (resid 53 and (name N or name CA or name C or name O or name CB \ )) or (resid 54 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (re \ sid 55 and (name N or name CA or name C or name O or name CB )) or (resid 56 and \ (name N or name CA or name C or name O or name CB or name CG or name CD )) or ( \ resid 57 through 58 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name CE or name NZ )) or (resid 59 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or ( \ resid 60 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD1 or name CD2)) or (resid 61 and (name N or name CA or name C or name O or n \ ame CB or name CG1 or name CG2 or name CD1)) or (resid 62 and (name N or name CA \ or name C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 6 \ 3 and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 \ or name CD1)) or (resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ )) or (resid 65 and (name N or name \ CA or name C or name O )) or (resid 66 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1)) or (resid 67 and (name N or \ name CA or name C or name O or name CB or name OG )) or (resid 68 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or nam \ e OE2)) or (resid 69 and (name N or name CA or name C or name O or name CB )) or \ (resid 70 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ )) or (resid 71 and (name N or name CA or name C or \ name O or name CB )) or (resid 72 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name OD2)) or (resid 73 and (name N or name C \ A or name C or name O or name CB or name CG or name CD or name CE or name NZ )) \ or (resid 74 and (name N or name CA or name C or name O or name CB or name CG1 o \ r name CG2 or name CD1)) or (resid 75 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2)) or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 77 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 78 through 79 and (name N or name CA or name C or name O or name CB )) or (r \ esid 80 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE or name NZ )) or (resid 81 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD1 or name CD2)) or (resid 82 and (name N or \ name CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 83 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD )) or \ (resid 84 and (name N or name CA or name C or name O or name CB or name CG or n \ ame SD or name CE )) or (resid 85 and (name N or name CA or name C or name O )) \ or (resid 86 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 87 through \ 88 and (name N or name CA or name C or name O or name CB or name OG1 or name CG \ 2)) or (resid 89 and (name N or name CA or name C or name O or name CB )) or (re \ sid 90 and (name N or name CA or name C or name O or name CB or name OG1 or name \ CG2)) or (resid 91 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name OE1 or name OE2)) or (resid 92 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or n \ ame CE2 or name CZ )) or (resid 93 and (name N or name CA or name C or name O or \ name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid \ 94 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name OE1 or name NE2)) or (resid 95 through 96 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2)) or (resid 97 and (name N or name CA or name C or name O or name CB \ or name OG )) or (resid 98 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2)) or (resid 99 through 100 and (n \ ame N or name CA or name C or name O or name CB or name CG1 or name CG2 or name \ CD1)) or (resid 101 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name OE1 or name NE2)) or (resid 102 and (name N or name CA o \ r name C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 10 \ 3 through 104 and (name N or name CA or name C or name O or name CB or name OG1 \ or name CG2)) or (resid 105 and (name N or name CA or name C or name O )) or (re \ sid 106 and (name N or name CA or name C or name O or name CB or name OG )) or ( \ resid 107 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name CE or name NZ )) or (resid 108 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name OE2)) or (resid 109 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2)) or (resid 110 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name OD2)) or (resid 111 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ )) or (resi \ d 112 through 113 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2)) or (resid 114 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD or name OE1 or name NE2)) or (resid 115 t \ hrough 116 and (name N or name CA or name C or name O )) or (resid 117 and (name \ N or name CA or name C or name O or name CB or name CG1 or name CG2 or name CD1 \ )) or (resid 118 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name OE1 or name OE2)) or (resid 119 and (name N or name CA or n \ ame C or name O or name CB or name OG1 or name CG2)) or (resid 120 and (name N o \ r name CA or name C or name O )) or (resid 121 and (name N or name CA or name C \ or name O or name CB or name OG )) or (resid 122 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 123 and ( \ name N or name CA or name C or name O or name CB or name OG1 or name CG2)) or (r \ esid 124 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name OE1 or name OE2)) or (resid 125 and (name N or name CA or name C or \ name O or name CB or name CG or name SD or name CE )) or (resid 126 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name CE1 or name CE2 or name CZ )) or (resid 127 and (name N or name CA or name \ C or name O )) or (resid 128 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name OE1 or name OE2)) or (resid 129 and (name N or \ name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or na \ me CE1 or name CE2 or name CZ )) or (resid 130 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 131 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2)) or (resid 132 and (name N or name CA or name C or name \ O )) or (resid 133 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name CE or name NZ )) or (resid 134 and (name N or name CA or \ name C or name O or name CB or name OG1 or name CG2)) or (resid 135 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name OE1 or n \ ame NE2)) or (resid 136 and (name N or name CA or name C or name O or name CB or \ name CG1 or name CG2 or name CD1)) or (resid 137 and (name N or name CA or name \ C or name O or name CB or name SG )) or (resid 138 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2)) or (resid 139 and (name N or name CA or name C or name O or name CB or na \ me OG1 or name CG2)) or (resid 140 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CD2)) or (resid 141 and (name N or name \ CA or name C or name O or name CB )) or (resid 142 and (name N or name CA or nam \ e C or name O or name CB or name CG1 or name CG2)) or (resid 143 and (name N or \ name CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 144 a \ nd (name N or name CA or name C or name O or name CB or name SG )) or (resid 145 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name OE1 or name NE2)) or (resid 146 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2)) or (resid 147 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD )) or (resid 148 and ( \ name N or name CA or name C or name O or name CB or name CG1 or name CG2 or name \ CD1)) or (resid 149 and (name N or name CA or name C or name O or name CB or na \ me CG or name OD1 or name OD2)) or (resid 150 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or n \ ame NH2)) or (resid 151 through 153 and (name N or name CA or name C or name O ) \ ) or (resid 154 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name OE2)) or (resid 155 and (name N or name CA or na \ me C or name O )) or (resid 156 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name CE or name NZ )) or (resid 157 and (name N o \ r name CA or name C or name O or name CB )) or (resid 158 and (name N or name CA \ or name C or name O or name CB or name CG or name SD or name CE )) or (resid 15 \ 9 and (name N or name CA or name C or name O or name CB or name CG or name CD1 o \ r name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 160 and (n \ ame N or name CA or name C or name O or name CB or name CG1 or name CG2 or name \ CD1)) or (resid 161 and (name N or name CA or name C or name O or name CB or nam \ e CG or name OD1 or name OD2)) or (resid 162 and (name N or name CA or name C or \ name O or name CB or name OG1 or name CG2)) or (resid 163 and (name N or name C \ A or name C or name O or name CB or name CG or name CD or name OE1 or name OE2)) \ or (resid 164 and (name N or name CA or name C or name O )) or (resid 165 and ( \ name N or name CA or name C or name O or name CB or name OG1 or name CG2)) or (r \ esid 166 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 167 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name NE or \ name CZ or name NH1 or name NH2)) or (resid 168 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )) or (resid 169 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name OE1 or name OE2 \ )) or (resid 170 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 171 throu \ gh 172 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or (resid 173 and (name N or name CA or name C or name O or na \ me CB )) or (resid 174 and (name N or name CA or name C or name O or name CB or \ name CG1 or name CG2)) or (resid 175 and (name N or name CA or name C or name O \ or name CB )) or (resid 176 and (name N or name CA or name C or name O or name C \ B or name CG or name CD or name OE1 or name OE2)) or (resid 177 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name NE or name C \ Z or name NH1 or name NH2)) or (resid 178 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or na \ me CZ or name OH )) or (resid 179 and (name N or name CA or name C or name O )) \ or (resid 180 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD1 or name CD2)) or (resid 181 and (name N or name CA or name C or name \ O or name CB or name OG )) or (resid 182 and (name N or name CA or name C or nam \ e O )) or (resid 183 and (name N or name CA or name C or name O or name CB or na \ me OG )) or (resid 184 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name OD2)) or (resid 185 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2)) or (resid 186 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or (res \ id 187 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name OD2)) or (resid 188 and (name N or name CA or name C or name O or na \ me CB or name CG or name OD1 or name ND2)) or (resid 189 and (name N or name CA \ or name C or name O or name CB or name CG1 or name CG2)) or (resid 190 and (name \ N or name CA or name C or name O or name CB )) or (resid 191 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name C \ E1 or name CE2 or name CZ or name OH )) or (resid 192 and (name N or name CA or \ name C or name O or name CB )) or (resid 193 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or na \ me NH2)) or (resid 194 and (name N or name CA or name C or name O or name CB )) \ or (resid 195 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 196 and ( \ name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2)) or (resid 197 and (name N or name CA or name C or name O or name CB or nam \ e OG1 or name CG2)) or (resid 198 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name OD2)) or (resid 199 and (name N or name C \ A or name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 \ or name NE2)) or (resid 200 and (name N or name CA or name C or name O or name C \ B or name CG or name CD or name OE1 or name NE2)) or (resid 201 and (name N or n \ ame CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 202 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ e OE1 or name NE2)) or (resid 203 through 204 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD1 or name CD2)) or (resid 205 and (name \ N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ or name CE1 or name CE2 or name CZ or name OH )) or (resid 206 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD or name OE1 or name N \ E2)) or (resid 207 and (name N or name CA or name C or name O or name CB )) or ( \ resid 208 and (name N or name CA or name C or name O or name CB or name OG )) or \ (resid 209 and (name N or name CA or name C or name O or name CB )) or (resid 2 \ 10 through 211 and (name N or name CA or name C or name O or name CB or name CG \ or name SD or name CE )) or (resid 212 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2)) or (resid 213 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (r \ esid 214 and (name N or name CA or name C or name O or name CB or name OG )) or \ (resid 215 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name NE or name CZ or name NH1 or name NH2)) or (resid 216 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name CE1 or name CE2 or name CZ or name OH )) or (resid 217 and (name N or name \ CA or name C or name O or name CB )) or (resid 218 through 219 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or (r \ esid 220 and (name N or name CA or name C or name O or name CB or name CG1 or na \ me CG2 or name CD1)) or (resid 221 and (name N or name CA or name C or name O or \ name CB or name CG1 or name CG2)) or (resid 222 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2)) or (resid 223 and (n \ ame N or name CA or name C or name O or name CB or name OG )) or (resid 224 and \ (name N or name CA or name C or name O or name CB )) or (resid 225 and (name N o \ r name CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 226 \ and (name N or name CA or name C or name O or name CB )) or (resid 227 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ )) or (resid 228 and (name N or name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (r \ esid 229 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name NE or name CZ or name NH1 or name NH2)) or (resid 238 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or \ (resid 239 and (name N or name CA or name C or name O or name CB or name OG )) \ or (resid 240 and (name N or name CA or name C or name O or name CB )) or (resid \ 241 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name NE or name CZ or name NH1 or name NH2)) or (resid 242 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD or name OE1 or name N \ E2)) or (resid 243 and (name N or name CA or name C or name O or name CB or name \ CG or name SD or name CE )) or (resid 244 and (name N or name CA or name C or n \ ame O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2)) or \ (resid 245 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2)) or (resid 246 and (name N or name CA or name C or name O \ or name CB )) or (resid 247 and (name N or name CA or name C or name O or name C \ B or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resi \ d 248 and (name N or name CA or name C or name O or name CB or name CG or name C \ D1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 249 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or \ (resid 250 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 251 and (name \ N or name CA or name C or name O or name CB or name CG or name SD or name CE )) \ or (resid 252 through 253 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2)) or (resid 254 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)) or (resid 255 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2)) or (resid 256 and (name N or name CA or \ name C or name O or name CB )) or (resid 257 and (name N or name CA or name C or \ name O or name CB or name CG or name OD1 or name OD2)) or (resid 258 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name OE1 or \ name OE2)) or (resid 259 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (res \ id 260 and (name N or name CA or name C or name O )) or (resid 261 and (name N o \ r name CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 262 \ and (name N or name CA or name C or name O or name CB )) or (resid 263 through \ 264 and (name N or name CA or name C or name O or name CB or name CG1 or name CG \ 2)) or (resid 265 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1)) or (resid 266 and (name N or name CA or name C or \ name O or name CB or name OG1 or name CG2)) or (resid 267 and (name N or name CA \ or name C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 2 \ 68 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name OE1 or name NE2)) or (resid 287 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1)) or (resid 288 through 289 and \ (name N or name CA or name C or name O )) or (resid 290 and (name N or name CA \ or name C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 29 \ 1 through 292 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2 or name CD1)) or (resid 293 and (name N or name CA or name C or name \ O or name CB )) or (resid 294 and (name N or name CA or name C or name O or nam \ e CB or name CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 295 \ and (name N or name CA or name C or name O or name CB )) or (resid 296 and (name \ N or name CA or name C or name O or name CB or name OG )) or (resid 297 through \ 298 and (name N or name CA or name C or name O or name CB or name OG1 or name C \ G2)) or (resid 299 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 300 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or nam \ e CD2)) or (resid 301 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) \ or (resid 302 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD1 or name CD2)) or (resid 303 through 310 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)) or (resid 311 and (name N or name CA or name C or name O or name \ CB or name CG1 or name CG2 or name CD1)) or (resid 312 and (name N or name CA or \ name C or name O or name CB or name SG )) or (resid 313 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name CE or name NZ )) or \ (resid 314 and (name N or name CA or name C or name O or name CB or name CG1 or \ name CG2 or name CD1)) or (resid 315 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name C \ Z or name OH )) or (resid 316 and (name N or name CA or name C or name O or name \ CB or name CG or name OD1 or name OD2)) or (resid 317 and (name N or name CA or \ name C or name O or name CB or name OG )) or (resid 318 and (name N or name CA \ or name C or name O or name CB or name CG or name CD )) or (resid 319 and (name \ N or name CA or name C or name O or name CB or name SG )) or (resid 320 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ )) or (resid 321 and (name N or name CA or name C or name O or name CB or name C \ G or name CD )) or (resid 322 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name OE1 or name OE2)) or (resid 323 and (name N or \ name CA or name C or name O or name CB )) or (resid 324 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name OE1 or name OE2)) o \ r (resid 325 and (name N or name CA or name C or name O or name CB )) or (resid \ 326 and (name N or name CA or name C or name O or name CB or name CG or name SD \ or name CE )) or (resid 327 and (name N or name CA or name C or name O or name C \ B or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (r \ esid 328 and (name N or name CA or name C or name O or name CB )) or (resid 329 \ and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or \ name CD1)) or (resid 330 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2)) or (resid 331 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 332 and (name N or name CA or name C or na \ me O or name CB or name CG or name OD1 or name OD2)) or (resid 333 and (name N o \ r name CA or name C or name O )) or (resid 334 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2)) or (resid 335 and (name N or name \ CA or name C or name O )) or (resid 336 and (name N or name CA or name C or nam \ e O or name CB or name CG or name OD1 or name OD2)))) } 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: 6.800 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: 0.140 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.770 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 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 0.034 14391 Z= 0.104 Angle : 0.514 13.655 19516 Z= 0.254 Chirality : 0.054 1.690 2280 Planarity : 0.003 0.038 2439 Dihedral : 10.880 125.294 5434 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.78 % Favored : 98.17 % Rotamer: Outliers : 0.60 % Allowed : 2.54 % Favored : 96.86 % 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: 1.88 (0.21), residues: 1744 helix: 2.57 (0.19), residues: 806 sheet: 0.22 (0.30), residues: 307 loop : 0.10 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 130 TYR 0.007 0.001 TYR X 187 PHE 0.007 0.001 PHE I 248 TRP 0.004 0.001 TRP X 231 HIS 0.003 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00215 (14391) covalent geometry : angle 0.51392 (19516) hydrogen bonds : bond 0.16636 ( 743) hydrogen bonds : angle 6.60218 ( 2133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 407 time to evaluate : 0.794 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: 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 32 PHE cc_start: 0.8534 (m-80) cc_final: 0.8317 (m-80) REVERT: C 54 LYS cc_start: 0.8229 (mttt) cc_final: 0.7984 (tppt) REVERT: C 62 GLN cc_start: 0.8133 (mt0) cc_final: 0.7915 (mt0) REVERT: C 101 ILE cc_start: 0.8037 (mt) cc_final: 0.7746 (pt) REVERT: C 110 ILE cc_start: 0.8328 (mt) cc_final: 0.8052 (OUTLIER) REVERT: C 194 LYS cc_start: 0.8828 (tttt) cc_final: 0.8432 (tppp) REVERT: C 277 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7845 (mtm110) REVERT: C 303 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7543 (pt0) REVERT: C 319 ARG cc_start: 0.8355 (mtt180) cc_final: 0.8121 (mmp-170) REVERT: D 1 MET cc_start: 0.1708 (mtt) cc_final: 0.1274 (ptt) REVERT: D 43 CYS cc_start: 0.8253 (m) cc_final: 0.7366 (m) REVERT: D 123 ASN cc_start: 0.8581 (t0) cc_final: 0.8284 (t160) REVERT: D 138 ASN cc_start: 0.8598 (m-40) cc_final: 0.8350 (m-40) REVERT: G 29 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7845 (mm-30) REVERT: G 58 LYS cc_start: 0.8331 (ttmt) cc_final: 0.8125 (mmtt) REVERT: G 59 GLU cc_start: 0.7498 (mt-10) cc_final: 0.6611 (mm-30) REVERT: G 81 LEU cc_start: 0.8357 (mt) cc_final: 0.8110 (mt) REVERT: G 118 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7154 (mm-30) REVERT: G 200 GLN cc_start: 0.8499 (tt0) cc_final: 0.8278 (tt0) REVERT: I 47 HIS cc_start: 0.7478 (m-70) cc_final: 0.7152 (m90) REVERT: I 88 THR cc_start: 0.8688 (p) cc_final: 0.8399 (t) REVERT: I 156 LYS cc_start: 0.7947 (mttt) cc_final: 0.7654 (mtpt) REVERT: I 199 HIS cc_start: 0.8085 (t-170) cc_final: 0.7655 (t-170) REVERT: I 253 LEU cc_start: 0.9240 (tp) cc_final: 0.8892 (tp) REVERT: R 192 GLU cc_start: 0.8229 (tt0) cc_final: 0.7928 (tm-30) REVERT: R 213 ASP cc_start: 0.8764 (t70) cc_final: 0.8561 (t0) REVERT: R 244 GLU cc_start: 0.7821 (tt0) cc_final: 0.7619 (mt-10) REVERT: R 297 LEU cc_start: 0.8760 (tp) cc_final: 0.8552 (tm) REVERT: R 316 ARG cc_start: 0.7731 (ttm170) cc_final: 0.7468 (ttm110) REVERT: R 335 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7582 (mp0) REVERT: X 24 LEU cc_start: 0.7995 (mt) cc_final: 0.7613 (mt) REVERT: X 64 ARG cc_start: 0.8063 (ttt180) cc_final: 0.7767 (mtp85) REVERT: X 102 GLN cc_start: 0.8925 (mt0) cc_final: 0.8331 (tp-100) REVERT: X 229 LYS cc_start: 0.8551 (mttt) cc_final: 0.7881 (mmmt) REVERT: X 236 LYS cc_start: 0.8214 (mttt) cc_final: 0.7532 (mmpt) REVERT: X 258 ARG cc_start: 0.7961 (ttt180) cc_final: 0.7652 (ttm-80) outliers start: 9 outliers final: 5 residues processed: 411 average time/residue: 1.4684 time to fit residues: 650.4239 Evaluate side-chains 224 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 220 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain X residue 39 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 233 HIS C 267 GLN C 294 GLN C 340 GLN G 36 ASN G 62 ASN G 188 ASN G 294 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.116900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.080561 restraints weight = 64473.229| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.84 r_work: 0.2953 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14391 Z= 0.191 Angle : 0.580 6.106 19516 Z= 0.296 Chirality : 0.041 0.166 2280 Planarity : 0.004 0.039 2439 Dihedral : 11.166 123.641 2139 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.64 % Favored : 97.31 % Rotamer: Outliers : 1.80 % Allowed : 13.96 % Favored : 84.24 % 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: 1.31 (0.21), residues: 1744 helix: 2.04 (0.18), residues: 838 sheet: -0.15 (0.28), residues: 311 loop : -0.17 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 193 TYR 0.016 0.001 TYR I 191 PHE 0.020 0.001 PHE X 270 TRP 0.007 0.001 TRP R 47 HIS 0.007 0.001 HIS I 138 Details of bonding type rmsd covalent geometry : bond 0.00434 (14391) covalent geometry : angle 0.58000 (19516) hydrogen bonds : bond 0.04135 ( 743) hydrogen bonds : angle 5.06197 ( 2133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 0.724 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: symmetry clash REVERT: C 101 ILE cc_start: 0.8174 (mt) cc_final: 0.7918 (pt) REVERT: C 110 ILE cc_start: 0.8442 (mt) cc_final: 0.8178 (mp) REVERT: C 194 LYS cc_start: 0.8771 (tttt) cc_final: 0.8530 (tppt) REVERT: C 277 ARG cc_start: 0.8534 (mtt180) cc_final: 0.8094 (mtm110) REVERT: C 303 GLU cc_start: 0.8499 (mm-30) cc_final: 0.7700 (pt0) REVERT: C 319 ARG cc_start: 0.8706 (mtt180) cc_final: 0.8359 (mmp-170) REVERT: D 1 MET cc_start: 0.2119 (mtt) cc_final: 0.1409 (ptt) REVERT: D 292 MET cc_start: 0.8105 (tpp) cc_final: 0.7897 (tpp) REVERT: G 29 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7756 (mm-30) REVERT: G 118 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7327 (mm-30) REVERT: G 176 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8954 (mm-30) REVERT: G 200 GLN cc_start: 0.8715 (tt0) cc_final: 0.8444 (tt0) REVERT: I 166 PHE cc_start: 0.7677 (p90) cc_final: 0.7437 (p90) REVERT: I 253 LEU cc_start: 0.9182 (tp) cc_final: 0.8978 (tp) REVERT: I 254 ARG cc_start: 0.9068 (ttm170) cc_final: 0.8697 (tpp80) REVERT: I 313 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7928 (tttt) REVERT: R 22 LYS cc_start: 0.8693 (mttt) cc_final: 0.8396 (mppt) REVERT: R 192 GLU cc_start: 0.8483 (tt0) cc_final: 0.8135 (tm-30) REVERT: R 244 GLU cc_start: 0.8080 (tt0) cc_final: 0.7772 (tp30) REVERT: R 316 ARG cc_start: 0.8064 (ttm170) cc_final: 0.7809 (ttm110) REVERT: X 24 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7599 (mt) REVERT: X 102 GLN cc_start: 0.9039 (mt0) cc_final: 0.8417 (tp-100) REVERT: X 236 LYS cc_start: 0.8588 (mttt) cc_final: 0.7959 (mmpt) outliers start: 27 outliers final: 13 residues processed: 236 average time/residue: 1.2782 time to fit residues: 328.3909 Evaluate side-chains 197 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain G residue 34 ASN Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 250 ARG Chi-restraints excluded: chain I residue 313 LYS Chi-restraints excluded: chain R residue 345 SER Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 106 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 112 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 140 optimal weight: 0.0980 chunk 65 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 36 ASN G 135 GLN G 244 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.113345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.077367 restraints weight = 65446.814| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.73 r_work: 0.2872 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14391 Z= 0.227 Angle : 0.578 7.005 19516 Z= 0.294 Chirality : 0.042 0.175 2280 Planarity : 0.004 0.059 2439 Dihedral : 10.966 118.641 2139 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.64 % Favored : 97.31 % Rotamer: Outliers : 2.07 % Allowed : 15.30 % Favored : 82.63 % 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: 0.93 (0.20), residues: 1744 helix: 1.82 (0.18), residues: 839 sheet: -0.57 (0.27), residues: 309 loop : -0.37 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 65 TYR 0.012 0.001 TYR G 301 PHE 0.015 0.001 PHE G 92 TRP 0.008 0.001 TRP R 47 HIS 0.012 0.001 HIS I 138 Details of bonding type rmsd covalent geometry : bond 0.00519 (14391) covalent geometry : angle 0.57756 (19516) hydrogen bonds : bond 0.03849 ( 743) hydrogen bonds : angle 4.81042 ( 2133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.644 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 84 LYS cc_start: 0.7732 (mtpt) cc_final: 0.7486 (tmmm) REVERT: C 101 ILE cc_start: 0.8274 (mt) cc_final: 0.8027 (pt) REVERT: C 110 ILE cc_start: 0.8522 (mt) cc_final: 0.8249 (mp) REVERT: C 193 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7512 (tmm-80) REVERT: C 194 LYS cc_start: 0.8864 (tttt) cc_final: 0.8610 (tppt) REVERT: C 277 ARG cc_start: 0.8588 (mtt180) cc_final: 0.8129 (mtm110) REVERT: C 303 GLU cc_start: 0.8580 (mm-30) cc_final: 0.7721 (pt0) REVERT: C 319 ARG cc_start: 0.8718 (mtt180) cc_final: 0.8358 (mmp-170) REVERT: D 19 LEU cc_start: 0.9225 (mt) cc_final: 0.9007 (mt) REVERT: D 23 HIS cc_start: 0.8598 (m-70) cc_final: 0.7973 (m-70) REVERT: G 29 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7713 (mm-30) REVERT: G 118 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7725 (mp0) REVERT: G 176 GLU cc_start: 0.9284 (OUTLIER) cc_final: 0.9055 (mm-30) REVERT: G 243 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7582 (tpt) REVERT: I 247 ARG cc_start: 0.8917 (mmm160) cc_final: 0.8625 (mmm160) REVERT: I 248 PHE cc_start: 0.8788 (t80) cc_final: 0.8579 (t80) REVERT: I 254 ARG cc_start: 0.8939 (ttm170) cc_final: 0.8663 (tpp80) REVERT: I 313 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8077 (tttt) REVERT: R 22 LYS cc_start: 0.8881 (mttt) cc_final: 0.8595 (mtpt) REVERT: R 192 GLU cc_start: 0.8544 (tt0) cc_final: 0.8306 (tm-30) REVERT: R 244 GLU cc_start: 0.8344 (tt0) cc_final: 0.8123 (tp30) REVERT: R 316 ARG cc_start: 0.8318 (ttm170) cc_final: 0.8071 (ttm110) REVERT: X 102 GLN cc_start: 0.9046 (mt0) cc_final: 0.8461 (tp-100) REVERT: X 236 LYS cc_start: 0.8715 (mttt) cc_final: 0.8287 (mmtm) outliers start: 31 outliers final: 19 residues processed: 205 average time/residue: 1.2644 time to fit residues: 282.6826 Evaluate side-chains 186 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 250 ARG Chi-restraints excluded: chain I residue 313 LYS Chi-restraints excluded: chain R residue 345 SER Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 106 GLU Chi-restraints excluded: chain X residue 275 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 23 HIS D 138 ASN D 301 GLN G 36 ASN G 200 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.114300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.078787 restraints weight = 64995.821| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.69 r_work: 0.2910 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14391 Z= 0.155 Angle : 0.537 8.061 19516 Z= 0.270 Chirality : 0.040 0.145 2280 Planarity : 0.004 0.042 2439 Dihedral : 10.581 117.456 2133 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.64 % Favored : 97.31 % Rotamer: Outliers : 2.34 % Allowed : 14.90 % Favored : 82.77 % 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: 1.04 (0.21), residues: 1744 helix: 1.96 (0.18), residues: 839 sheet: -0.66 (0.28), residues: 308 loop : -0.32 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 128 TYR 0.011 0.001 TYR G 301 PHE 0.027 0.001 PHE I 166 TRP 0.007 0.001 TRP D 268 HIS 0.021 0.001 HIS I 138 Details of bonding type rmsd covalent geometry : bond 0.00355 (14391) covalent geometry : angle 0.53677 (19516) hydrogen bonds : bond 0.03213 ( 743) hydrogen bonds : angle 4.57301 ( 2133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.726 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 84 LYS cc_start: 0.7716 (mtpt) cc_final: 0.7500 (tmmm) REVERT: C 101 ILE cc_start: 0.8236 (mt) cc_final: 0.7958 (pt) REVERT: C 110 ILE cc_start: 0.8537 (mt) cc_final: 0.8283 (mp) REVERT: C 194 LYS cc_start: 0.8882 (tttt) cc_final: 0.8627 (tppt) REVERT: C 216 TYR cc_start: 0.9135 (p90) cc_final: 0.8767 (p90) REVERT: C 277 ARG cc_start: 0.8579 (mtt180) cc_final: 0.8072 (mtm110) REVERT: C 303 GLU cc_start: 0.8537 (mm-30) cc_final: 0.7769 (pt0) REVERT: C 319 ARG cc_start: 0.8699 (mtt180) cc_final: 0.8334 (mmp-170) REVERT: D 221 ARG cc_start: 0.7998 (mpt-90) cc_final: 0.7639 (mtm180) REVERT: G 29 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7694 (mm-30) REVERT: G 59 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7730 (pp20) REVERT: G 118 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7692 (mp0) REVERT: G 176 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.9085 (mm-30) REVERT: G 232 TYR cc_start: 0.8395 (m-80) cc_final: 0.8184 (m-80) REVERT: G 243 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7589 (tpt) REVERT: I 247 ARG cc_start: 0.8887 (mmm160) cc_final: 0.8600 (mmm160) REVERT: I 254 ARG cc_start: 0.8944 (ttm170) cc_final: 0.8631 (tpp80) REVERT: I 313 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8076 (tttt) REVERT: I 315 TYR cc_start: 0.8470 (t80) cc_final: 0.8105 (t80) REVERT: R 22 LYS cc_start: 0.8968 (mttt) cc_final: 0.8599 (mtpt) REVERT: R 192 GLU cc_start: 0.8523 (tt0) cc_final: 0.8303 (tm-30) REVERT: R 244 GLU cc_start: 0.8295 (tt0) cc_final: 0.8058 (tp30) REVERT: R 316 ARG cc_start: 0.8276 (ttm170) cc_final: 0.8029 (ttm110) REVERT: X 28 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7766 (tm-30) REVERT: X 102 GLN cc_start: 0.9025 (mt0) cc_final: 0.8469 (tp-100) REVERT: X 229 LYS cc_start: 0.8373 (mttt) cc_final: 0.7983 (mmmt) REVERT: X 236 LYS cc_start: 0.8728 (mttt) cc_final: 0.8250 (mmtm) outliers start: 35 outliers final: 16 residues processed: 200 average time/residue: 1.3308 time to fit residues: 289.1828 Evaluate side-chains 191 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 250 ARG Chi-restraints excluded: chain I residue 313 LYS Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 345 SER Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 155 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN D 301 GLN G 36 ASN G 62 ASN X 263 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.113819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.078540 restraints weight = 65476.828| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.68 r_work: 0.2898 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14391 Z= 0.173 Angle : 0.541 7.982 19516 Z= 0.273 Chirality : 0.040 0.144 2280 Planarity : 0.004 0.067 2439 Dihedral : 10.508 115.400 2133 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.69 % Favored : 97.25 % Rotamer: Outliers : 1.94 % Allowed : 16.30 % Favored : 81.76 % 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: 1.03 (0.21), residues: 1744 helix: 1.97 (0.18), residues: 841 sheet: -0.63 (0.28), residues: 316 loop : -0.36 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 193 TYR 0.011 0.001 TYR G 301 PHE 0.016 0.001 PHE I 166 TRP 0.007 0.001 TRP R 47 HIS 0.005 0.001 HIS I 138 Details of bonding type rmsd covalent geometry : bond 0.00396 (14391) covalent geometry : angle 0.54063 (19516) hydrogen bonds : bond 0.03207 ( 743) hydrogen bonds : angle 4.53884 ( 2133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 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: 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 84 LYS cc_start: 0.7706 (mtpt) cc_final: 0.7494 (tmmm) REVERT: C 101 ILE cc_start: 0.8273 (mt) cc_final: 0.8001 (pt) REVERT: C 110 ILE cc_start: 0.8567 (mt) cc_final: 0.8322 (mp) REVERT: C 182 LEU cc_start: 0.8740 (mm) cc_final: 0.8516 (tt) REVERT: C 193 ARG cc_start: 0.7899 (mtm110) cc_final: 0.7509 (tmm-80) REVERT: C 194 LYS cc_start: 0.8875 (tttt) cc_final: 0.8651 (tppt) REVERT: C 216 TYR cc_start: 0.9136 (p90) cc_final: 0.8766 (p90) REVERT: C 277 ARG cc_start: 0.8581 (mtt180) cc_final: 0.8129 (mtm110) REVERT: C 303 GLU cc_start: 0.8542 (mm-30) cc_final: 0.7762 (pt0) REVERT: C 319 ARG cc_start: 0.8714 (mtt180) cc_final: 0.8357 (mmp-170) REVERT: D 221 ARG cc_start: 0.8021 (mpt-90) cc_final: 0.7630 (mtm180) REVERT: G 29 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7668 (mm-30) REVERT: G 59 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7769 (pp20) REVERT: G 118 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7885 (mt-10) REVERT: G 232 TYR cc_start: 0.8418 (m-80) cc_final: 0.8212 (m-80) REVERT: G 243 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7529 (tpt) REVERT: I 125 MET cc_start: 0.8387 (mtm) cc_final: 0.8083 (mtm) REVERT: I 247 ARG cc_start: 0.8848 (mmm160) cc_final: 0.8543 (mmm160) REVERT: I 313 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8144 (tttt) REVERT: I 315 TYR cc_start: 0.8489 (t80) cc_final: 0.8142 (t80) REVERT: R 22 LYS cc_start: 0.8963 (mttt) cc_final: 0.8583 (mtpt) REVERT: R 128 ARG cc_start: 0.8658 (ttm110) cc_final: 0.8385 (ttt-90) REVERT: R 192 GLU cc_start: 0.8516 (tt0) cc_final: 0.8313 (tm-30) REVERT: R 244 GLU cc_start: 0.8318 (tt0) cc_final: 0.8087 (tp30) REVERT: R 316 ARG cc_start: 0.8298 (ttm170) cc_final: 0.8053 (ttm110) REVERT: X 28 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7828 (tm-30) REVERT: X 102 GLN cc_start: 0.9052 (mt0) cc_final: 0.8528 (tp-100) REVERT: X 229 LYS cc_start: 0.8481 (mttt) cc_final: 0.8092 (mmmt) REVERT: X 236 LYS cc_start: 0.8655 (mttt) cc_final: 0.8182 (mmtm) REVERT: X 275 SER cc_start: 0.9326 (OUTLIER) cc_final: 0.9059 (t) outliers start: 29 outliers final: 18 residues processed: 199 average time/residue: 1.3320 time to fit residues: 287.7863 Evaluate side-chains 199 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 250 ARG Chi-restraints excluded: chain I residue 313 LYS Chi-restraints excluded: chain R residue 345 SER Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 106 GLU Chi-restraints excluded: chain X residue 275 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 ASN D 301 GLN G 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.113842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.078191 restraints weight = 65227.955| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.70 r_work: 0.2897 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14391 Z= 0.148 Angle : 0.534 8.281 19516 Z= 0.269 Chirality : 0.040 0.141 2280 Planarity : 0.004 0.043 2439 Dihedral : 10.395 113.952 2133 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.58 % Favored : 97.36 % Rotamer: Outliers : 1.74 % Allowed : 16.83 % Favored : 81.43 % 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: 1.06 (0.21), residues: 1744 helix: 2.00 (0.18), residues: 842 sheet: -0.63 (0.28), residues: 315 loop : -0.34 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 65 TYR 0.011 0.001 TYR I 178 PHE 0.015 0.001 PHE I 166 TRP 0.006 0.001 TRP R 47 HIS 0.006 0.001 HIS I 138 Details of bonding type rmsd covalent geometry : bond 0.00338 (14391) covalent geometry : angle 0.53408 (19516) hydrogen bonds : bond 0.03068 ( 743) hydrogen bonds : angle 4.44814 ( 2133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.692 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LYS cc_start: 0.7771 (mtpt) cc_final: 0.7544 (tmmm) REVERT: C 101 ILE cc_start: 0.8274 (mt) cc_final: 0.8007 (pt) REVERT: C 110 ILE cc_start: 0.8569 (mt) cc_final: 0.8323 (OUTLIER) REVERT: C 182 LEU cc_start: 0.8730 (mm) cc_final: 0.8516 (tt) REVERT: C 194 LYS cc_start: 0.8875 (tttt) cc_final: 0.8649 (tppt) REVERT: C 277 ARG cc_start: 0.8590 (mtt180) cc_final: 0.8076 (mtm110) REVERT: C 303 GLU cc_start: 0.8546 (mm-30) cc_final: 0.7785 (pt0) REVERT: C 319 ARG cc_start: 0.8736 (mtt180) cc_final: 0.8392 (mmp-170) REVERT: D 221 ARG cc_start: 0.8025 (mpt-90) cc_final: 0.7639 (mtm180) REVERT: D 292 MET cc_start: 0.8228 (tpp) cc_final: 0.7616 (mmt) REVERT: G 29 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7647 (mm-30) REVERT: G 59 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7763 (pp20) REVERT: G 118 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7893 (mt-10) REVERT: G 232 TYR cc_start: 0.8407 (m-80) cc_final: 0.8139 (m-80) REVERT: G 243 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7458 (tpt) REVERT: G 258 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7115 (mt-10) REVERT: I 125 MET cc_start: 0.8428 (mtm) cc_final: 0.8104 (mtm) REVERT: I 313 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8154 (tttt) REVERT: R 22 LYS cc_start: 0.8967 (mttt) cc_final: 0.8621 (mtpt) REVERT: R 244 GLU cc_start: 0.8270 (tt0) cc_final: 0.8042 (tp30) REVERT: R 316 ARG cc_start: 0.8307 (ttm170) cc_final: 0.8064 (ttm110) REVERT: X 28 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7820 (tm-30) REVERT: X 102 GLN cc_start: 0.9077 (mt0) cc_final: 0.8535 (tp-100) REVERT: X 229 LYS cc_start: 0.8484 (mttt) cc_final: 0.8089 (mmmt) REVERT: X 236 LYS cc_start: 0.8640 (mttt) cc_final: 0.8173 (mmtm) REVERT: X 243 LYS cc_start: 0.9045 (tttt) cc_final: 0.8798 (tttm) REVERT: X 275 SER cc_start: 0.9305 (OUTLIER) cc_final: 0.9042 (t) outliers start: 26 outliers final: 15 residues processed: 204 average time/residue: 1.3185 time to fit residues: 292.3496 Evaluate side-chains 195 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 250 ARG Chi-restraints excluded: chain I residue 313 LYS Chi-restraints excluded: chain R residue 345 SER Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 106 GLU Chi-restraints excluded: chain X residue 275 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 112 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 ASN D 301 GLN G 36 ASN X 263 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.112523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.076582 restraints weight = 65063.801| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.71 r_work: 0.2874 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14391 Z= 0.198 Angle : 0.556 8.277 19516 Z= 0.282 Chirality : 0.040 0.148 2280 Planarity : 0.004 0.067 2439 Dihedral : 10.483 111.140 2133 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.13 % Rotamer: Outliers : 2.14 % Allowed : 16.97 % Favored : 80.90 % 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: 0.99 (0.21), residues: 1744 helix: 1.94 (0.18), residues: 841 sheet: -0.63 (0.28), residues: 320 loop : -0.40 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 193 TYR 0.011 0.001 TYR G 301 PHE 0.031 0.001 PHE I 166 TRP 0.007 0.001 TRP R 47 HIS 0.007 0.001 HIS R 29 Details of bonding type rmsd covalent geometry : bond 0.00454 (14391) covalent geometry : angle 0.55578 (19516) hydrogen bonds : bond 0.03252 ( 743) hydrogen bonds : angle 4.53472 ( 2133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.725 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7512 (tmmm) REVERT: C 101 ILE cc_start: 0.8259 (mt) cc_final: 0.7996 (pt) REVERT: C 110 ILE cc_start: 0.8568 (mt) cc_final: 0.8329 (mp) REVERT: C 182 LEU cc_start: 0.8710 (mm) cc_final: 0.8500 (tt) REVERT: C 193 ARG cc_start: 0.7882 (mtm110) cc_final: 0.7485 (tmm-80) REVERT: C 277 ARG cc_start: 0.8559 (mtt180) cc_final: 0.8093 (mtm110) REVERT: C 303 GLU cc_start: 0.8550 (mm-30) cc_final: 0.7708 (pt0) REVERT: C 319 ARG cc_start: 0.8711 (mtt180) cc_final: 0.8350 (mmp-170) REVERT: D 91 LYS cc_start: 0.8935 (ttmm) cc_final: 0.8543 (ttpp) REVERT: D 221 ARG cc_start: 0.8024 (mpt-90) cc_final: 0.7625 (mtm180) REVERT: D 279 ASP cc_start: 0.8327 (t0) cc_final: 0.8108 (t0) REVERT: G 29 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7676 (mm-30) REVERT: G 59 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7777 (pp20) REVERT: G 118 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7869 (mt-10) REVERT: G 243 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7480 (tpt) REVERT: G 258 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7187 (mt-10) REVERT: I 125 MET cc_start: 0.8409 (mtm) cc_final: 0.7931 (mtm) REVERT: I 247 ARG cc_start: 0.8793 (mmm160) cc_final: 0.8456 (mtp85) REVERT: I 313 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8145 (tttt) REVERT: I 315 TYR cc_start: 0.8397 (t80) cc_final: 0.8063 (t80) REVERT: R 22 LYS cc_start: 0.8990 (mttt) cc_final: 0.8614 (mtpt) REVERT: R 108 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7196 (mtp180) REVERT: R 244 GLU cc_start: 0.8312 (tt0) cc_final: 0.8063 (tp30) REVERT: R 316 ARG cc_start: 0.8250 (ttm170) cc_final: 0.8007 (ttm110) REVERT: X 28 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7825 (tm-30) REVERT: X 102 GLN cc_start: 0.9077 (mt0) cc_final: 0.8540 (tp-100) REVERT: X 198 ILE cc_start: 0.8948 (mm) cc_final: 0.8747 (mt) REVERT: X 229 LYS cc_start: 0.8522 (mttt) cc_final: 0.8135 (mmmt) REVERT: X 236 LYS cc_start: 0.8617 (mttt) cc_final: 0.8154 (mmtm) REVERT: X 243 LYS cc_start: 0.9059 (tttt) cc_final: 0.8844 (tttm) REVERT: X 275 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.9022 (t) outliers start: 32 outliers final: 20 residues processed: 200 average time/residue: 1.2941 time to fit residues: 281.8016 Evaluate side-chains 195 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 250 ARG Chi-restraints excluded: chain I residue 313 LYS Chi-restraints excluded: chain R residue 108 ARG Chi-restraints excluded: chain R residue 345 SER Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 106 GLU Chi-restraints excluded: chain X residue 275 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 55 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 ASN D 301 GLN G 36 ASN G 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.113152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.077272 restraints weight = 64733.239| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.71 r_work: 0.2899 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14391 Z= 0.140 Angle : 0.537 8.212 19516 Z= 0.270 Chirality : 0.040 0.223 2280 Planarity : 0.004 0.053 2439 Dihedral : 10.359 109.867 2133 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.29 % Favored : 97.65 % Rotamer: Outliers : 2.00 % Allowed : 17.43 % Favored : 80.56 % 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: 1.07 (0.21), residues: 1744 helix: 2.03 (0.18), residues: 842 sheet: -0.64 (0.28), residues: 319 loop : -0.37 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 65 TYR 0.010 0.001 TYR G 301 PHE 0.025 0.001 PHE I 166 TRP 0.006 0.001 TRP D 268 HIS 0.008 0.001 HIS R 29 Details of bonding type rmsd covalent geometry : bond 0.00318 (14391) covalent geometry : angle 0.53671 (19516) hydrogen bonds : bond 0.03028 ( 743) hydrogen bonds : angle 4.40960 ( 2133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.728 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LYS cc_start: 0.7776 (mtpt) cc_final: 0.7536 (tmmm) REVERT: C 101 ILE cc_start: 0.8250 (mt) cc_final: 0.7983 (pt) REVERT: C 110 ILE cc_start: 0.8584 (mt) cc_final: 0.8355 (OUTLIER) REVERT: C 182 LEU cc_start: 0.8712 (mm) cc_final: 0.8509 (tt) REVERT: C 193 ARG cc_start: 0.7904 (mtm110) cc_final: 0.7488 (tmm-80) REVERT: C 277 ARG cc_start: 0.8566 (mtt180) cc_final: 0.8109 (mtm110) REVERT: C 303 GLU cc_start: 0.8548 (mm-30) cc_final: 0.7752 (pt0) REVERT: C 319 ARG cc_start: 0.8723 (mtt180) cc_final: 0.8409 (mmp-170) REVERT: D 221 ARG cc_start: 0.8022 (mpt-90) cc_final: 0.7630 (mtm180) REVERT: D 279 ASP cc_start: 0.8410 (t0) cc_final: 0.8173 (t0) REVERT: D 292 MET cc_start: 0.8211 (tpp) cc_final: 0.7572 (mmt) REVERT: G 29 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7682 (mm-30) REVERT: G 118 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7874 (mt-10) REVERT: G 243 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7371 (tpt) REVERT: G 258 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7145 (mt-10) REVERT: I 125 MET cc_start: 0.8438 (mtm) cc_final: 0.7958 (mtm) REVERT: I 247 ARG cc_start: 0.8779 (mmm160) cc_final: 0.8456 (mtp85) REVERT: R 22 LYS cc_start: 0.8992 (mttt) cc_final: 0.8619 (mtpt) REVERT: R 108 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7232 (mtp180) REVERT: R 244 GLU cc_start: 0.8257 (tt0) cc_final: 0.8019 (tp30) REVERT: R 316 ARG cc_start: 0.8267 (ttm170) cc_final: 0.8027 (ttm110) REVERT: X 28 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7809 (tm-30) REVERT: X 102 GLN cc_start: 0.9087 (mt0) cc_final: 0.8501 (tp-100) REVERT: X 198 ILE cc_start: 0.8937 (mm) cc_final: 0.8732 (mt) REVERT: X 229 LYS cc_start: 0.8529 (mttt) cc_final: 0.8178 (mmmt) REVERT: X 236 LYS cc_start: 0.8637 (mttt) cc_final: 0.8179 (mmtm) REVERT: X 275 SER cc_start: 0.9291 (OUTLIER) cc_final: 0.9041 (t) outliers start: 30 outliers final: 17 residues processed: 194 average time/residue: 1.3558 time to fit residues: 285.6963 Evaluate side-chains 184 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 250 ARG Chi-restraints excluded: chain R residue 108 ARG Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 275 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 89 optimal weight: 0.2980 chunk 175 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 116 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 ASN D 301 GLN G 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.114037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.078316 restraints weight = 64599.926| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.72 r_work: 0.2894 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14391 Z= 0.123 Angle : 0.533 8.054 19516 Z= 0.267 Chirality : 0.039 0.136 2280 Planarity : 0.004 0.056 2439 Dihedral : 10.228 108.913 2133 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.29 % Favored : 97.65 % Rotamer: Outliers : 1.60 % Allowed : 17.90 % Favored : 80.49 % 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: 1.17 (0.21), residues: 1744 helix: 2.10 (0.18), residues: 844 sheet: -0.64 (0.28), residues: 322 loop : -0.28 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 65 TYR 0.010 0.001 TYR G 301 PHE 0.024 0.001 PHE I 166 TRP 0.006 0.001 TRP R 47 HIS 0.007 0.001 HIS R 29 Details of bonding type rmsd covalent geometry : bond 0.00279 (14391) covalent geometry : angle 0.53310 (19516) hydrogen bonds : bond 0.02879 ( 743) hydrogen bonds : angle 4.33462 ( 2133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.637 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LYS cc_start: 0.7768 (mtpt) cc_final: 0.7548 (tmmm) REVERT: C 101 ILE cc_start: 0.8225 (mt) cc_final: 0.7962 (pt) REVERT: C 110 ILE cc_start: 0.8613 (mt) cc_final: 0.8388 (mp) REVERT: C 193 ARG cc_start: 0.7886 (mtm110) cc_final: 0.7482 (tmm-80) REVERT: C 216 TYR cc_start: 0.9094 (p90) cc_final: 0.8621 (p90) REVERT: C 277 ARG cc_start: 0.8564 (mtt180) cc_final: 0.8090 (mtm110) REVERT: C 303 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7757 (pt0) REVERT: C 319 ARG cc_start: 0.8725 (mtt180) cc_final: 0.8371 (mmp-170) REVERT: D 91 LYS cc_start: 0.8951 (ttmm) cc_final: 0.8558 (ttpp) REVERT: D 221 ARG cc_start: 0.8007 (mpt-90) cc_final: 0.7614 (mtm180) REVERT: D 279 ASP cc_start: 0.8419 (t0) cc_final: 0.8179 (t0) REVERT: D 292 MET cc_start: 0.8192 (tpp) cc_final: 0.7545 (mmt) REVERT: G 29 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7693 (mm-30) REVERT: G 118 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7853 (mt-10) REVERT: G 243 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7326 (tpt) REVERT: G 258 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7134 (mt-10) REVERT: I 125 MET cc_start: 0.8382 (mtm) cc_final: 0.7892 (mtm) REVERT: I 315 TYR cc_start: 0.8268 (t80) cc_final: 0.7863 (t80) REVERT: R 22 LYS cc_start: 0.8998 (mttt) cc_final: 0.8617 (mtpt) REVERT: R 108 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7204 (mtp180) REVERT: R 244 GLU cc_start: 0.8239 (tt0) cc_final: 0.7995 (tp30) REVERT: R 316 ARG cc_start: 0.8248 (ttm170) cc_final: 0.8013 (ttm110) REVERT: X 28 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7780 (tm-30) REVERT: X 102 GLN cc_start: 0.9105 (mt0) cc_final: 0.8515 (tp-100) REVERT: X 229 LYS cc_start: 0.8522 (mttt) cc_final: 0.8180 (mmmt) REVERT: X 236 LYS cc_start: 0.8632 (mttt) cc_final: 0.8139 (mmtm) REVERT: X 275 SER cc_start: 0.9283 (OUTLIER) cc_final: 0.8926 (t) outliers start: 24 outliers final: 15 residues processed: 187 average time/residue: 1.3187 time to fit residues: 268.8655 Evaluate side-chains 187 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 250 ARG Chi-restraints excluded: chain R residue 108 ARG Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 275 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 166 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 66 optimal weight: 0.0050 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 36 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 ASN D 301 GLN G 36 ASN G 135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.113650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.077893 restraints weight = 64497.819| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.72 r_work: 0.2910 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14391 Z= 0.125 Angle : 0.532 8.176 19516 Z= 0.266 Chirality : 0.039 0.150 2280 Planarity : 0.004 0.062 2439 Dihedral : 10.159 107.570 2133 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.18 % Favored : 97.76 % Rotamer: Outliers : 1.40 % Allowed : 18.17 % Favored : 80.43 % 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: 1.22 (0.21), residues: 1744 helix: 2.15 (0.18), residues: 844 sheet: -0.60 (0.28), residues: 322 loop : -0.28 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 65 TYR 0.016 0.001 TYR C 327 PHE 0.024 0.001 PHE I 166 TRP 0.006 0.001 TRP X 156 HIS 0.007 0.001 HIS R 29 Details of bonding type rmsd covalent geometry : bond 0.00285 (14391) covalent geometry : angle 0.53150 (19516) hydrogen bonds : bond 0.02857 ( 743) hydrogen bonds : angle 4.29853 ( 2133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.703 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LYS cc_start: 0.7778 (mtpt) cc_final: 0.7556 (tmmm) REVERT: C 101 ILE cc_start: 0.8234 (mt) cc_final: 0.7976 (pt) REVERT: C 110 ILE cc_start: 0.8609 (mt) cc_final: 0.8384 (mp) REVERT: C 193 ARG cc_start: 0.7892 (mtm110) cc_final: 0.7480 (tmm-80) REVERT: C 216 TYR cc_start: 0.9087 (p90) cc_final: 0.8581 (p90) REVERT: C 277 ARG cc_start: 0.8587 (mtt180) cc_final: 0.8117 (mtm110) REVERT: C 303 GLU cc_start: 0.8576 (mm-30) cc_final: 0.7815 (pt0) REVERT: C 319 ARG cc_start: 0.8714 (mtt180) cc_final: 0.8378 (mmp-170) REVERT: D 24 ARG cc_start: 0.8794 (mpp80) cc_final: 0.8164 (ptp90) REVERT: D 91 LYS cc_start: 0.8943 (ttmm) cc_final: 0.8541 (ttpp) REVERT: D 221 ARG cc_start: 0.8010 (mpt-90) cc_final: 0.7615 (mtm180) REVERT: D 279 ASP cc_start: 0.8414 (t0) cc_final: 0.8163 (t0) REVERT: D 292 MET cc_start: 0.8206 (tpp) cc_final: 0.7560 (mmt) REVERT: G 118 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7863 (mt-10) REVERT: G 243 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7339 (tpt) REVERT: G 258 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7133 (mt-10) REVERT: I 125 MET cc_start: 0.8396 (mtm) cc_final: 0.7813 (mtm) REVERT: R 22 LYS cc_start: 0.9026 (mttt) cc_final: 0.8640 (mtpt) REVERT: R 108 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7262 (mtp180) REVERT: R 244 GLU cc_start: 0.8248 (tt0) cc_final: 0.8005 (tp30) REVERT: R 316 ARG cc_start: 0.8278 (ttm170) cc_final: 0.8021 (ttm110) REVERT: X 28 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7783 (tm-30) REVERT: X 102 GLN cc_start: 0.9093 (mt0) cc_final: 0.8525 (tp-100) REVERT: X 229 LYS cc_start: 0.8542 (mttt) cc_final: 0.8200 (mmmt) REVERT: X 236 LYS cc_start: 0.8649 (mttt) cc_final: 0.8165 (mmtm) REVERT: X 275 SER cc_start: 0.9277 (OUTLIER) cc_final: 0.8950 (t) outliers start: 21 outliers final: 16 residues processed: 190 average time/residue: 1.2729 time to fit residues: 263.9746 Evaluate side-chains 186 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 250 ARG Chi-restraints excluded: chain R residue 13 ILE Chi-restraints excluded: chain R residue 108 ARG Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 275 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 169 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 172 optimal weight: 0.2980 chunk 63 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 ASN D 301 GLN G 36 ASN G 135 GLN I 294 HIS I 330 ASN X 167 ASN X 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.114374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.078775 restraints weight = 64336.417| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.71 r_work: 0.2917 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14391 Z= 0.118 Angle : 0.530 7.997 19516 Z= 0.264 Chirality : 0.039 0.145 2280 Planarity : 0.004 0.078 2439 Dihedral : 10.082 106.090 2133 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.95 % Favored : 97.99 % Rotamer: Outliers : 1.60 % Allowed : 18.17 % Favored : 80.23 % 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: 1.26 (0.21), residues: 1744 helix: 2.17 (0.18), residues: 844 sheet: -0.56 (0.28), residues: 322 loop : -0.26 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 65 TYR 0.016 0.001 TYR C 327 PHE 0.023 0.001 PHE I 166 TRP 0.005 0.001 TRP R 47 HIS 0.007 0.001 HIS R 29 Details of bonding type rmsd covalent geometry : bond 0.00270 (14391) covalent geometry : angle 0.52964 (19516) hydrogen bonds : bond 0.02767 ( 743) hydrogen bonds : angle 4.24942 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9888.19 seconds wall clock time: 167 minutes 33.90 seconds (10053.90 seconds total)