Starting phenix.real_space_refine on Wed Mar 4 12:48:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6q2s_20579/03_2026/6q2s_20579_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q2s_20579/03_2026/6q2s_20579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6q2s_20579/03_2026/6q2s_20579_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q2s_20579/03_2026/6q2s_20579_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6q2s_20579/03_2026/6q2s_20579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q2s_20579/03_2026/6q2s_20579.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 124 5.16 5 C 8558 2.51 5 N 2466 2.21 5 O 2570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13726 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 743 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 8, 'TRANS': 89} Chain: "C" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1527 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain: "E" Number of atoms: 4491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4491 Classifications: {'peptide': 570} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 535} Chain breaks: 5 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Unusual residues: {' CA': 4, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Restraints were copied for chains: B, D, F Time building chain proxies: 3.53, per 1000 atoms: 0.26 Number of scatterers: 13726 At special positions: 0 Unit cell: (133.75, 209.72, 75.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 124 16.00 O 2570 8.00 N 2466 7.00 C 8558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A 123 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 216 " distance=2.02 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 218 " distance=2.02 Simple disulfide: pdb=" SG CYS A 187 " - pdb=" SG CYS B 187 " distance=2.05 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 218 " distance=2.02 Simple disulfide: pdb=" SG CYS C 169 " - pdb=" SG CYS C 175 " distance=2.02 Simple disulfide: pdb=" SG CYS C 186 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 248 " - pdb=" SG CYS C 316 " distance=2.04 Simple disulfide: pdb=" SG CYS C 255 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS C 272 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 328 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 142 " distance=2.02 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 197 " distance=2.03 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 243 " distance=2.03 Simple disulfide: pdb=" SG CYS E 426 " - pdb=" SG CYS E 430 " distance=2.02 Simple disulfide: pdb=" SG CYS E 449 " - pdb=" SG CYS E 478 " distance=2.03 Simple disulfide: pdb=" SG CYS E 515 " - pdb=" SG CYS E 531 " distance=2.03 Simple disulfide: pdb=" SG CYS E 519 " - pdb=" SG CYS E 541 " distance=2.03 Simple disulfide: pdb=" SG CYS E 528 " - pdb=" SG CYS E 558 " distance=2.02 Simple disulfide: pdb=" SG CYS E 565 " - pdb=" SG CYS E 581 " distance=2.02 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 585 " distance=2.03 Simple disulfide: pdb=" SG CYS E 609 " - pdb=" SG CYS E 620 " distance=2.04 Simple disulfide: pdb=" SG CYS E 611 " - pdb=" SG CYS E 618 " distance=2.03 Simple disulfide: pdb=" SG CYS B 123 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 216 " distance=2.02 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 218 " distance=2.02 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 218 " distance=2.02 Simple disulfide: pdb=" SG CYS D 169 " - pdb=" SG CYS D 175 " distance=2.02 Simple disulfide: pdb=" SG CYS D 186 " - pdb=" SG CYS D 196 " distance=2.02 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 248 " - pdb=" SG CYS D 316 " distance=2.04 Simple disulfide: pdb=" SG CYS D 255 " - pdb=" SG CYS D 261 " distance=2.03 Simple disulfide: pdb=" SG CYS D 272 " - pdb=" SG CYS D 288 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 328 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS F 142 " distance=2.02 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS F 166 " - pdb=" SG CYS F 243 " distance=2.03 Simple disulfide: pdb=" SG CYS F 426 " - pdb=" SG CYS F 430 " distance=2.02 Simple disulfide: pdb=" SG CYS F 449 " - pdb=" SG CYS F 478 " distance=2.03 Simple disulfide: pdb=" SG CYS F 515 " - pdb=" SG CYS F 531 " distance=2.03 Simple disulfide: pdb=" SG CYS F 519 " - pdb=" SG CYS F 541 " distance=2.03 Simple disulfide: pdb=" SG CYS F 528 " - pdb=" SG CYS F 558 " distance=2.02 Simple disulfide: pdb=" SG CYS F 565 " - pdb=" SG CYS F 581 " distance=2.02 Simple disulfide: pdb=" SG CYS F 570 " - pdb=" SG CYS F 585 " distance=2.03 Simple disulfide: pdb=" SG CYS F 609 " - pdb=" SG CYS F 620 " distance=2.04 Simple disulfide: pdb=" SG CYS F 611 " - pdb=" SG CYS F 618 " distance=2.03 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 Links applied NAG-ASN " NAG C1100 " - " ASN C 309 " " NAG D1100 " - " ASN D 309 " " NAG E 701 " - " ASN E 336 " " NAG E 702 " - " ASN E 377 " " NAG E 703 " - " ASN E 394 " " NAG E 704 " - " ASN E 468 " " NAG E 705 " - " ASN E 98 " " NAG E 706 " - " ASN E 361 " " NAG F 701 " - " ASN F 336 " " NAG F 702 " - " ASN F 377 " " NAG F 703 " - " ASN F 394 " " NAG F 704 " - " ASN F 468 " " NAG F 705 " - " ASN F 98 " " NAG F 706 " - " ASN F 361 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 621.6 milliseconds 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3256 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 36 sheets defined 23.4% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 133 through 136 removed outlier: 3.742A pdb=" N GLY A 136 " --> pdb=" O ARG A 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 133 through 136' Processing helix chain 'A' and resid 159 through 169 removed outlier: 3.521A pdb=" N LEU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 171 removed outlier: 3.614A pdb=" N LYS C 164 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA C 166 " --> pdb=" O CYS C 162 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS C 169 " --> pdb=" O PHE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 184 removed outlier: 3.653A pdb=" N ASP C 176 " --> pdb=" O ASN C 172 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 206 removed outlier: 3.689A pdb=" N THR C 202 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 217 removed outlier: 3.600A pdb=" N GLY C 214 " --> pdb=" O PRO C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 removed outlier: 3.647A pdb=" N GLY C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG C 230 " --> pdb=" O GLY C 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG C 231 " --> pdb=" O CYS C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 249 through 258 removed outlier: 3.635A pdb=" N ASP C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 272 removed outlier: 3.592A pdb=" N ASP C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 268 " --> pdb=" O ARG C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 293 removed outlier: 3.981A pdb=" N ARG C 290 " --> pdb=" O SER C 286 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 325 through 337 removed outlier: 3.867A pdb=" N LEU C 331 " --> pdb=" O GLU C 327 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 356 removed outlier: 3.752A pdb=" N GLN C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE C 356 " --> pdb=" O HIS C 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 109 Processing helix chain 'E' and resid 156 through 160 removed outlier: 3.503A pdb=" N SER E 159 " --> pdb=" O ALA E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 167 removed outlier: 3.641A pdb=" N CYS E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE E 167 " --> pdb=" O ARG E 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 162 through 167' Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 309 through 314 removed outlier: 3.782A pdb=" N ARG E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 329 removed outlier: 3.873A pdb=" N GLN E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 522 removed outlier: 3.786A pdb=" N VAL E 521 " --> pdb=" O SER E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 530 removed outlier: 3.706A pdb=" N GLU E 529 " --> pdb=" O ARG E 525 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 525 through 530' Processing helix chain 'E' and resid 581 through 585 removed outlier: 3.786A pdb=" N ASP E 584 " --> pdb=" O CYS E 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 136 removed outlier: 3.742A pdb=" N GLY B 136 " --> pdb=" O ARG B 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 133 through 136' Processing helix chain 'B' and resid 159 through 169 removed outlier: 3.521A pdb=" N LEU B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 171 removed outlier: 3.613A pdb=" N LYS D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA D 166 " --> pdb=" O CYS D 162 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS D 169 " --> pdb=" O PHE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 184 removed outlier: 3.653A pdb=" N ASP D 176 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG D 177 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 206 removed outlier: 3.690A pdb=" N THR D 202 " --> pdb=" O ARG D 198 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 217 removed outlier: 3.600A pdb=" N GLY D 214 " --> pdb=" O PRO D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 removed outlier: 3.647A pdb=" N GLY D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG D 230 " --> pdb=" O GLY D 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG D 231 " --> pdb=" O CYS D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 241 Processing helix chain 'D' and resid 249 through 258 removed outlier: 3.635A pdb=" N ASP D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.592A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 293 removed outlier: 3.981A pdb=" N ARG D 290 " --> pdb=" O SER D 286 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 296 No H-bonds generated for 'chain 'D' and resid 294 through 296' Processing helix chain 'D' and resid 325 through 337 removed outlier: 3.866A pdb=" N LEU D 331 " --> pdb=" O GLU D 327 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 356 removed outlier: 3.752A pdb=" N GLN D 354 " --> pdb=" O ARG D 350 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE D 356 " --> pdb=" O HIS D 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 109 Processing helix chain 'F' and resid 156 through 160 removed outlier: 3.503A pdb=" N SER F 159 " --> pdb=" O ALA F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 removed outlier: 3.642A pdb=" N CYS F 166 " --> pdb=" O PRO F 162 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 162 through 167' Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 309 through 314 removed outlier: 3.782A pdb=" N ARG F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 329 removed outlier: 3.873A pdb=" N GLN F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 522 removed outlier: 3.786A pdb=" N VAL F 521 " --> pdb=" O SER F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 530 removed outlier: 3.707A pdb=" N GLU F 529 " --> pdb=" O ARG F 525 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU F 530 " --> pdb=" O LEU F 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 525 through 530' Processing helix chain 'F' and resid 581 through 585 removed outlier: 3.786A pdb=" N ASP F 584 " --> pdb=" O CYS F 581 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 125 removed outlier: 3.551A pdb=" N SER A 151 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 187 through 199 removed outlier: 6.959A pdb=" N CYS A 188 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N CYS A 218 " --> pdb=" O CYS A 188 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N CYS A 216 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG A 192 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL A 196 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG A 210 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE A 198 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL A 208 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 303 through 304 Processing sheet with id=AA5, first strand: chain 'E' and resid 30 through 31 removed outlier: 3.578A pdb=" N TYR E 30 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.515A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU E 40 " --> pdb=" O PHE E 150 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR E 152 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.515A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 48 through 52 removed outlier: 3.924A pdb=" N THR E 48 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU E 95 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 174 through 176 removed outlier: 3.576A pdb=" N THR E 261 " --> pdb=" O PHE E 174 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL E 256 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA E 241 " --> pdb=" O VAL E 256 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 184 through 187 removed outlier: 6.665A pdb=" N THR E 184 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N THR E 225 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS E 186 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 292 through 300 removed outlier: 4.064A pdb=" N ALA E 294 " --> pdb=" O LEU E 356 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP E 353 " --> pdb=" O TRP E 334 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP E 334 " --> pdb=" O ASP E 353 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 316 through 318 removed outlier: 3.734A pdb=" N VAL E 395 " --> pdb=" O MET E 370 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 407 through 413 removed outlier: 7.220A pdb=" N TYR E 408 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR E 503 " --> pdb=" O TYR E 408 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU E 410 " --> pdb=" O THR E 503 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLU E 505 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL E 412 " --> pdb=" O GLU E 505 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU E 500 " --> pdb=" O TYR E 483 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR E 483 " --> pdb=" O LEU E 500 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 407 through 413 removed outlier: 7.220A pdb=" N TYR E 408 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR E 503 " --> pdb=" O TYR E 408 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU E 410 " --> pdb=" O THR E 503 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLU E 505 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL E 412 " --> pdb=" O GLU E 505 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL E 502 " --> pdb=" O LEU E 481 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU E 481 " --> pdb=" O VAL E 502 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 421 through 425 removed outlier: 7.346A pdb=" N GLN E 421 " --> pdb=" O VAL E 467 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL E 467 " --> pdb=" O GLN E 421 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY E 423 " --> pdb=" O LEU E 465 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU E 465 " --> pdb=" O GLY E 423 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER E 462 " --> pdb=" O SER E 457 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 542 through 544 Processing sheet with id=AB8, first strand: chain 'E' and resid 551 through 552 removed outlier: 4.345A pdb=" N THR E 552 " --> pdb=" O GLY E 605 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY E 605 " --> pdb=" O THR E 552 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 589 through 591 removed outlier: 6.519A pdb=" N SER E 589 " --> pdb=" O CYS E 618 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N CYS E 620 " --> pdb=" O SER E 589 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL E 591 " --> pdb=" O CYS E 620 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 124 through 125 removed outlier: 3.552A pdb=" N SER B 151 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 128 through 131 Processing sheet with id=AC3, first strand: chain 'B' and resid 187 through 199 removed outlier: 6.959A pdb=" N CYS B 188 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N CYS B 218 " --> pdb=" O CYS B 188 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N CYS B 216 " --> pdb=" O PRO B 190 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG B 192 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL B 196 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG B 210 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE B 198 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL B 208 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 303 through 304 Processing sheet with id=AC5, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.578A pdb=" N TYR F 30 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.514A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU F 40 " --> pdb=" O PHE F 150 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR F 152 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.514A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 48 through 52 removed outlier: 3.924A pdb=" N THR F 48 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU F 95 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 174 through 176 removed outlier: 3.576A pdb=" N THR F 261 " --> pdb=" O PHE F 174 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL F 256 " --> pdb=" O ALA F 241 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA F 241 " --> pdb=" O VAL F 256 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 184 through 187 removed outlier: 6.664A pdb=" N THR F 184 " --> pdb=" O THR F 225 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N THR F 225 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS F 186 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 292 through 300 removed outlier: 4.063A pdb=" N ALA F 294 " --> pdb=" O LEU F 356 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP F 353 " --> pdb=" O TRP F 334 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP F 334 " --> pdb=" O ASP F 353 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 316 through 318 removed outlier: 3.734A pdb=" N VAL F 395 " --> pdb=" O MET F 370 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 407 through 413 removed outlier: 7.220A pdb=" N TYR F 408 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR F 503 " --> pdb=" O TYR F 408 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU F 410 " --> pdb=" O THR F 503 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLU F 505 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL F 412 " --> pdb=" O GLU F 505 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU F 500 " --> pdb=" O TYR F 483 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR F 483 " --> pdb=" O LEU F 500 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 407 through 413 removed outlier: 7.220A pdb=" N TYR F 408 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR F 503 " --> pdb=" O TYR F 408 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU F 410 " --> pdb=" O THR F 503 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLU F 505 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL F 412 " --> pdb=" O GLU F 505 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL F 502 " --> pdb=" O LEU F 481 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU F 481 " --> pdb=" O VAL F 502 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 421 through 425 removed outlier: 7.346A pdb=" N GLN F 421 " --> pdb=" O VAL F 467 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL F 467 " --> pdb=" O GLN F 421 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY F 423 " --> pdb=" O LEU F 465 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU F 465 " --> pdb=" O GLY F 423 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER F 462 " --> pdb=" O SER F 457 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AD8, first strand: chain 'F' and resid 551 through 552 removed outlier: 4.345A pdb=" N THR F 552 " --> pdb=" O GLY F 605 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY F 605 " --> pdb=" O THR F 552 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 589 through 591 removed outlier: 6.520A pdb=" N SER F 589 " --> pdb=" O CYS F 618 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N CYS F 620 " --> pdb=" O SER F 589 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL F 591 " --> pdb=" O CYS F 620 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 948 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: 2.16 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4593 1.34 - 1.47: 3334 1.47 - 1.59: 5949 1.59 - 1.72: 0 1.72 - 1.84: 142 Bond restraints: 14018 Sorted by residual: bond pdb=" C1 NAG F 706 " pdb=" O5 NAG F 706 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.43e+00 bond pdb=" C1 NAG F 702 " pdb=" O5 NAG F 702 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.16e+00 bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.09e+00 bond pdb=" C CYS F 565 " pdb=" N PRO F 566 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.09e+00 ... (remaining 14013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 18690 3.12 - 6.24: 290 6.24 - 9.37: 32 9.37 - 12.49: 4 12.49 - 15.61: 2 Bond angle restraints: 19018 Sorted by residual: angle pdb=" C VAL F 427 " pdb=" N GLU F 428 " pdb=" CA GLU F 428 " ideal model delta sigma weight residual 120.38 127.46 -7.08 1.46e+00 4.69e-01 2.35e+01 angle pdb=" C VAL E 427 " pdb=" N GLU E 428 " pdb=" CA GLU E 428 " ideal model delta sigma weight residual 120.38 127.45 -7.07 1.46e+00 4.69e-01 2.35e+01 angle pdb=" C TYR E 76 " pdb=" N ARG E 77 " pdb=" CA ARG E 77 " ideal model delta sigma weight residual 121.54 129.60 -8.06 1.91e+00 2.74e-01 1.78e+01 angle pdb=" C TYR F 76 " pdb=" N ARG F 77 " pdb=" CA ARG F 77 " ideal model delta sigma weight residual 121.54 129.57 -8.03 1.91e+00 2.74e-01 1.77e+01 angle pdb=" N VAL E 304 " pdb=" CA VAL E 304 " pdb=" C VAL E 304 " ideal model delta sigma weight residual 108.88 116.52 -7.64 2.16e+00 2.14e-01 1.25e+01 ... (remaining 19013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 8468 17.62 - 35.24: 279 35.24 - 52.86: 46 52.86 - 70.49: 12 70.49 - 88.11: 4 Dihedral angle restraints: 8809 sinusoidal: 3791 harmonic: 5018 Sorted by residual: dihedral pdb=" CB CYS E 515 " pdb=" SG CYS E 515 " pdb=" SG CYS E 531 " pdb=" CB CYS E 531 " ideal model delta sinusoidal sigma weight residual 93.00 -178.89 -88.11 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS F 515 " pdb=" SG CYS F 515 " pdb=" SG CYS F 531 " pdb=" CB CYS F 531 " ideal model delta sinusoidal sigma weight residual 93.00 -178.90 -88.10 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS F 426 " pdb=" SG CYS F 426 " pdb=" SG CYS F 430 " pdb=" CB CYS F 430 " ideal model delta sinusoidal sigma weight residual -86.00 -168.97 82.97 1 1.00e+01 1.00e-02 8.43e+01 ... (remaining 8806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2118 0.132 - 0.264: 32 0.264 - 0.396: 2 0.396 - 0.528: 0 0.528 - 0.660: 4 Chirality restraints: 2156 Sorted by residual: chirality pdb=" C1 NAG E 704 " pdb=" ND2 ASN E 468 " pdb=" C2 NAG E 704 " pdb=" O5 NAG E 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" C1 NAG F 704 " pdb=" ND2 ASN F 468 " pdb=" C2 NAG F 704 " pdb=" O5 NAG F 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" C1 NAG F 702 " pdb=" ND2 ASN F 377 " pdb=" C2 NAG F 702 " pdb=" O5 NAG F 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.51e+00 ... (remaining 2153 not shown) Planarity restraints: 2492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 59 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.52e+00 pdb=" N PRO E 60 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 60 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 60 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 59 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO F 60 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO F 60 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 60 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 258 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO D 259 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 259 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 259 " 0.033 5.00e-02 4.00e+02 ... (remaining 2489 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.07: 12 2.07 - 2.78: 2967 2.78 - 3.49: 16353 3.49 - 4.19: 30175 4.19 - 4.90: 51736 Nonbonded interactions: 101243 Sorted by model distance: nonbonded pdb=" OD2 ASP F 300 " pdb=" OH TYR F 314 " model vdw 1.366 3.040 nonbonded pdb=" OD2 ASP E 300 " pdb=" OH TYR E 314 " model vdw 1.367 3.040 nonbonded pdb=" OD1 ASP E 266 " pdb=" OD2 ASP E 302 " model vdw 1.613 3.040 nonbonded pdb=" OD1 ASP F 266 " pdb=" OD2 ASP F 302 " model vdw 1.613 3.040 nonbonded pdb=" O THR F 564 " pdb=" OD2 ASP F 567 " model vdw 1.692 3.040 ... (remaining 101238 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.510 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5127 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 : 0.008 0.061 14081 Z= 0.343 Angle : 1.096 15.609 19158 Z= 0.587 Chirality : 0.062 0.660 2156 Planarity : 0.007 0.069 2478 Dihedral : 9.187 57.568 5406 Min Nonbonded Distance : 1.366 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.13 % Allowed : 1.72 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.58 (0.15), residues: 1702 helix: -4.22 (0.13), residues: 320 sheet: -2.35 (0.23), residues: 434 loop : -3.01 (0.15), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 544 TYR 0.037 0.004 TYR F 122 PHE 0.026 0.003 PHE F 433 TRP 0.035 0.005 TRP F 139 HIS 0.015 0.002 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00763 (14018) covalent geometry : angle 1.06410 (19018) SS BOND : bond 0.00696 ( 49) SS BOND : angle 1.83711 ( 98) hydrogen bonds : bond 0.19172 ( 352) hydrogen bonds : angle 9.06621 ( 948) link_NAG-ASN : bond 0.01913 ( 14) link_NAG-ASN : angle 5.22879 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 417 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.5898 (p90) cc_final: 0.5300 (p90) REVERT: C 249 LEU cc_start: 0.7440 (mt) cc_final: 0.6798 (mm) REVERT: C 296 ILE cc_start: 0.7425 (mt) cc_final: 0.7215 (mt) REVERT: D 199 GLN cc_start: 0.7314 (mm-40) cc_final: 0.7082 (mm-40) REVERT: D 283 THR cc_start: 0.4763 (p) cc_final: 0.4223 (m) REVERT: F 471 LYS cc_start: 0.7210 (mmtt) cc_final: 0.6804 (pptt) outliers start: 2 outliers final: 0 residues processed: 419 average time/residue: 0.1547 time to fit residues: 85.9839 Evaluate side-chains 170 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS C 194 HIS C 247 ASN C 338 ASN E 44 GLN E 103 HIS E 187 GLN E 333 HIS E 403 HIS E 443 HIS F 44 GLN F 81 HIS F 89 GLN F 103 HIS F 187 GLN F 333 HIS F 403 HIS F 443 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.128023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.107439 restraints weight = 56134.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.110100 restraints weight = 30386.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.111840 restraints weight = 19651.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.112993 restraints weight = 14335.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.113793 restraints weight = 11379.235| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14081 Z= 0.159 Angle : 0.783 12.847 19158 Z= 0.387 Chirality : 0.048 0.322 2156 Planarity : 0.006 0.055 2478 Dihedral : 6.982 50.239 2202 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.92 % Allowed : 10.54 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.17), residues: 1702 helix: -2.71 (0.23), residues: 328 sheet: -1.64 (0.24), residues: 420 loop : -2.79 (0.16), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 156 TYR 0.028 0.002 TYR E 122 PHE 0.025 0.002 PHE D 203 TRP 0.028 0.002 TRP E 139 HIS 0.005 0.001 HIS C 273 Details of bonding type rmsd covalent geometry : bond 0.00359 (14018) covalent geometry : angle 0.75756 (19018) SS BOND : bond 0.00479 ( 49) SS BOND : angle 1.63842 ( 98) hydrogen bonds : bond 0.03745 ( 352) hydrogen bonds : angle 6.69704 ( 948) link_NAG-ASN : bond 0.00984 ( 14) link_NAG-ASN : angle 3.67353 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 0.518 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: C 176 ASP cc_start: 0.8412 (t70) cc_final: 0.8144 (t70) REVERT: C 265 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7129 (tt) REVERT: C 268 PHE cc_start: 0.7805 (t80) cc_final: 0.7594 (t80) REVERT: C 349 MET cc_start: 0.7172 (mmm) cc_final: 0.6958 (mmt) REVERT: E 56 LEU cc_start: 0.6209 (OUTLIER) cc_final: 0.5655 (mm) REVERT: E 370 MET cc_start: 0.4274 (pmm) cc_final: 0.3778 (pmm) REVERT: E 392 HIS cc_start: 0.7407 (p-80) cc_final: 0.7058 (p-80) REVERT: F 102 ASP cc_start: 0.8005 (p0) cc_final: 0.7693 (p0) REVERT: F 484 MET cc_start: 0.6334 (tpp) cc_final: 0.6079 (tmm) outliers start: 44 outliers final: 27 residues processed: 235 average time/residue: 0.1100 time to fit residues: 38.4236 Evaluate side-chains 177 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 439 GLN Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain F residue 227 TRP Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 467 VAL Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain F residue 579 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 13 optimal weight: 0.1980 chunk 134 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN C 303 ASN D 323 ASN ** D 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.124961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.104370 restraints weight = 57539.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.106892 restraints weight = 31495.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.108501 restraints weight = 20466.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.109651 restraints weight = 15038.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.110342 restraints weight = 12067.014| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14081 Z= 0.136 Angle : 0.697 10.654 19158 Z= 0.340 Chirality : 0.045 0.296 2156 Planarity : 0.006 0.088 2478 Dihedral : 5.697 40.189 2202 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.51 % Allowed : 13.26 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.18), residues: 1702 helix: -1.90 (0.26), residues: 324 sheet: -1.47 (0.24), residues: 444 loop : -2.38 (0.17), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 156 TYR 0.027 0.002 TYR E 122 PHE 0.020 0.002 PHE B 198 TRP 0.013 0.002 TRP E 139 HIS 0.003 0.001 HIS E 569 Details of bonding type rmsd covalent geometry : bond 0.00305 (14018) covalent geometry : angle 0.67335 (19018) SS BOND : bond 0.00363 ( 49) SS BOND : angle 1.40377 ( 98) hydrogen bonds : bond 0.03354 ( 352) hydrogen bonds : angle 6.07150 ( 948) link_NAG-ASN : bond 0.00948 ( 14) link_NAG-ASN : angle 3.39736 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 178 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 176 ASP cc_start: 0.8560 (t70) cc_final: 0.8106 (t70) REVERT: C 326 GLU cc_start: 0.8546 (tt0) cc_final: 0.8331 (tt0) REVERT: E 56 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5697 (mm) REVERT: E 278 THR cc_start: 0.4447 (m) cc_final: 0.3774 (m) REVERT: E 392 HIS cc_start: 0.7337 (p-80) cc_final: 0.7137 (p-80) REVERT: B 174 LEU cc_start: 0.3609 (OUTLIER) cc_final: 0.3260 (mp) REVERT: D 234 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7699 (m) REVERT: D 247 ASN cc_start: 0.5615 (t0) cc_final: 0.4914 (p0) REVERT: F 102 ASP cc_start: 0.8260 (p0) cc_final: 0.7944 (p0) REVERT: F 256 VAL cc_start: 0.7360 (OUTLIER) cc_final: 0.7126 (m) outliers start: 53 outliers final: 32 residues processed: 213 average time/residue: 0.1104 time to fit residues: 34.9512 Evaluate side-chains 178 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain F residue 227 TRP Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 467 VAL Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 579 ASN Chi-restraints excluded: chain F residue 589 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 13 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 153 optimal weight: 0.1980 chunk 2 optimal weight: 0.3980 chunk 9 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 108 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN E 439 GLN E 490 GLN B 128 GLN B 161 HIS D 323 ASN ** D 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.125026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.104580 restraints weight = 56571.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.107083 restraints weight = 31276.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.108702 restraints weight = 20336.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.109806 restraints weight = 14978.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.110532 restraints weight = 12064.534| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.6439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14081 Z= 0.105 Angle : 0.652 10.468 19158 Z= 0.310 Chirality : 0.043 0.256 2156 Planarity : 0.004 0.041 2478 Dihedral : 4.880 38.579 2202 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.25 % Allowed : 13.53 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.19), residues: 1702 helix: -1.26 (0.28), residues: 320 sheet: -1.12 (0.25), residues: 434 loop : -2.08 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 253 TYR 0.027 0.001 TYR E 122 PHE 0.016 0.001 PHE D 165 TRP 0.009 0.001 TRP E 139 HIS 0.006 0.001 HIS F 333 Details of bonding type rmsd covalent geometry : bond 0.00235 (14018) covalent geometry : angle 0.63486 (19018) SS BOND : bond 0.00204 ( 49) SS BOND : angle 1.05347 ( 98) hydrogen bonds : bond 0.02787 ( 352) hydrogen bonds : angle 5.72458 ( 948) link_NAG-ASN : bond 0.01093 ( 14) link_NAG-ASN : angle 2.94326 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 163 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 GLN cc_start: 0.6990 (mp10) cc_final: 0.6493 (mt0) REVERT: C 293 LEU cc_start: 0.8313 (pp) cc_final: 0.8107 (pp) REVERT: C 326 GLU cc_start: 0.8680 (tt0) cc_final: 0.8453 (tt0) REVERT: C 334 PHE cc_start: 0.7547 (t80) cc_final: 0.7184 (t80) REVERT: C 349 MET cc_start: 0.7225 (mmt) cc_final: 0.6936 (ptp) REVERT: E 188 PHE cc_start: 0.8064 (m-10) cc_final: 0.7751 (m-10) REVERT: E 358 LEU cc_start: 0.8543 (mt) cc_final: 0.8171 (tp) REVERT: E 500 LEU cc_start: 0.4247 (tp) cc_final: 0.4020 (tp) REVERT: D 234 THR cc_start: 0.8036 (t) cc_final: 0.7735 (m) REVERT: F 102 ASP cc_start: 0.8197 (p0) cc_final: 0.7815 (p0) REVERT: F 187 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6638 (tm-30) REVERT: F 256 VAL cc_start: 0.7548 (OUTLIER) cc_final: 0.7313 (m) REVERT: F 289 GLU cc_start: 0.6309 (mp0) cc_final: 0.6073 (mp0) REVERT: F 595 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7705 (mt-10) outliers start: 49 outliers final: 31 residues processed: 199 average time/residue: 0.1045 time to fit residues: 31.5197 Evaluate side-chains 172 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 439 GLN Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 328 CYS Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 227 TRP Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 467 VAL Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 589 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 0.0770 chunk 96 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 139 optimal weight: 0.0070 chunk 83 optimal weight: 0.9990 chunk 62 optimal weight: 30.0000 overall best weight: 1.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN C 247 ASN E 392 HIS ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 ASN D 352 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.122310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.101701 restraints weight = 57322.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.104164 restraints weight = 31782.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.105812 restraints weight = 20925.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.106909 restraints weight = 15492.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.107621 restraints weight = 12550.265| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.7154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14081 Z= 0.124 Angle : 0.658 9.985 19158 Z= 0.316 Chirality : 0.044 0.266 2156 Planarity : 0.004 0.039 2478 Dihedral : 4.742 37.271 2202 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.18 % Allowed : 14.92 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.19), residues: 1702 helix: -1.01 (0.28), residues: 320 sheet: -0.77 (0.25), residues: 434 loop : -2.06 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 600 TYR 0.026 0.001 TYR E 122 PHE 0.014 0.001 PHE D 165 TRP 0.007 0.001 TRP F 543 HIS 0.034 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00275 (14018) covalent geometry : angle 0.64298 (19018) SS BOND : bond 0.00516 ( 49) SS BOND : angle 1.07699 ( 98) hydrogen bonds : bond 0.03113 ( 352) hydrogen bonds : angle 5.64191 ( 948) link_NAG-ASN : bond 0.00858 ( 14) link_NAG-ASN : angle 2.72023 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 0.418 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: C 171 LEU cc_start: 0.7679 (mt) cc_final: 0.7387 (mt) REVERT: C 213 GLN cc_start: 0.7084 (mp10) cc_final: 0.6792 (mt0) REVERT: C 293 LEU cc_start: 0.8296 (pp) cc_final: 0.7859 (mt) REVERT: C 326 GLU cc_start: 0.8700 (tt0) cc_final: 0.8399 (tt0) REVERT: C 329 GLU cc_start: 0.7780 (tt0) cc_final: 0.6974 (tp30) REVERT: C 334 PHE cc_start: 0.7710 (t80) cc_final: 0.7340 (t80) REVERT: C 349 MET cc_start: 0.7400 (mmt) cc_final: 0.6967 (mmt) REVERT: E 56 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.6076 (mm) REVERT: E 76 TYR cc_start: 0.8323 (t80) cc_final: 0.7955 (m-80) REVERT: E 188 PHE cc_start: 0.8221 (m-80) cc_final: 0.7844 (m-10) REVERT: E 358 LEU cc_start: 0.8457 (mt) cc_final: 0.8101 (tp) REVERT: D 234 THR cc_start: 0.8025 (t) cc_final: 0.7728 (m) REVERT: D 319 ARG cc_start: 0.5930 (ttm-80) cc_final: 0.5243 (mmp-170) REVERT: F 102 ASP cc_start: 0.8249 (p0) cc_final: 0.7874 (p0) REVERT: F 187 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6708 (tm-30) REVERT: F 256 VAL cc_start: 0.7721 (m) cc_final: 0.7483 (m) outliers start: 48 outliers final: 34 residues processed: 190 average time/residue: 0.0996 time to fit residues: 28.8690 Evaluate side-chains 177 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 328 CYS Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 227 TRP Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 467 VAL Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 61 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 149 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 HIS ** E 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 HIS D 271 HIS F 84 ASN F 371 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.114778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.094872 restraints weight = 57818.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.097297 restraints weight = 35107.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.098593 restraints weight = 21762.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.098950 restraints weight = 17410.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.099112 restraints weight = 15192.698| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.9208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 14081 Z= 0.243 Angle : 0.841 9.323 19158 Z= 0.418 Chirality : 0.050 0.400 2156 Planarity : 0.006 0.067 2478 Dihedral : 6.029 42.340 2202 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.18 % Allowed : 15.32 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.19), residues: 1702 helix: -1.50 (0.27), residues: 328 sheet: -1.02 (0.24), residues: 426 loop : -2.27 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 600 TYR 0.025 0.002 TYR E 122 PHE 0.024 0.002 PHE D 165 TRP 0.013 0.002 TRP B 205 HIS 0.033 0.002 HIS E 569 Details of bonding type rmsd covalent geometry : bond 0.00514 (14018) covalent geometry : angle 0.82414 (19018) SS BOND : bond 0.00663 ( 49) SS BOND : angle 1.67585 ( 98) hydrogen bonds : bond 0.04151 ( 352) hydrogen bonds : angle 6.58478 ( 948) link_NAG-ASN : bond 0.00997 ( 14) link_NAG-ASN : angle 2.88392 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 155 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 ARG cc_start: 0.8521 (ttt-90) cc_final: 0.8207 (ttm110) REVERT: C 300 MET cc_start: 0.8545 (mmm) cc_final: 0.8062 (tpp) REVERT: C 326 GLU cc_start: 0.8432 (tt0) cc_final: 0.8135 (tt0) REVERT: C 329 GLU cc_start: 0.8058 (tt0) cc_final: 0.7264 (tp30) REVERT: C 349 MET cc_start: 0.7400 (mmt) cc_final: 0.7151 (mmt) REVERT: E 52 TYR cc_start: 0.7543 (m-10) cc_final: 0.7339 (m-80) REVERT: D 290 ARG cc_start: 0.8436 (mtt180) cc_final: 0.8182 (ttm-80) REVERT: F 102 ASP cc_start: 0.8341 (p0) cc_final: 0.8013 (p0) REVERT: F 187 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: F 255 MET cc_start: 0.7548 (mmp) cc_final: 0.7246 (mpp) REVERT: F 256 VAL cc_start: 0.8094 (OUTLIER) cc_final: 0.7868 (m) REVERT: F 559 SER cc_start: 0.7827 (p) cc_final: 0.7626 (t) outliers start: 63 outliers final: 37 residues processed: 200 average time/residue: 0.0957 time to fit residues: 29.8381 Evaluate side-chains 168 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 122 TYR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 227 TRP Chi-restraints excluded: chain F residue 235 GLU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 579 ASN Chi-restraints excluded: chain F residue 580 ILE Chi-restraints excluded: chain F residue 586 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 21 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 139 optimal weight: 0.0270 chunk 108 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 168 optimal weight: 7.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 GLN E 403 HIS B 128 GLN B 202 ASN F 371 GLN F 491 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.118680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.098700 restraints weight = 56282.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.101148 restraints weight = 31642.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.102781 restraints weight = 20861.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.103891 restraints weight = 15417.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.104593 restraints weight = 12406.382| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.9289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14081 Z= 0.114 Angle : 0.683 9.737 19158 Z= 0.330 Chirality : 0.044 0.266 2156 Planarity : 0.004 0.040 2478 Dihedral : 4.997 39.115 2202 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.05 % Allowed : 17.51 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.19), residues: 1702 helix: -0.86 (0.29), residues: 302 sheet: -0.73 (0.25), residues: 410 loop : -1.99 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 181 TYR 0.028 0.001 TYR E 122 PHE 0.020 0.001 PHE F 619 TRP 0.014 0.001 TRP B 205 HIS 0.005 0.001 HIS F 333 Details of bonding type rmsd covalent geometry : bond 0.00247 (14018) covalent geometry : angle 0.66661 (19018) SS BOND : bond 0.00305 ( 49) SS BOND : angle 1.33741 ( 98) hydrogen bonds : bond 0.03158 ( 352) hydrogen bonds : angle 5.80974 ( 948) link_NAG-ASN : bond 0.00784 ( 14) link_NAG-ASN : angle 2.71623 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 ARG cc_start: 0.8581 (ttt-90) cc_final: 0.8368 (tpt-90) REVERT: C 326 GLU cc_start: 0.8403 (tt0) cc_final: 0.8157 (tt0) REVERT: C 329 GLU cc_start: 0.7942 (tt0) cc_final: 0.7127 (tp30) REVERT: C 349 MET cc_start: 0.7222 (mmt) cc_final: 0.6954 (mmt) REVERT: E 358 LEU cc_start: 0.8546 (mt) cc_final: 0.8237 (tp) REVERT: E 600 ARG cc_start: 0.7444 (ptp-170) cc_final: 0.7176 (ptp-170) REVERT: F 102 ASP cc_start: 0.8235 (p0) cc_final: 0.7812 (p0) REVERT: F 118 LEU cc_start: 0.7839 (tp) cc_final: 0.7606 (tp) REVERT: F 122 TYR cc_start: 0.6765 (p90) cc_final: 0.6455 (p90) REVERT: F 187 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: F 255 MET cc_start: 0.7859 (mmp) cc_final: 0.7374 (mmp) REVERT: F 256 VAL cc_start: 0.8062 (OUTLIER) cc_final: 0.7838 (m) REVERT: F 559 SER cc_start: 0.7833 (p) cc_final: 0.7622 (t) REVERT: F 616 GLU cc_start: 0.6360 (tp30) cc_final: 0.5215 (tt0) outliers start: 46 outliers final: 32 residues processed: 199 average time/residue: 0.1035 time to fit residues: 31.1180 Evaluate side-chains 179 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 227 TRP Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 578 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 129 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 134 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 164 optimal weight: 9.9990 chunk 150 optimal weight: 0.0670 chunk 42 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 126 optimal weight: 30.0000 chunk 139 optimal weight: 0.0570 overall best weight: 3.4240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 GLN E 392 HIS ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN F 371 GLN F 437 ASN F 569 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.115044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.095050 restraints weight = 56618.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.097362 restraints weight = 32445.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.098934 restraints weight = 21649.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.099962 restraints weight = 16049.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.100700 restraints weight = 12991.155| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.9861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14081 Z= 0.173 Angle : 0.740 9.586 19158 Z= 0.365 Chirality : 0.047 0.324 2156 Planarity : 0.005 0.056 2478 Dihedral : 5.375 40.792 2202 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.45 % Allowed : 17.37 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.19), residues: 1702 helix: -0.88 (0.29), residues: 320 sheet: -0.70 (0.25), residues: 430 loop : -2.11 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 544 TYR 0.028 0.002 TYR E 122 PHE 0.020 0.002 PHE D 165 TRP 0.052 0.002 TRP E 543 HIS 0.010 0.001 HIS F 569 Details of bonding type rmsd covalent geometry : bond 0.00383 (14018) covalent geometry : angle 0.72308 (19018) SS BOND : bond 0.00438 ( 49) SS BOND : angle 1.67603 ( 98) hydrogen bonds : bond 0.03567 ( 352) hydrogen bonds : angle 6.07166 ( 948) link_NAG-ASN : bond 0.01040 ( 14) link_NAG-ASN : angle 2.55381 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 ARG cc_start: 0.8636 (ttt-90) cc_final: 0.8188 (ttm110) REVERT: C 326 GLU cc_start: 0.8383 (tt0) cc_final: 0.8174 (tt0) REVERT: C 329 GLU cc_start: 0.8035 (tt0) cc_final: 0.7243 (tp30) REVERT: E 370 MET cc_start: 0.4293 (pmm) cc_final: 0.3956 (pmm) REVERT: E 600 ARG cc_start: 0.7502 (ptp-170) cc_final: 0.7204 (ptp-170) REVERT: D 287 ARG cc_start: 0.7940 (mtt180) cc_final: 0.7679 (mtp180) REVERT: F 102 ASP cc_start: 0.8241 (p0) cc_final: 0.7859 (p0) REVERT: F 187 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: F 238 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7406 (tp30) REVERT: F 255 MET cc_start: 0.7862 (mmp) cc_final: 0.7325 (mmp) REVERT: F 256 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7906 (m) outliers start: 52 outliers final: 41 residues processed: 191 average time/residue: 0.0994 time to fit residues: 29.5823 Evaluate side-chains 179 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 185 PHE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 392 HIS Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 227 TRP Chi-restraints excluded: chain F residue 235 GLU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 133 optimal weight: 20.0000 chunk 159 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 86 optimal weight: 0.0050 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 overall best weight: 2.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN C 190 HIS E 84 ASN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 HIS F 421 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.115598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.095610 restraints weight = 56939.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.098007 restraints weight = 32365.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.099576 restraints weight = 21355.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.100627 restraints weight = 15873.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.101384 restraints weight = 12805.815| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 1.0169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14081 Z= 0.142 Angle : 0.707 9.254 19158 Z= 0.349 Chirality : 0.046 0.295 2156 Planarity : 0.004 0.036 2478 Dihedral : 5.197 40.456 2202 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.18 % Allowed : 18.17 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.19), residues: 1702 helix: -0.78 (0.29), residues: 322 sheet: -0.81 (0.25), residues: 424 loop : -1.99 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 206 TYR 0.029 0.001 TYR E 122 PHE 0.015 0.002 PHE F 619 TRP 0.009 0.001 TRP E 334 HIS 0.036 0.001 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00321 (14018) covalent geometry : angle 0.69169 (19018) SS BOND : bond 0.00345 ( 49) SS BOND : angle 1.38502 ( 98) hydrogen bonds : bond 0.03403 ( 352) hydrogen bonds : angle 5.93490 ( 948) link_NAG-ASN : bond 0.00830 ( 14) link_NAG-ASN : angle 2.60404 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 148 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 ARG cc_start: 0.8680 (ttt-90) cc_final: 0.8185 (ttm110) REVERT: C 329 GLU cc_start: 0.8021 (tt0) cc_final: 0.7255 (tp30) REVERT: E 39 LYS cc_start: 0.6715 (ttmt) cc_final: 0.6349 (ttpt) REVERT: E 148 SER cc_start: 0.6487 (m) cc_final: 0.5961 (p) REVERT: E 370 MET cc_start: 0.4308 (pmm) cc_final: 0.3908 (pmm) REVERT: E 429 ASN cc_start: 0.6638 (m-40) cc_final: 0.6191 (t0) REVERT: E 600 ARG cc_start: 0.7407 (ptp-170) cc_final: 0.7169 (ptp-170) REVERT: D 287 ARG cc_start: 0.7998 (mtt180) cc_final: 0.7661 (mtp180) REVERT: F 102 ASP cc_start: 0.8175 (p0) cc_final: 0.7774 (p0) REVERT: F 122 TYR cc_start: 0.6713 (p90) cc_final: 0.6446 (p90) REVERT: F 187 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: F 190 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7636 (mp) REVERT: F 255 MET cc_start: 0.7821 (mmp) cc_final: 0.7279 (mmp) REVERT: F 256 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7915 (m) outliers start: 48 outliers final: 41 residues processed: 181 average time/residue: 0.1007 time to fit residues: 27.7663 Evaluate side-chains 178 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain E residue 185 PHE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 392 HIS Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 227 TRP Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 578 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 152 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN C 190 HIS C 213 GLN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 GLN E 392 HIS F 421 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.116379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.096532 restraints weight = 56738.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.098900 restraints weight = 32229.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.100490 restraints weight = 21448.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.101567 restraints weight = 15947.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.102329 restraints weight = 12843.236| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 1.0334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14081 Z= 0.120 Angle : 0.689 9.495 19158 Z= 0.337 Chirality : 0.045 0.271 2156 Planarity : 0.004 0.038 2478 Dihedral : 4.970 38.884 2202 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.25 % Allowed : 18.57 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.19), residues: 1702 helix: -0.63 (0.29), residues: 322 sheet: -0.62 (0.25), residues: 420 loop : -1.91 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 181 TYR 0.030 0.001 TYR E 122 PHE 0.014 0.001 PHE C 256 TRP 0.013 0.001 TRP B 205 HIS 0.047 0.002 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00273 (14018) covalent geometry : angle 0.67568 (19018) SS BOND : bond 0.00285 ( 49) SS BOND : angle 1.17024 ( 98) hydrogen bonds : bond 0.03216 ( 352) hydrogen bonds : angle 5.75041 ( 948) link_NAG-ASN : bond 0.00788 ( 14) link_NAG-ASN : angle 2.61000 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 149 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 PHE cc_start: 0.7230 (p90) cc_final: 0.6875 (p90) REVERT: A 200 ASP cc_start: 0.7028 (t0) cc_final: 0.6438 (t70) REVERT: C 177 ARG cc_start: 0.8639 (ttt-90) cc_final: 0.8174 (ttm110) REVERT: E 39 LYS cc_start: 0.6996 (ttmt) cc_final: 0.6655 (ttpt) REVERT: E 148 SER cc_start: 0.6631 (m) cc_final: 0.6194 (p) REVERT: E 258 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7965 (m-80) REVERT: E 358 LEU cc_start: 0.8337 (mt) cc_final: 0.8053 (tp) REVERT: E 370 MET cc_start: 0.4356 (pmm) cc_final: 0.3969 (pmm) REVERT: E 429 ASN cc_start: 0.6595 (m-40) cc_final: 0.6189 (t0) REVERT: E 600 ARG cc_start: 0.7299 (ptp-170) cc_final: 0.7045 (ptp-170) REVERT: D 231 ARG cc_start: 0.8080 (ttp-170) cc_final: 0.7806 (ptp-170) REVERT: D 287 ARG cc_start: 0.8002 (mtt180) cc_final: 0.7645 (mtp180) REVERT: F 102 ASP cc_start: 0.8136 (p0) cc_final: 0.7705 (p0) REVERT: F 122 TYR cc_start: 0.6660 (p90) cc_final: 0.6389 (p90) REVERT: F 187 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: F 255 MET cc_start: 0.7841 (mmp) cc_final: 0.7322 (mmp) REVERT: F 256 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7869 (m) REVERT: F 470 THR cc_start: 0.7185 (m) cc_final: 0.6985 (m) REVERT: F 543 TRP cc_start: 0.6327 (t-100) cc_final: 0.5628 (t-100) outliers start: 49 outliers final: 40 residues processed: 184 average time/residue: 0.1066 time to fit residues: 29.6116 Evaluate side-chains 177 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 316 CYS Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 258 PHE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 392 HIS Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 227 TRP Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 608 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 137 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 80 optimal weight: 0.3980 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 129 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN C 190 HIS ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.116522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.096750 restraints weight = 56987.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.099139 restraints weight = 32197.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.100697 restraints weight = 21385.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.101792 restraints weight = 15909.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.102556 restraints weight = 12797.758| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 1.0477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14081 Z= 0.117 Angle : 0.687 9.486 19158 Z= 0.334 Chirality : 0.044 0.261 2156 Planarity : 0.004 0.037 2478 Dihedral : 4.853 37.758 2202 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.85 % Allowed : 19.30 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.20), residues: 1702 helix: -0.61 (0.29), residues: 328 sheet: -0.48 (0.26), residues: 420 loop : -1.83 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 181 TYR 0.030 0.001 TYR E 122 PHE 0.014 0.001 PHE C 256 TRP 0.010 0.001 TRP B 205 HIS 0.050 0.001 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00265 (14018) covalent geometry : angle 0.67419 (19018) SS BOND : bond 0.00271 ( 49) SS BOND : angle 1.13685 ( 98) hydrogen bonds : bond 0.03187 ( 352) hydrogen bonds : angle 5.65652 ( 948) link_NAG-ASN : bond 0.00766 ( 14) link_NAG-ASN : angle 2.59975 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2541.14 seconds wall clock time: 44 minutes 22.78 seconds (2662.78 seconds total)