Starting phenix.real_space_refine on Wed Mar 4 14:19:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u2n_26316/03_2026/7u2n_26316_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u2n_26316/03_2026/7u2n_26316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u2n_26316/03_2026/7u2n_26316_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u2n_26316/03_2026/7u2n_26316_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u2n_26316/03_2026/7u2n_26316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u2n_26316/03_2026/7u2n_26316.map" } resolution = 2.8 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= 0.005 sd= 2.345 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 9165 2.51 5 N 2255 2.21 5 O 2555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s 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: 14080 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2771 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: D, B, C, E, G, H, I, J Time building chain proxies: 2.41, per 1000 atoms: 0.17 Number of scatterers: 14080 At special positions: 0 Unit cell: (104.706, 106.368, 135.453, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 2555 8.00 N 2255 7.00 C 9165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.04 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN D 54 " " NAG H 1 " - " ASN B 54 " " NAG I 1 " - " ASN C 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 679.9 milliseconds 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3310 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 30 sheets defined 40.3% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.840A pdb=" N ASP A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.200A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.937A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 244 through 257 removed outlier: 4.197A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 287 removed outlier: 3.942A pdb=" N VAL A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 325 removed outlier: 3.575A pdb=" N ILE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 307 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 426 removed outlier: 4.253A pdb=" N LEU A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 4.162A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 35 removed outlier: 3.841A pdb=" N ASP D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.201A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 102 through 108 removed outlier: 3.937A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 237 No H-bonds generated for 'chain 'D' and resid 235 through 237' Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 244 through 257 removed outlier: 4.197A pdb=" N ILE D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 287 removed outlier: 3.942A pdb=" N VAL D 269 " --> pdb=" O ALA D 265 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 325 removed outlier: 3.576A pdb=" N ILE D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP D 302 " --> pdb=" O ALA D 298 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 307 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 426 removed outlier: 4.253A pdb=" N LEU D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA D 399 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE D 402 " --> pdb=" O ARG D 398 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 4.161A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 35 removed outlier: 3.841A pdb=" N ASP B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.201A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 102 through 108 removed outlier: 3.937A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 244 through 257 removed outlier: 4.197A pdb=" N ILE B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 287 removed outlier: 3.941A pdb=" N VAL B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 325 removed outlier: 3.576A pdb=" N ILE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 307 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 426 removed outlier: 4.253A pdb=" N LEU B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA B 399 " --> pdb=" O PHE B 395 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE B 402 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 4.163A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.841A pdb=" N ASP C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 4.201A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 102 through 108 removed outlier: 3.936A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 244 through 257 removed outlier: 4.197A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 287 removed outlier: 3.941A pdb=" N VAL C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 325 removed outlier: 3.576A pdb=" N ILE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 307 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 426 removed outlier: 4.254A pdb=" N LEU C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA C 399 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 4.162A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.841A pdb=" N ASP E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 40 removed outlier: 4.200A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 102 through 108 removed outlier: 3.936A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 237 No H-bonds generated for 'chain 'E' and resid 235 through 237' Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 244 through 257 removed outlier: 4.197A pdb=" N ILE E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 287 removed outlier: 3.942A pdb=" N VAL E 269 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 325 removed outlier: 3.575A pdb=" N ILE E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP E 302 " --> pdb=" O ALA E 298 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E 307 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA E 319 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 426 removed outlier: 4.253A pdb=" N LEU E 394 " --> pdb=" O GLU E 390 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA E 399 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE E 402 " --> pdb=" O ARG E 398 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 4.162A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 124 removed outlier: 3.713A pdb=" N TRP A 84 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.299A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 168 Processing sheet with id=AA5, first strand: chain 'A' and resid 211 through 213 Processing sheet with id=AA6, first strand: chain 'A' and resid 216 through 218 Processing sheet with id=AA7, first strand: chain 'D' and resid 122 through 124 removed outlier: 3.713A pdb=" N TRP D 84 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 122 through 124 removed outlier: 6.299A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AB1, first strand: chain 'D' and resid 167 through 168 Processing sheet with id=AB2, first strand: chain 'D' and resid 211 through 213 Processing sheet with id=AB3, first strand: chain 'D' and resid 216 through 218 Processing sheet with id=AB4, first strand: chain 'B' and resid 122 through 124 removed outlier: 3.714A pdb=" N TRP B 84 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.300A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB7, first strand: chain 'B' and resid 167 through 168 Processing sheet with id=AB8, first strand: chain 'B' and resid 211 through 213 Processing sheet with id=AB9, first strand: chain 'B' and resid 216 through 218 Processing sheet with id=AC1, first strand: chain 'C' and resid 122 through 124 removed outlier: 3.713A pdb=" N TRP C 84 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.299A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AC4, first strand: chain 'C' and resid 167 through 168 Processing sheet with id=AC5, first strand: chain 'C' and resid 211 through 213 Processing sheet with id=AC6, first strand: chain 'C' and resid 216 through 218 Processing sheet with id=AC7, first strand: chain 'E' and resid 122 through 124 removed outlier: 3.714A pdb=" N TRP E 84 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 122 through 124 removed outlier: 6.298A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AD1, first strand: chain 'E' and resid 167 through 168 Processing sheet with id=AD2, first strand: chain 'E' and resid 211 through 213 Processing sheet with id=AD3, first strand: chain 'E' and resid 216 through 218 585 hydrogen bonds defined for protein. 1590 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: 2.30 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4264 1.34 - 1.46: 3283 1.46 - 1.58: 6703 1.58 - 1.70: 0 1.70 - 1.82: 175 Bond restraints: 14425 Sorted by residual: bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 4.03e+00 bond pdb=" C1 BMA J 3 " pdb=" C2 BMA J 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 3.96e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 3.96e+00 bond pdb=" C1 BMA H 3 " pdb=" C2 BMA H 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.90e+00 ... (remaining 14420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 19171 2.21 - 4.43: 352 4.43 - 6.64: 62 6.64 - 8.85: 0 8.85 - 11.07: 5 Bond angle restraints: 19590 Sorted by residual: angle pdb=" N ASN B 261 " pdb=" CA ASN B 261 " pdb=" CB ASN B 261 " ideal model delta sigma weight residual 114.17 109.93 4.24 1.14e+00 7.69e-01 1.38e+01 angle pdb=" N ASN E 261 " pdb=" CA ASN E 261 " pdb=" CB ASN E 261 " ideal model delta sigma weight residual 114.17 109.93 4.24 1.14e+00 7.69e-01 1.38e+01 angle pdb=" N ASN A 261 " pdb=" CA ASN A 261 " pdb=" CB ASN A 261 " ideal model delta sigma weight residual 114.17 109.94 4.23 1.14e+00 7.69e-01 1.38e+01 angle pdb=" O04 L2L C 600 " pdb=" S03 L2L C 600 " pdb=" O05 L2L C 600 " ideal model delta sigma weight residual 112.97 101.90 11.07 3.00e+00 1.11e-01 1.36e+01 angle pdb=" N ASN D 261 " pdb=" CA ASN D 261 " pdb=" CB ASN D 261 " ideal model delta sigma weight residual 114.17 109.96 4.21 1.14e+00 7.69e-01 1.36e+01 ... (remaining 19585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 8463 17.68 - 35.35: 252 35.35 - 53.02: 25 53.02 - 70.70: 0 70.70 - 88.37: 70 Dihedral angle restraints: 8810 sinusoidal: 3710 harmonic: 5100 Sorted by residual: dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual 93.00 41.46 51.54 1 1.00e+01 1.00e-02 3.63e+01 dihedral pdb=" CB CYS E 154 " pdb=" SG CYS E 154 " pdb=" SG CYS E 168 " pdb=" CB CYS E 168 " ideal model delta sinusoidal sigma weight residual 93.00 41.49 51.51 1 1.00e+01 1.00e-02 3.63e+01 dihedral pdb=" CB CYS B 154 " pdb=" SG CYS B 154 " pdb=" SG CYS B 168 " pdb=" CB CYS B 168 " ideal model delta sinusoidal sigma weight residual 93.00 41.50 51.50 1 1.00e+01 1.00e-02 3.62e+01 ... (remaining 8807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1784 0.052 - 0.104: 390 0.104 - 0.157: 71 0.157 - 0.209: 5 0.209 - 0.261: 5 Chirality restraints: 2255 Sorted by residual: chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 2252 not shown) Planarity restraints: 2425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 151 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C VAL C 151 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL C 151 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU C 152 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 151 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C VAL A 151 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL A 151 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 152 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 151 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.22e+00 pdb=" C VAL E 151 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL E 151 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU E 152 " 0.013 2.00e-02 2.50e+03 ... (remaining 2422 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1544 2.74 - 3.28: 14295 3.28 - 3.82: 22022 3.82 - 4.36: 27975 4.36 - 4.90: 46917 Nonbonded interactions: 112753 Sorted by model distance: nonbonded pdb=" O THR B 128 " pdb=" OG1 THR B 129 " model vdw 2.195 3.040 nonbonded pdb=" O THR C 128 " pdb=" OG1 THR C 129 " model vdw 2.195 3.040 nonbonded pdb=" OE2 GLU B 69 " pdb=" NH2 ARG B 234 " model vdw 2.195 3.120 nonbonded pdb=" OE2 GLU C 69 " pdb=" NH2 ARG C 234 " model vdw 2.196 3.120 nonbonded pdb=" O THR D 128 " pdb=" OG1 THR D 129 " model vdw 2.196 3.040 ... (remaining 112748 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'B' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.030 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.007 0.049 14450 Z= 0.324 Angle : 0.809 11.067 19655 Z= 0.432 Chirality : 0.048 0.261 2255 Planarity : 0.005 0.044 2420 Dihedral : 12.412 88.373 5470 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 23.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.23 (0.18), residues: 1705 helix: -2.95 (0.19), residues: 535 sheet: -3.24 (0.22), residues: 370 loop : -2.33 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 147 TYR 0.012 0.002 TYR A 74 PHE 0.021 0.002 PHE A 115 TRP 0.018 0.003 TRP B 259 HIS 0.004 0.001 HIS D 217 Details of bonding type rmsd covalent geometry : bond 0.00736 (14425) covalent geometry : angle 0.80385 (19590) SS BOND : bond 0.00703 ( 10) SS BOND : angle 2.49666 ( 20) hydrogen bonds : bond 0.30839 ( 535) hydrogen bonds : angle 10.52262 ( 1590) link_BETA1-4 : bond 0.00655 ( 10) link_BETA1-4 : angle 1.44442 ( 30) link_NAG-ASN : bond 0.00216 ( 5) link_NAG-ASN : angle 1.27793 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 481 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7857 (tp30) cc_final: 0.7503 (tp30) REVERT: A 96 ASP cc_start: 0.7708 (m-30) cc_final: 0.7261 (m-30) REVERT: A 108 SER cc_start: 0.8592 (t) cc_final: 0.8309 (t) REVERT: A 126 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7204 (pm20) REVERT: A 130 ASP cc_start: 0.8395 (m-30) cc_final: 0.8132 (m-30) REVERT: A 132 LYS cc_start: 0.8163 (mttm) cc_final: 0.7951 (mtmp) REVERT: A 189 LYS cc_start: 0.8608 (ptpt) cc_final: 0.8385 (ptpp) REVERT: A 206 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7979 (mttt) REVERT: A 312 SER cc_start: 0.8172 (m) cc_final: 0.7819 (p) REVERT: D 63 SER cc_start: 0.8337 (t) cc_final: 0.7751 (p) REVERT: D 75 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7467 (ttm-80) REVERT: D 96 ASP cc_start: 0.7877 (m-30) cc_final: 0.7503 (m-30) REVERT: D 102 ASP cc_start: 0.8025 (t0) cc_final: 0.7811 (t0) REVERT: D 126 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6896 (pm20) REVERT: D 132 LYS cc_start: 0.8195 (mttm) cc_final: 0.7801 (mtmt) REVERT: D 189 LYS cc_start: 0.8581 (ptpt) cc_final: 0.8364 (ptpp) REVERT: D 206 LYS cc_start: 0.8334 (mtpt) cc_final: 0.7876 (mttm) REVERT: D 210 ASP cc_start: 0.8283 (m-30) cc_final: 0.7976 (m-30) REVERT: D 235 GLN cc_start: 0.8053 (mm110) cc_final: 0.7746 (mt0) REVERT: D 312 SER cc_start: 0.8196 (m) cc_final: 0.7911 (p) REVERT: B 28 GLU cc_start: 0.7877 (tp30) cc_final: 0.7590 (tp30) REVERT: B 31 ASP cc_start: 0.8304 (m-30) cc_final: 0.7894 (m-30) REVERT: B 96 ASP cc_start: 0.7720 (m-30) cc_final: 0.7141 (m-30) REVERT: B 108 SER cc_start: 0.8576 (t) cc_final: 0.8365 (t) REVERT: B 126 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7174 (pm20) REVERT: B 132 LYS cc_start: 0.8143 (mttm) cc_final: 0.7866 (mtmp) REVERT: B 206 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7991 (mttm) REVERT: B 210 ASP cc_start: 0.8300 (m-30) cc_final: 0.8000 (m-30) REVERT: B 229 ARG cc_start: 0.7960 (mtt-85) cc_final: 0.7607 (mtt-85) REVERT: B 312 SER cc_start: 0.8159 (m) cc_final: 0.7846 (p) REVERT: C 28 GLU cc_start: 0.7845 (tp30) cc_final: 0.7550 (tp30) REVERT: C 96 ASP cc_start: 0.7756 (m-30) cc_final: 0.7356 (m-30) REVERT: C 108 SER cc_start: 0.8746 (t) cc_final: 0.8505 (t) REVERT: C 126 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7106 (pm20) REVERT: C 130 ASP cc_start: 0.8482 (m-30) cc_final: 0.8176 (m-30) REVERT: C 132 LYS cc_start: 0.8216 (mttm) cc_final: 0.7936 (mtmp) REVERT: C 189 LYS cc_start: 0.8559 (ptpt) cc_final: 0.8290 (ptpp) REVERT: C 206 LYS cc_start: 0.8311 (mtpt) cc_final: 0.7995 (mttm) REVERT: C 210 ASP cc_start: 0.8236 (m-30) cc_final: 0.7891 (m-30) REVERT: C 235 GLN cc_start: 0.7989 (mm110) cc_final: 0.7673 (mt0) REVERT: C 312 SER cc_start: 0.8218 (m) cc_final: 0.7936 (p) REVERT: E 28 GLU cc_start: 0.7947 (tp30) cc_final: 0.7647 (tp30) REVERT: E 75 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7615 (ttm-80) REVERT: E 96 ASP cc_start: 0.7711 (m-30) cc_final: 0.7201 (m-30) REVERT: E 108 SER cc_start: 0.8681 (t) cc_final: 0.8388 (t) REVERT: E 126 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7224 (pm20) REVERT: E 132 LYS cc_start: 0.8127 (mttm) cc_final: 0.7843 (mtmp) REVERT: E 189 LYS cc_start: 0.8466 (ptpt) cc_final: 0.8238 (ptpp) REVERT: E 210 ASP cc_start: 0.8281 (m-30) cc_final: 0.7934 (m-30) REVERT: E 235 GLN cc_start: 0.8057 (mm110) cc_final: 0.7851 (mm110) REVERT: E 312 SER cc_start: 0.8193 (m) cc_final: 0.7910 (p) outliers start: 0 outliers final: 0 residues processed: 481 average time/residue: 0.5417 time to fit residues: 287.2930 Evaluate side-chains 374 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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: 8.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.0470 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0040 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.0030 chunk 149 optimal weight: 2.9990 overall best weight: 0.3300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 77 ASN A 82 GLN A 141 ASN A 202 GLN A 231 HIS D 77 ASN D 82 GLN D 141 ASN D 202 GLN D 418 ASN B 62 ASN B 77 ASN B 82 GLN B 141 ASN B 219 ASN B 321 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 77 ASN C 82 GLN C 141 ASN C 219 ASN C 321 ASN E 62 ASN E 77 ASN E 82 GLN E 141 ASN E 171 GLN E 418 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.166429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.118005 restraints weight = 16872.891| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.91 r_work: 0.3100 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14450 Z= 0.159 Angle : 0.744 6.142 19655 Z= 0.385 Chirality : 0.048 0.167 2255 Planarity : 0.006 0.059 2420 Dihedral : 12.333 79.113 2190 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.64 % Allowed : 13.20 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.19), residues: 1705 helix: -1.28 (0.21), residues: 560 sheet: -2.59 (0.23), residues: 370 loop : -1.72 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 229 TYR 0.014 0.002 TYR D 317 PHE 0.025 0.002 PHE D 414 TRP 0.015 0.001 TRP A 259 HIS 0.004 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00329 (14425) covalent geometry : angle 0.73503 (19590) SS BOND : bond 0.00302 ( 10) SS BOND : angle 1.39985 ( 20) hydrogen bonds : bond 0.05469 ( 535) hydrogen bonds : angle 5.80698 ( 1590) link_BETA1-4 : bond 0.00651 ( 10) link_BETA1-4 : angle 2.95346 ( 30) link_NAG-ASN : bond 0.00275 ( 5) link_NAG-ASN : angle 0.26643 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 404 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 PRO cc_start: 0.6711 (Cg_exo) cc_final: 0.6490 (Cg_endo) REVERT: A 104 SER cc_start: 0.8178 (t) cc_final: 0.7631 (p) REVERT: A 126 GLU cc_start: 0.7769 (mt-10) cc_final: 0.6929 (pm20) REVERT: A 132 LYS cc_start: 0.7864 (mttm) cc_final: 0.7652 (mtmp) REVERT: A 135 ARG cc_start: 0.7911 (ptp-170) cc_final: 0.7503 (ptp-170) REVERT: A 141 ASN cc_start: 0.8178 (m110) cc_final: 0.7857 (m110) REVERT: A 189 LYS cc_start: 0.8398 (ptpt) cc_final: 0.8135 (ptmm) REVERT: A 235 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7682 (mt0) REVERT: D 49 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8766 (mmmm) REVERT: D 63 SER cc_start: 0.8384 (t) cc_final: 0.7828 (p) REVERT: D 75 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7584 (ttm-80) REVERT: D 96 ASP cc_start: 0.8011 (m-30) cc_final: 0.7534 (m-30) REVERT: D 97 ASP cc_start: 0.7957 (m-30) cc_final: 0.7591 (t0) REVERT: D 126 GLU cc_start: 0.7564 (mt-10) cc_final: 0.6454 (pm20) REVERT: D 130 ASP cc_start: 0.8432 (m-30) cc_final: 0.8128 (m-30) REVERT: D 132 LYS cc_start: 0.7838 (mttm) cc_final: 0.7531 (mtmm) REVERT: D 135 ARG cc_start: 0.7750 (ptp-170) cc_final: 0.7138 (ptp-170) REVERT: D 141 ASN cc_start: 0.8055 (m110) cc_final: 0.7674 (m110) REVERT: D 179 MET cc_start: 0.8077 (mmm) cc_final: 0.7769 (mmm) REVERT: D 189 LYS cc_start: 0.8256 (ptpt) cc_final: 0.8040 (ptpp) REVERT: D 206 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7703 (mttm) REVERT: D 210 ASP cc_start: 0.8331 (m-30) cc_final: 0.8129 (m-30) REVERT: D 212 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6862 (ptt90) REVERT: D 235 GLN cc_start: 0.7959 (mm110) cc_final: 0.7632 (mt0) REVERT: D 262 MET cc_start: 0.8254 (mpp) cc_final: 0.7053 (tmt) REVERT: B 94 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.8269 (t80) REVERT: B 108 SER cc_start: 0.8724 (t) cc_final: 0.8438 (p) REVERT: B 126 GLU cc_start: 0.7799 (mt-10) cc_final: 0.6986 (pm20) REVERT: B 132 LYS cc_start: 0.7885 (mttm) cc_final: 0.7671 (mtmp) REVERT: B 135 ARG cc_start: 0.7775 (ptp-170) cc_final: 0.7478 (ptp-170) REVERT: B 179 MET cc_start: 0.8047 (mmm) cc_final: 0.7584 (mmm) REVERT: B 206 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7963 (mttt) REVERT: B 210 ASP cc_start: 0.8284 (m-30) cc_final: 0.7705 (m-30) REVERT: B 212 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7579 (pmm-80) REVERT: B 219 ASN cc_start: 0.8264 (p0) cc_final: 0.8038 (p0) REVERT: B 229 ARG cc_start: 0.8170 (mtt-85) cc_final: 0.7857 (mmm-85) REVERT: B 235 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7658 (mt0) REVERT: B 262 MET cc_start: 0.8063 (mpp) cc_final: 0.6999 (tmt) REVERT: C 94 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7253 (t80) REVERT: C 96 ASP cc_start: 0.7949 (m-30) cc_final: 0.7711 (m-30) REVERT: C 100 ASP cc_start: 0.7973 (m-30) cc_final: 0.7698 (t70) REVERT: C 126 GLU cc_start: 0.7678 (mt-10) cc_final: 0.6766 (pm20) REVERT: C 130 ASP cc_start: 0.8497 (m-30) cc_final: 0.8186 (m-30) REVERT: C 135 ARG cc_start: 0.7858 (ptp-170) cc_final: 0.7269 (mtp180) REVERT: C 156 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8555 (mmp) REVERT: C 179 MET cc_start: 0.8078 (mmm) cc_final: 0.7844 (mmm) REVERT: C 189 LYS cc_start: 0.8324 (ptpt) cc_final: 0.8107 (ptpp) REVERT: C 206 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7940 (mttm) REVERT: C 210 ASP cc_start: 0.8317 (m-30) cc_final: 0.8116 (m-30) REVERT: C 235 GLN cc_start: 0.7940 (mm110) cc_final: 0.7618 (mt0) REVERT: C 401 ARG cc_start: 0.8727 (mmm160) cc_final: 0.8351 (mmm-85) REVERT: E 28 GLU cc_start: 0.8212 (tp30) cc_final: 0.7878 (tp30) REVERT: E 62 ASN cc_start: 0.7992 (m-40) cc_final: 0.7789 (m-40) REVERT: E 75 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7670 (ttm-80) REVERT: E 105 MET cc_start: 0.7312 (tpp) cc_final: 0.7044 (tpp) REVERT: E 126 GLU cc_start: 0.7837 (mt-10) cc_final: 0.6741 (pm20) REVERT: E 132 LYS cc_start: 0.7918 (mttm) cc_final: 0.7636 (mtmp) REVERT: E 135 ARG cc_start: 0.7706 (ptp-170) cc_final: 0.7217 (ttp-170) REVERT: E 141 ASN cc_start: 0.8136 (m110) cc_final: 0.7935 (m110) REVERT: E 189 LYS cc_start: 0.8107 (ptpt) cc_final: 0.7862 (ptpp) REVERT: E 210 ASP cc_start: 0.8268 (m-30) cc_final: 0.7891 (m-30) REVERT: E 235 GLN cc_start: 0.8001 (mm110) cc_final: 0.7496 (mt0) REVERT: E 262 MET cc_start: 0.8281 (mpp) cc_final: 0.7093 (tmt) outliers start: 40 outliers final: 15 residues processed: 411 average time/residue: 0.5542 time to fit residues: 251.1364 Evaluate side-chains 375 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 353 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 424 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 110 optimal weight: 0.1980 chunk 1 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 58 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 202 GLN B 418 ASN C 62 ASN C 219 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.165854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.115463 restraints weight = 16562.286| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.92 r_work: 0.3139 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14450 Z= 0.143 Angle : 0.672 7.115 19655 Z= 0.346 Chirality : 0.045 0.152 2255 Planarity : 0.005 0.055 2420 Dihedral : 11.342 68.810 2190 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.37 % Allowed : 16.83 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.94 (0.20), residues: 1705 helix: -0.21 (0.22), residues: 550 sheet: -2.18 (0.24), residues: 370 loop : -1.52 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 212 TYR 0.018 0.001 TYR C 317 PHE 0.016 0.001 PHE E 29 TRP 0.013 0.001 TRP C 259 HIS 0.003 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00322 (14425) covalent geometry : angle 0.66074 (19590) SS BOND : bond 0.00364 ( 10) SS BOND : angle 1.68362 ( 20) hydrogen bonds : bond 0.04391 ( 535) hydrogen bonds : angle 5.24129 ( 1590) link_BETA1-4 : bond 0.00596 ( 10) link_BETA1-4 : angle 2.89440 ( 30) link_NAG-ASN : bond 0.00032 ( 5) link_NAG-ASN : angle 0.56497 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 353 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 PRO cc_start: 0.6775 (Cg_exo) cc_final: 0.6512 (Cg_endo) REVERT: A 104 SER cc_start: 0.8277 (t) cc_final: 0.7720 (p) REVERT: A 126 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7198 (pm20) REVERT: A 135 ARG cc_start: 0.7942 (ptp-170) cc_final: 0.7404 (ptp-170) REVERT: A 141 ASN cc_start: 0.8405 (m110) cc_final: 0.8094 (m110) REVERT: A 235 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8063 (mt0) REVERT: D 49 LYS cc_start: 0.9036 (mmmt) cc_final: 0.8767 (mmmm) REVERT: D 63 SER cc_start: 0.8734 (t) cc_final: 0.8243 (p) REVERT: D 72 MET cc_start: 0.9234 (mtt) cc_final: 0.9015 (mmt) REVERT: D 75 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7805 (ttm-80) REVERT: D 126 GLU cc_start: 0.7806 (mt-10) cc_final: 0.6799 (pm20) REVERT: D 130 ASP cc_start: 0.8540 (m-30) cc_final: 0.8299 (m-30) REVERT: D 132 LYS cc_start: 0.8026 (mttm) cc_final: 0.7802 (mtmm) REVERT: D 135 ARG cc_start: 0.7869 (ptp-170) cc_final: 0.7441 (ptp-170) REVERT: D 189 LYS cc_start: 0.8363 (ptpt) cc_final: 0.8152 (ptpp) REVERT: D 206 LYS cc_start: 0.8439 (mtpt) cc_final: 0.8030 (mttm) REVERT: D 227 GLU cc_start: 0.8532 (pt0) cc_final: 0.8250 (pt0) REVERT: D 235 GLN cc_start: 0.8040 (mm110) cc_final: 0.7817 (mt0) REVERT: D 262 MET cc_start: 0.8261 (mpp) cc_final: 0.6767 (tmt) REVERT: B 32 LYS cc_start: 0.8204 (tmtt) cc_final: 0.7976 (tmtt) REVERT: B 94 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.8299 (t80) REVERT: B 126 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7140 (pm20) REVERT: B 135 ARG cc_start: 0.7911 (ptp-170) cc_final: 0.7665 (ptp-170) REVERT: B 179 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7857 (mmm) REVERT: B 206 LYS cc_start: 0.8441 (mtpt) cc_final: 0.8201 (mttp) REVERT: B 210 ASP cc_start: 0.8511 (m-30) cc_final: 0.8268 (m-30) REVERT: B 219 ASN cc_start: 0.8309 (p0) cc_final: 0.8065 (p0) REVERT: B 229 ARG cc_start: 0.8491 (mtt-85) cc_final: 0.7788 (mmm-85) REVERT: B 235 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7890 (mt0) REVERT: B 262 MET cc_start: 0.8087 (mpp) cc_final: 0.6746 (tmt) REVERT: C 94 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7121 (t80) REVERT: C 96 ASP cc_start: 0.7948 (m-30) cc_final: 0.7597 (m-30) REVERT: C 102 ASP cc_start: 0.7638 (t70) cc_final: 0.7157 (t0) REVERT: C 126 GLU cc_start: 0.7853 (mt-10) cc_final: 0.6989 (pm20) REVERT: C 135 ARG cc_start: 0.8017 (ptp-170) cc_final: 0.7708 (ptp-170) REVERT: C 206 LYS cc_start: 0.8424 (mtpt) cc_final: 0.8170 (mttm) REVERT: C 227 GLU cc_start: 0.8512 (pt0) cc_final: 0.8289 (pt0) REVERT: C 235 GLN cc_start: 0.8111 (mm110) cc_final: 0.7860 (mt0) REVERT: C 243 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7563 (mtt) REVERT: C 401 ARG cc_start: 0.8693 (mmm160) cc_final: 0.8300 (mmm-85) REVERT: E 71 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.9026 (p) REVERT: E 75 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7913 (ttm-80) REVERT: E 126 GLU cc_start: 0.7933 (mt-10) cc_final: 0.6939 (pm20) REVERT: E 132 LYS cc_start: 0.8129 (mttm) cc_final: 0.7908 (mtmp) REVERT: E 135 ARG cc_start: 0.7843 (ptp-170) cc_final: 0.7442 (ptp-170) REVERT: E 210 ASP cc_start: 0.8472 (m-30) cc_final: 0.8183 (m-30) REVERT: E 235 GLN cc_start: 0.8060 (mm110) cc_final: 0.7774 (mt0) REVERT: E 262 MET cc_start: 0.8251 (mpp) cc_final: 0.6892 (tmt) outliers start: 51 outliers final: 29 residues processed: 366 average time/residue: 0.5638 time to fit residues: 227.0564 Evaluate side-chains 361 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 325 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 135 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 129 optimal weight: 0.3980 chunk 112 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS C 219 ASN C 231 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.165773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116010 restraints weight = 16245.806| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.89 r_work: 0.3133 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14450 Z= 0.138 Angle : 0.657 7.487 19655 Z= 0.334 Chirality : 0.044 0.153 2255 Planarity : 0.004 0.049 2420 Dihedral : 10.127 59.426 2190 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.89 % Allowed : 18.81 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.20), residues: 1705 helix: 0.35 (0.23), residues: 550 sheet: -1.83 (0.25), residues: 370 loop : -1.46 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 229 TYR 0.017 0.001 TYR C 317 PHE 0.015 0.001 PHE D 414 TRP 0.011 0.001 TRP C 259 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00313 (14425) covalent geometry : angle 0.64474 (19590) SS BOND : bond 0.00392 ( 10) SS BOND : angle 1.49501 ( 20) hydrogen bonds : bond 0.03853 ( 535) hydrogen bonds : angle 4.90670 ( 1590) link_BETA1-4 : bond 0.00483 ( 10) link_BETA1-4 : angle 3.06846 ( 30) link_NAG-ASN : bond 0.00015 ( 5) link_NAG-ASN : angle 0.47396 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 335 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 PRO cc_start: 0.6698 (Cg_exo) cc_final: 0.6482 (Cg_endo) REVERT: A 43 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.8268 (mtm180) REVERT: A 104 SER cc_start: 0.8132 (t) cc_final: 0.7592 (p) REVERT: A 126 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7187 (pm20) REVERT: A 135 ARG cc_start: 0.7927 (ptp-170) cc_final: 0.7453 (ptp-170) REVERT: A 141 ASN cc_start: 0.8405 (m110) cc_final: 0.8089 (m110) REVERT: A 243 MET cc_start: 0.8358 (mpp) cc_final: 0.7843 (mtt) REVERT: A 391 MET cc_start: 0.5164 (pmm) cc_final: 0.4853 (pmm) REVERT: D 63 SER cc_start: 0.8720 (t) cc_final: 0.8236 (p) REVERT: D 72 MET cc_start: 0.9232 (mtt) cc_final: 0.9017 (mmt) REVERT: D 75 ARG cc_start: 0.8106 (ttm-80) cc_final: 0.7759 (ttm-80) REVERT: D 96 ASP cc_start: 0.8062 (p0) cc_final: 0.7787 (p0) REVERT: D 126 GLU cc_start: 0.7808 (mt-10) cc_final: 0.6811 (pm20) REVERT: D 132 LYS cc_start: 0.7951 (mttm) cc_final: 0.7543 (mtmt) REVERT: D 135 ARG cc_start: 0.7862 (ptp-170) cc_final: 0.7391 (ptp-170) REVERT: D 206 LYS cc_start: 0.8410 (mtpt) cc_final: 0.8171 (mttt) REVERT: D 235 GLN cc_start: 0.8020 (mm110) cc_final: 0.7787 (mt0) REVERT: D 243 MET cc_start: 0.8264 (mpp) cc_final: 0.7730 (mtt) REVERT: D 262 MET cc_start: 0.8179 (mpp) cc_final: 0.6703 (tmt) REVERT: B 102 ASP cc_start: 0.7606 (t70) cc_final: 0.7110 (t0) REVERT: B 126 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7163 (pm20) REVERT: B 135 ARG cc_start: 0.7935 (ptp-170) cc_final: 0.7653 (ptp-170) REVERT: B 179 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7907 (mmm) REVERT: B 206 LYS cc_start: 0.8467 (mtpt) cc_final: 0.8249 (mttp) REVERT: B 210 ASP cc_start: 0.8511 (m-30) cc_final: 0.8279 (m-30) REVERT: B 229 ARG cc_start: 0.8534 (mtt-85) cc_final: 0.7889 (mmm-85) REVERT: B 235 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8012 (mt0) REVERT: B 262 MET cc_start: 0.8074 (mpp) cc_final: 0.6606 (tmt) REVERT: C 102 ASP cc_start: 0.7801 (t70) cc_final: 0.7163 (t0) REVERT: C 126 GLU cc_start: 0.7796 (mt-10) cc_final: 0.6865 (pm20) REVERT: C 135 ARG cc_start: 0.7915 (ptp-170) cc_final: 0.7630 (ptp-170) REVERT: C 206 LYS cc_start: 0.8410 (mtpt) cc_final: 0.8162 (mttm) REVERT: C 235 GLN cc_start: 0.8090 (mm110) cc_final: 0.7864 (mt0) REVERT: C 243 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7667 (mtt) REVERT: C 401 ARG cc_start: 0.8701 (mmm160) cc_final: 0.8298 (mmm-85) REVERT: E 71 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8980 (p) REVERT: E 75 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.7872 (ttm-80) REVERT: E 96 ASP cc_start: 0.7927 (p0) cc_final: 0.7716 (p0) REVERT: E 126 GLU cc_start: 0.7912 (mt-10) cc_final: 0.6899 (pm20) REVERT: E 132 LYS cc_start: 0.8063 (mttm) cc_final: 0.7817 (mtmp) REVERT: E 135 ARG cc_start: 0.7811 (ptp-170) cc_final: 0.7317 (ttp-170) REVERT: E 138 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8812 (mtmt) REVERT: E 206 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7913 (mttt) REVERT: E 210 ASP cc_start: 0.8471 (m-30) cc_final: 0.8168 (m-30) REVERT: E 219 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.8125 (p0) REVERT: E 235 GLN cc_start: 0.8056 (mm110) cc_final: 0.7763 (mt0) REVERT: E 262 MET cc_start: 0.8219 (mpp) cc_final: 0.6809 (tmt) outliers start: 59 outliers final: 27 residues processed: 354 average time/residue: 0.5468 time to fit residues: 212.9784 Evaluate side-chains 350 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 317 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 219 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 84 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 121 optimal weight: 0.0370 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.163234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.113037 restraints weight = 16418.703| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.89 r_work: 0.3250 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14450 Z= 0.187 Angle : 0.685 8.212 19655 Z= 0.350 Chirality : 0.046 0.139 2255 Planarity : 0.005 0.050 2420 Dihedral : 8.914 50.136 2190 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.87 % Allowed : 17.10 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.20), residues: 1705 helix: 0.62 (0.23), residues: 565 sheet: -1.61 (0.26), residues: 370 loop : -1.65 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 212 TYR 0.016 0.002 TYR B 317 PHE 0.014 0.002 PHE A 124 TRP 0.012 0.002 TRP C 259 HIS 0.003 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00444 (14425) covalent geometry : angle 0.67356 (19590) SS BOND : bond 0.00502 ( 10) SS BOND : angle 1.81240 ( 20) hydrogen bonds : bond 0.03814 ( 535) hydrogen bonds : angle 4.78575 ( 1590) link_BETA1-4 : bond 0.00522 ( 10) link_BETA1-4 : angle 3.00911 ( 30) link_NAG-ASN : bond 0.00114 ( 5) link_NAG-ASN : angle 0.63852 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 314 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 PRO cc_start: 0.6587 (Cg_exo) cc_final: 0.6357 (Cg_endo) REVERT: A 94 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.7538 (t80) REVERT: A 126 GLU cc_start: 0.7785 (mt-10) cc_final: 0.6917 (pm20) REVERT: A 135 ARG cc_start: 0.7798 (ptp-170) cc_final: 0.7533 (ptp-170) REVERT: A 141 ASN cc_start: 0.8166 (m110) cc_final: 0.7854 (m110) REVERT: A 243 MET cc_start: 0.8215 (mpp) cc_final: 0.7616 (mtt) REVERT: A 312 SER cc_start: 0.8045 (OUTLIER) cc_final: 0.7649 (p) REVERT: A 391 MET cc_start: 0.4901 (pmm) cc_final: 0.4616 (pmm) REVERT: D 63 SER cc_start: 0.8460 (t) cc_final: 0.7905 (p) REVERT: D 72 MET cc_start: 0.9052 (mtt) cc_final: 0.8799 (mmt) REVERT: D 75 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7478 (ttm-80) REVERT: D 81 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.8024 (mpp80) REVERT: D 102 ASP cc_start: 0.7871 (t0) cc_final: 0.7651 (t0) REVERT: D 126 GLU cc_start: 0.7604 (mt-10) cc_final: 0.6766 (pm20) REVERT: D 135 ARG cc_start: 0.7683 (ptp-170) cc_final: 0.7243 (ptp-170) REVERT: D 206 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7801 (mttt) REVERT: D 219 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7773 (p0) REVERT: D 227 GLU cc_start: 0.8455 (pt0) cc_final: 0.8065 (pt0) REVERT: D 235 GLN cc_start: 0.8023 (mm110) cc_final: 0.7683 (mt0) REVERT: D 262 MET cc_start: 0.8102 (mpp) cc_final: 0.6661 (tmt) REVERT: B 126 GLU cc_start: 0.7758 (mt-10) cc_final: 0.6872 (pm20) REVERT: B 135 ARG cc_start: 0.7742 (ptp-170) cc_final: 0.7420 (ptp-170) REVERT: B 179 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7698 (mmm) REVERT: B 206 LYS cc_start: 0.8350 (mtpt) cc_final: 0.8003 (mttt) REVERT: B 210 ASP cc_start: 0.8479 (m-30) cc_final: 0.8241 (m-30) REVERT: B 219 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7861 (p0) REVERT: B 229 ARG cc_start: 0.8427 (mtt-85) cc_final: 0.7741 (mmm-85) REVERT: B 235 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7904 (mt0) REVERT: B 262 MET cc_start: 0.7993 (mpp) cc_final: 0.6730 (tmt) REVERT: C 94 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.7142 (t80) REVERT: C 126 GLU cc_start: 0.7608 (mt-10) cc_final: 0.6667 (pm20) REVERT: C 130 ASP cc_start: 0.8471 (m-30) cc_final: 0.8264 (m-30) REVERT: C 135 ARG cc_start: 0.7742 (ptp-170) cc_final: 0.7440 (ptp-170) REVERT: C 179 MET cc_start: 0.8105 (mmm) cc_final: 0.7882 (mmm) REVERT: C 189 LYS cc_start: 0.8239 (ptpp) cc_final: 0.7705 (ptpp) REVERT: C 206 LYS cc_start: 0.8238 (mtpt) cc_final: 0.7916 (mttm) REVERT: C 235 GLN cc_start: 0.8068 (mm110) cc_final: 0.7743 (mt0) REVERT: C 243 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7517 (mtt) REVERT: C 401 ARG cc_start: 0.8747 (mmm160) cc_final: 0.8335 (mmm-85) REVERT: E 71 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8821 (p) REVERT: E 75 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7587 (ttm-80) REVERT: E 94 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.8224 (t80) REVERT: E 96 ASP cc_start: 0.8038 (p0) cc_final: 0.7777 (p0) REVERT: E 126 GLU cc_start: 0.7660 (mt-10) cc_final: 0.6699 (pm20) REVERT: E 132 LYS cc_start: 0.7842 (mttm) cc_final: 0.7481 (mtmp) REVERT: E 135 ARG cc_start: 0.7638 (ptp-170) cc_final: 0.7078 (ttp-170) REVERT: E 138 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8643 (mtmt) REVERT: E 141 ASN cc_start: 0.8174 (m110) cc_final: 0.7968 (m110) REVERT: E 206 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7637 (mttp) REVERT: E 210 ASP cc_start: 0.8348 (m-30) cc_final: 0.7993 (m-30) REVERT: E 219 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7942 (p0) REVERT: E 235 GLN cc_start: 0.8004 (mm110) cc_final: 0.7581 (mt0) REVERT: E 262 MET cc_start: 0.8051 (mpp) cc_final: 0.6738 (tmt) REVERT: E 284 SER cc_start: 0.9316 (p) cc_final: 0.9097 (p) REVERT: E 312 SER cc_start: 0.8065 (m) cc_final: 0.7677 (p) outliers start: 89 outliers final: 48 residues processed: 349 average time/residue: 0.5400 time to fit residues: 207.9845 Evaluate side-chains 360 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 299 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 96 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 169 optimal weight: 0.4980 chunk 139 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.164667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.115040 restraints weight = 16366.179| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.92 r_work: 0.3118 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14450 Z= 0.144 Angle : 0.669 8.374 19655 Z= 0.339 Chirality : 0.045 0.144 2255 Planarity : 0.004 0.041 2420 Dihedral : 7.524 38.891 2190 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.42 % Allowed : 19.47 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.21), residues: 1705 helix: 0.81 (0.23), residues: 560 sheet: -1.46 (0.26), residues: 370 loop : -1.40 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 212 TYR 0.015 0.001 TYR C 317 PHE 0.014 0.001 PHE C 322 TRP 0.010 0.001 TRP C 186 HIS 0.002 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00335 (14425) covalent geometry : angle 0.65810 (19590) SS BOND : bond 0.00369 ( 10) SS BOND : angle 1.71033 ( 20) hydrogen bonds : bond 0.03643 ( 535) hydrogen bonds : angle 4.65460 ( 1590) link_BETA1-4 : bond 0.00408 ( 10) link_BETA1-4 : angle 2.90297 ( 30) link_NAG-ASN : bond 0.00044 ( 5) link_NAG-ASN : angle 0.39191 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 311 time to evaluate : 0.493 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: A 25 PRO cc_start: 0.6722 (Cg_exo) cc_final: 0.6506 (Cg_endo) REVERT: A 94 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.7518 (t80) REVERT: A 126 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7180 (pm20) REVERT: A 135 ARG cc_start: 0.8014 (ptp-170) cc_final: 0.7620 (ptp-170) REVERT: A 141 ASN cc_start: 0.8407 (m110) cc_final: 0.8116 (m110) REVERT: A 243 MET cc_start: 0.8415 (tpp) cc_final: 0.7740 (mtt) REVERT: A 312 SER cc_start: 0.8094 (OUTLIER) cc_final: 0.7701 (p) REVERT: D 63 SER cc_start: 0.8707 (t) cc_final: 0.8220 (p) REVERT: D 75 ARG cc_start: 0.8105 (ttm-80) cc_final: 0.7752 (ttm-80) REVERT: D 81 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8309 (mpp80) REVERT: D 120 LYS cc_start: 0.8430 (ttmp) cc_final: 0.8205 (ttmt) REVERT: D 126 GLU cc_start: 0.7790 (mt-10) cc_final: 0.6806 (pm20) REVERT: D 135 ARG cc_start: 0.7880 (ptp-170) cc_final: 0.7397 (ptp-170) REVERT: D 206 LYS cc_start: 0.8419 (mtpt) cc_final: 0.8195 (mttp) REVERT: D 219 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7803 (p0) REVERT: D 235 GLN cc_start: 0.8246 (mm110) cc_final: 0.7985 (mt0) REVERT: D 243 MET cc_start: 0.8371 (mpp) cc_final: 0.8067 (mtt) REVERT: D 262 MET cc_start: 0.8081 (mpp) cc_final: 0.6636 (tmt) REVERT: B 49 LYS cc_start: 0.9150 (mmmm) cc_final: 0.8828 (mmmt) REVERT: B 126 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7168 (pm20) REVERT: B 135 ARG cc_start: 0.7943 (ptp-170) cc_final: 0.7673 (ptp-170) REVERT: B 179 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7911 (mmm) REVERT: B 206 LYS cc_start: 0.8501 (mtpt) cc_final: 0.8204 (mttp) REVERT: B 210 ASP cc_start: 0.8525 (m-30) cc_final: 0.8303 (m-30) REVERT: B 219 ASN cc_start: 0.8201 (OUTLIER) cc_final: 0.7891 (p0) REVERT: B 229 ARG cc_start: 0.8577 (mtt-85) cc_final: 0.7696 (mmm-85) REVERT: B 235 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8131 (mt0) REVERT: B 262 MET cc_start: 0.8020 (mpp) cc_final: 0.6762 (tmt) REVERT: C 104 SER cc_start: 0.8056 (OUTLIER) cc_final: 0.7568 (p) REVERT: C 126 GLU cc_start: 0.7794 (mt-10) cc_final: 0.6851 (pm20) REVERT: C 135 ARG cc_start: 0.7908 (ptp-170) cc_final: 0.7670 (ptp-170) REVERT: C 206 LYS cc_start: 0.8461 (mtpt) cc_final: 0.8196 (mttm) REVERT: C 243 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7841 (mtt) REVERT: C 401 ARG cc_start: 0.8698 (mmm160) cc_final: 0.8276 (mmm-85) REVERT: E 71 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8932 (p) REVERT: E 94 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.8086 (t80) REVERT: E 96 ASP cc_start: 0.7999 (p0) cc_final: 0.7727 (p0) REVERT: E 126 GLU cc_start: 0.7890 (mt-10) cc_final: 0.6932 (pm20) REVERT: E 132 LYS cc_start: 0.8044 (mttm) cc_final: 0.7761 (mtmp) REVERT: E 135 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7385 (mtp180) REVERT: E 138 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8813 (mtmt) REVERT: E 206 LYS cc_start: 0.8386 (mtpt) cc_final: 0.7945 (mttp) REVERT: E 210 ASP cc_start: 0.8461 (m-30) cc_final: 0.8143 (m-30) REVERT: E 219 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.7991 (p0) REVERT: E 235 GLN cc_start: 0.8129 (mm110) cc_final: 0.7823 (mt0) REVERT: E 262 MET cc_start: 0.8092 (mpp) cc_final: 0.6773 (tmt) REVERT: E 312 SER cc_start: 0.8112 (OUTLIER) cc_final: 0.7728 (p) outliers start: 67 outliers final: 33 residues processed: 333 average time/residue: 0.5793 time to fit residues: 212.2769 Evaluate side-chains 345 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 297 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 ARG Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 312 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 38 optimal weight: 0.1980 chunk 132 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 149 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.162216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.111166 restraints weight = 16693.522| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.03 r_work: 0.3097 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14450 Z= 0.147 Angle : 0.673 9.011 19655 Z= 0.340 Chirality : 0.045 0.140 2255 Planarity : 0.004 0.042 2420 Dihedral : 6.145 25.846 2190 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.16 % Allowed : 20.26 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.21), residues: 1705 helix: 0.99 (0.23), residues: 560 sheet: -1.36 (0.26), residues: 370 loop : -1.39 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 392 TYR 0.014 0.001 TYR C 317 PHE 0.014 0.001 PHE C 322 TRP 0.010 0.001 TRP C 186 HIS 0.002 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00344 (14425) covalent geometry : angle 0.66493 (19590) SS BOND : bond 0.00419 ( 10) SS BOND : angle 1.54783 ( 20) hydrogen bonds : bond 0.03534 ( 535) hydrogen bonds : angle 4.52530 ( 1590) link_BETA1-4 : bond 0.00492 ( 10) link_BETA1-4 : angle 2.58254 ( 30) link_NAG-ASN : bond 0.00019 ( 5) link_NAG-ASN : angle 0.43682 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 303 time to evaluate : 0.495 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 94 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.7477 (t80) REVERT: A 126 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7186 (pm20) REVERT: A 141 ASN cc_start: 0.8390 (m110) cc_final: 0.8114 (m110) REVERT: A 219 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7853 (p0) REVERT: A 243 MET cc_start: 0.8436 (tpp) cc_final: 0.7870 (mtt) REVERT: A 312 SER cc_start: 0.8070 (OUTLIER) cc_final: 0.7669 (p) REVERT: D 63 SER cc_start: 0.8684 (t) cc_final: 0.8190 (p) REVERT: D 75 ARG cc_start: 0.8136 (ttm-80) cc_final: 0.7772 (ttm-80) REVERT: D 81 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8319 (mpp80) REVERT: D 94 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.8074 (t80) REVERT: D 126 GLU cc_start: 0.7834 (mt-10) cc_final: 0.6845 (pm20) REVERT: D 135 ARG cc_start: 0.7894 (ptp-170) cc_final: 0.7415 (ptp-170) REVERT: D 206 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8217 (mttp) REVERT: D 235 GLN cc_start: 0.8246 (mm110) cc_final: 0.7988 (mt0) REVERT: D 262 MET cc_start: 0.8002 (mpp) cc_final: 0.6698 (tmt) REVERT: B 49 LYS cc_start: 0.9171 (mmmm) cc_final: 0.8855 (mmmt) REVERT: B 126 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7164 (pm20) REVERT: B 135 ARG cc_start: 0.7951 (ptp-170) cc_final: 0.7663 (ptp-170) REVERT: B 179 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7877 (mmt) REVERT: B 206 LYS cc_start: 0.8517 (mtpt) cc_final: 0.8169 (mttp) REVERT: B 210 ASP cc_start: 0.8520 (m-30) cc_final: 0.8260 (m-30) REVERT: B 219 ASN cc_start: 0.8200 (OUTLIER) cc_final: 0.7879 (p0) REVERT: B 229 ARG cc_start: 0.8578 (mtt-85) cc_final: 0.7719 (mmm-85) REVERT: B 235 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8141 (mt0) REVERT: B 262 MET cc_start: 0.7938 (mpp) cc_final: 0.6640 (tmt) REVERT: C 94 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.7234 (t80) REVERT: C 126 GLU cc_start: 0.7807 (mt-10) cc_final: 0.6934 (pm20) REVERT: C 135 ARG cc_start: 0.7912 (ptp-170) cc_final: 0.7658 (ptp-170) REVERT: C 206 LYS cc_start: 0.8471 (mtpt) cc_final: 0.8207 (mttm) REVERT: C 401 ARG cc_start: 0.8703 (mmm160) cc_final: 0.8274 (mmm-85) REVERT: E 71 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8839 (p) REVERT: E 94 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.7912 (t80) REVERT: E 96 ASP cc_start: 0.8037 (p0) cc_final: 0.7837 (p0) REVERT: E 120 LYS cc_start: 0.8430 (tttp) cc_final: 0.8142 (tttt) REVERT: E 126 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7004 (pm20) REVERT: E 132 LYS cc_start: 0.8079 (mttm) cc_final: 0.7812 (mtmp) REVERT: E 135 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7331 (mtp180) REVERT: E 138 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8761 (mtmt) REVERT: E 210 ASP cc_start: 0.8439 (m-30) cc_final: 0.8134 (m-30) REVERT: E 219 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7893 (p0) REVERT: E 235 GLN cc_start: 0.8163 (mm110) cc_final: 0.7854 (mt0) REVERT: E 262 MET cc_start: 0.8046 (mpp) cc_final: 0.6791 (tmt) REVERT: E 312 SER cc_start: 0.8139 (OUTLIER) cc_final: 0.7774 (p) REVERT: E 391 MET cc_start: 0.4880 (pmm) cc_final: 0.3874 (ppp) outliers start: 63 outliers final: 32 residues processed: 324 average time/residue: 0.5813 time to fit residues: 207.1842 Evaluate side-chains 340 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 293 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 ARG Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 312 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 34 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.163463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114087 restraints weight = 16509.711| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.86 r_work: 0.3112 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14450 Z= 0.158 Angle : 0.687 14.300 19655 Z= 0.345 Chirality : 0.045 0.141 2255 Planarity : 0.004 0.040 2420 Dihedral : 5.427 41.495 2190 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.22 % Allowed : 20.46 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.21), residues: 1705 helix: 1.17 (0.23), residues: 560 sheet: -1.32 (0.26), residues: 370 loop : -1.45 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 212 TYR 0.015 0.001 TYR B 317 PHE 0.015 0.001 PHE C 322 TRP 0.010 0.001 TRP C 259 HIS 0.002 0.001 HIS D 217 Details of bonding type rmsd covalent geometry : bond 0.00372 (14425) covalent geometry : angle 0.67846 (19590) SS BOND : bond 0.00387 ( 10) SS BOND : angle 2.28234 ( 20) hydrogen bonds : bond 0.03526 ( 535) hydrogen bonds : angle 4.48839 ( 1590) link_BETA1-4 : bond 0.00519 ( 10) link_BETA1-4 : angle 2.24408 ( 30) link_NAG-ASN : bond 0.00023 ( 5) link_NAG-ASN : angle 0.45486 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 292 time to evaluate : 0.519 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 94 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.7737 (t80) REVERT: A 126 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7182 (pm20) REVERT: A 132 LYS cc_start: 0.7963 (mttm) cc_final: 0.7728 (mtmp) REVERT: A 141 ASN cc_start: 0.8375 (m110) cc_final: 0.8106 (m110) REVERT: A 243 MET cc_start: 0.8488 (tpp) cc_final: 0.7902 (mtt) REVERT: A 312 SER cc_start: 0.8059 (OUTLIER) cc_final: 0.7653 (p) REVERT: D 75 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7761 (ttm-80) REVERT: D 81 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8325 (mpp80) REVERT: D 126 GLU cc_start: 0.7816 (mt-10) cc_final: 0.6848 (pm20) REVERT: D 135 ARG cc_start: 0.7932 (ptp-170) cc_final: 0.7547 (ptp-170) REVERT: D 206 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8135 (mttp) REVERT: D 235 GLN cc_start: 0.8278 (mm110) cc_final: 0.8032 (mt0) REVERT: D 262 MET cc_start: 0.7964 (mpp) cc_final: 0.6642 (tmt) REVERT: B 49 LYS cc_start: 0.9184 (mmmm) cc_final: 0.8904 (mmmt) REVERT: B 126 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7183 (pm20) REVERT: B 135 ARG cc_start: 0.7935 (ptp-170) cc_final: 0.7664 (ptp-170) REVERT: B 179 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7805 (mmm) REVERT: B 189 LYS cc_start: 0.7891 (ptpp) cc_final: 0.7546 (ptpp) REVERT: B 206 LYS cc_start: 0.8575 (mtpt) cc_final: 0.8192 (mttm) REVERT: B 210 ASP cc_start: 0.8495 (m-30) cc_final: 0.8234 (m-30) REVERT: B 219 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7888 (p0) REVERT: B 229 ARG cc_start: 0.8602 (mtt-85) cc_final: 0.7757 (mmm-85) REVERT: B 235 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: B 262 MET cc_start: 0.7904 (mpp) cc_final: 0.6599 (tmt) REVERT: C 94 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.7136 (t80) REVERT: C 126 GLU cc_start: 0.7782 (mt-10) cc_final: 0.6942 (pm20) REVERT: C 135 ARG cc_start: 0.7924 (ptp-170) cc_final: 0.7656 (ptp-170) REVERT: C 206 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8222 (mttm) REVERT: C 279 MET cc_start: 0.8680 (tpp) cc_final: 0.7009 (mpp) REVERT: C 312 SER cc_start: 0.8005 (OUTLIER) cc_final: 0.7677 (p) REVERT: E 94 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.7903 (t80) REVERT: E 96 ASP cc_start: 0.8083 (p0) cc_final: 0.7867 (p0) REVERT: E 126 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7050 (pm20) REVERT: E 132 LYS cc_start: 0.8093 (mttm) cc_final: 0.7826 (mtmp) REVERT: E 135 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7353 (mtp180) REVERT: E 138 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8765 (mtmt) REVERT: E 210 ASP cc_start: 0.8429 (m-30) cc_final: 0.8123 (m-30) REVERT: E 219 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7867 (p0) REVERT: E 235 GLN cc_start: 0.8177 (mm110) cc_final: 0.7875 (mt0) REVERT: E 243 MET cc_start: 0.8441 (mtt) cc_final: 0.8176 (mtt) REVERT: E 262 MET cc_start: 0.8019 (mpp) cc_final: 0.6800 (tmt) REVERT: E 312 SER cc_start: 0.8093 (OUTLIER) cc_final: 0.7733 (p) REVERT: E 391 MET cc_start: 0.4982 (pmm) cc_final: 0.4646 (pmm) outliers start: 64 outliers final: 34 residues processed: 319 average time/residue: 0.5707 time to fit residues: 199.9271 Evaluate side-chains 332 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 285 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 ARG Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 312 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 66 optimal weight: 0.9990 chunk 60 optimal weight: 0.0370 chunk 138 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 163 optimal weight: 0.0270 chunk 120 optimal weight: 2.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.166581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117024 restraints weight = 16478.998| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.88 r_work: 0.3148 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14450 Z= 0.122 Angle : 0.654 9.783 19655 Z= 0.328 Chirality : 0.044 0.143 2255 Planarity : 0.004 0.042 2420 Dihedral : 4.869 47.162 2190 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.57 % Allowed : 22.05 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.21), residues: 1705 helix: 1.34 (0.23), residues: 560 sheet: -1.46 (0.25), residues: 395 loop : -1.44 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 212 TYR 0.014 0.001 TYR E 317 PHE 0.016 0.001 PHE C 322 TRP 0.011 0.001 TRP A 186 HIS 0.002 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00278 (14425) covalent geometry : angle 0.64820 (19590) SS BOND : bond 0.00317 ( 10) SS BOND : angle 2.09674 ( 20) hydrogen bonds : bond 0.03338 ( 535) hydrogen bonds : angle 4.38802 ( 1590) link_BETA1-4 : bond 0.00506 ( 10) link_BETA1-4 : angle 1.74037 ( 30) link_NAG-ASN : bond 0.00106 ( 5) link_NAG-ASN : angle 0.28138 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 295 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.7641 (t80) REVERT: A 105 MET cc_start: 0.7288 (mtp) cc_final: 0.7010 (tpp) REVERT: A 126 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7111 (pm20) REVERT: A 132 LYS cc_start: 0.7942 (mttm) cc_final: 0.7676 (mtmp) REVERT: A 141 ASN cc_start: 0.8310 (m110) cc_final: 0.8059 (m110) REVERT: A 243 MET cc_start: 0.8479 (tpp) cc_final: 0.7925 (mtt) REVERT: A 312 SER cc_start: 0.8015 (OUTLIER) cc_final: 0.7592 (p) REVERT: D 63 SER cc_start: 0.8679 (t) cc_final: 0.8334 (p) REVERT: D 75 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7707 (ttm-80) REVERT: D 94 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7618 (t80) REVERT: D 135 ARG cc_start: 0.7832 (ptp-170) cc_final: 0.7377 (ptp-170) REVERT: D 206 LYS cc_start: 0.8371 (mtpt) cc_final: 0.7945 (mttm) REVERT: D 235 GLN cc_start: 0.8223 (mm110) cc_final: 0.7978 (mt0) REVERT: D 243 MET cc_start: 0.8360 (tpp) cc_final: 0.8050 (mtt) REVERT: D 262 MET cc_start: 0.8029 (mpp) cc_final: 0.6602 (tmt) REVERT: B 49 LYS cc_start: 0.9165 (mmmm) cc_final: 0.8886 (mmmt) REVERT: B 101 LEU cc_start: 0.7605 (mm) cc_final: 0.7402 (mp) REVERT: B 126 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7079 (pm20) REVERT: B 135 ARG cc_start: 0.7937 (ptp-170) cc_final: 0.7658 (ptp-170) REVERT: B 179 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7873 (mmm) REVERT: B 206 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8093 (mttm) REVERT: B 210 ASP cc_start: 0.8488 (m-30) cc_final: 0.8218 (m-30) REVERT: B 219 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7830 (p0) REVERT: B 229 ARG cc_start: 0.8556 (mtt-85) cc_final: 0.7696 (mmm-85) REVERT: B 235 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8155 (mt0) REVERT: B 262 MET cc_start: 0.7906 (mpp) cc_final: 0.6673 (tmt) REVERT: C 94 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.7002 (t80) REVERT: C 126 GLU cc_start: 0.7705 (mt-10) cc_final: 0.6804 (pm20) REVERT: C 135 ARG cc_start: 0.7875 (ptp-170) cc_final: 0.7652 (ptp-170) REVERT: C 206 LYS cc_start: 0.8478 (mtpt) cc_final: 0.8249 (mttp) REVERT: E 63 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.8311 (p) REVERT: E 94 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.7589 (t80) REVERT: E 101 LEU cc_start: 0.7733 (mp) cc_final: 0.7487 (mp) REVERT: E 120 LYS cc_start: 0.8474 (tttp) cc_final: 0.8221 (tttt) REVERT: E 126 GLU cc_start: 0.7942 (mt-10) cc_final: 0.6931 (pm20) REVERT: E 132 LYS cc_start: 0.8025 (mttm) cc_final: 0.7776 (mtmp) REVERT: E 135 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7385 (mtp180) REVERT: E 206 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7994 (mttm) REVERT: E 219 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7896 (p0) REVERT: E 235 GLN cc_start: 0.8086 (mm110) cc_final: 0.7842 (mt0) REVERT: E 243 MET cc_start: 0.8445 (mtt) cc_final: 0.8183 (mtt) REVERT: E 262 MET cc_start: 0.8098 (mpp) cc_final: 0.6899 (tmt) REVERT: E 312 SER cc_start: 0.8071 (m) cc_final: 0.7693 (p) REVERT: E 391 MET cc_start: 0.4931 (pmm) cc_final: 0.4600 (pmm) outliers start: 39 outliers final: 18 residues processed: 311 average time/residue: 0.5608 time to fit residues: 192.3078 Evaluate side-chains 306 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 277 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 135 ARG Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 293 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 139 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 231 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.164723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115190 restraints weight = 16688.526| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.89 r_work: 0.3253 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14450 Z= 0.148 Angle : 0.685 9.659 19655 Z= 0.345 Chirality : 0.044 0.138 2255 Planarity : 0.004 0.038 2420 Dihedral : 4.887 46.756 2190 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.38 % Allowed : 22.90 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.21), residues: 1705 helix: 1.42 (0.23), residues: 560 sheet: -1.45 (0.25), residues: 395 loop : -1.52 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 392 TYR 0.014 0.001 TYR E 317 PHE 0.016 0.001 PHE C 322 TRP 0.008 0.001 TRP A 186 HIS 0.002 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00350 (14425) covalent geometry : angle 0.68006 (19590) SS BOND : bond 0.00359 ( 10) SS BOND : angle 2.14085 ( 20) hydrogen bonds : bond 0.03390 ( 535) hydrogen bonds : angle 4.39332 ( 1590) link_BETA1-4 : bond 0.00530 ( 10) link_BETA1-4 : angle 1.64320 ( 30) link_NAG-ASN : bond 0.00021 ( 5) link_NAG-ASN : angle 0.45683 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 282 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7358 (t80) REVERT: A 126 GLU cc_start: 0.7711 (mt-10) cc_final: 0.6800 (pm20) REVERT: A 132 LYS cc_start: 0.7693 (mttm) cc_final: 0.7372 (mtmp) REVERT: A 141 ASN cc_start: 0.8007 (m110) cc_final: 0.7700 (m110) REVERT: A 243 MET cc_start: 0.8320 (tpp) cc_final: 0.7753 (mtt) REVERT: A 312 SER cc_start: 0.7990 (OUTLIER) cc_final: 0.7556 (p) REVERT: D 63 SER cc_start: 0.8410 (t) cc_final: 0.8005 (p) REVERT: D 75 ARG cc_start: 0.7761 (ttm-80) cc_final: 0.7358 (ttm-80) REVERT: D 94 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.7598 (t80) REVERT: D 135 ARG cc_start: 0.7617 (ptp-170) cc_final: 0.7141 (ptp-170) REVERT: D 206 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7780 (mttp) REVERT: D 235 GLN cc_start: 0.8130 (mm110) cc_final: 0.7780 (mt0) REVERT: D 262 MET cc_start: 0.8022 (mpp) cc_final: 0.6566 (tmt) REVERT: B 49 LYS cc_start: 0.9081 (mmmm) cc_final: 0.8777 (mmmt) REVERT: B 102 ASP cc_start: 0.7753 (t70) cc_final: 0.7258 (t0) REVERT: B 126 GLU cc_start: 0.7746 (mt-10) cc_final: 0.6721 (pm20) REVERT: B 179 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7727 (mmm) REVERT: B 206 LYS cc_start: 0.8275 (mtpt) cc_final: 0.7839 (mttm) REVERT: B 210 ASP cc_start: 0.8371 (m-30) cc_final: 0.8073 (m-30) REVERT: B 219 ASN cc_start: 0.8066 (p0) cc_final: 0.7768 (p0) REVERT: B 229 ARG cc_start: 0.8389 (mtt-85) cc_final: 0.7403 (mmm-85) REVERT: B 235 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7974 (mt0) REVERT: B 262 MET cc_start: 0.7908 (mpp) cc_final: 0.6641 (tmt) REVERT: C 63 SER cc_start: 0.8543 (t) cc_final: 0.8175 (p) REVERT: C 94 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.6838 (t80) REVERT: C 120 LYS cc_start: 0.8028 (ttmp) cc_final: 0.7740 (ttmm) REVERT: C 126 GLU cc_start: 0.7539 (mt-10) cc_final: 0.6538 (pm20) REVERT: C 135 ARG cc_start: 0.7660 (ptp-170) cc_final: 0.7379 (ptp-170) REVERT: C 206 LYS cc_start: 0.8253 (mtpt) cc_final: 0.7923 (mttm) REVERT: C 279 MET cc_start: 0.8428 (tpp) cc_final: 0.6893 (mpp) REVERT: C 312 SER cc_start: 0.8013 (m) cc_final: 0.7655 (p) REVERT: E 63 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.8018 (p) REVERT: E 94 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7467 (t80) REVERT: E 120 LYS cc_start: 0.8134 (tttp) cc_final: 0.7860 (tttt) REVERT: E 126 GLU cc_start: 0.7751 (mt-10) cc_final: 0.6713 (pm20) REVERT: E 132 LYS cc_start: 0.7783 (mttm) cc_final: 0.7444 (mtmp) REVERT: E 219 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7827 (p0) REVERT: E 235 GLN cc_start: 0.7997 (mm110) cc_final: 0.7628 (mt0) REVERT: E 243 MET cc_start: 0.8280 (mtt) cc_final: 0.8039 (mtt) REVERT: E 262 MET cc_start: 0.8097 (mpp) cc_final: 0.6777 (tmt) REVERT: E 312 SER cc_start: 0.8062 (OUTLIER) cc_final: 0.7673 (p) REVERT: E 391 MET cc_start: 0.5060 (pmm) cc_final: 0.4739 (pmm) outliers start: 36 outliers final: 21 residues processed: 298 average time/residue: 0.5605 time to fit residues: 183.6210 Evaluate side-chains 303 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 272 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 312 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 144 optimal weight: 0.9990 chunk 44 optimal weight: 0.0670 chunk 87 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 89 optimal weight: 0.1980 chunk 20 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.165987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.116602 restraints weight = 16617.482| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.88 r_work: 0.3141 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14450 Z= 0.128 Angle : 0.662 9.680 19655 Z= 0.332 Chirality : 0.044 0.140 2255 Planarity : 0.004 0.037 2420 Dihedral : 4.739 46.526 2190 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.11 % Allowed : 23.23 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.21), residues: 1705 helix: 1.45 (0.23), residues: 570 sheet: -1.39 (0.25), residues: 395 loop : -1.71 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 135 TYR 0.014 0.001 TYR A 317 PHE 0.017 0.001 PHE C 322 TRP 0.010 0.001 TRP A 186 HIS 0.001 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00296 (14425) covalent geometry : angle 0.65759 (19590) SS BOND : bond 0.00328 ( 10) SS BOND : angle 2.03184 ( 20) hydrogen bonds : bond 0.03268 ( 535) hydrogen bonds : angle 4.34913 ( 1590) link_BETA1-4 : bond 0.00448 ( 10) link_BETA1-4 : angle 1.49901 ( 30) link_NAG-ASN : bond 0.00086 ( 5) link_NAG-ASN : angle 0.32712 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5991.34 seconds wall clock time: 102 minutes 25.41 seconds (6145.41 seconds total)