Starting phenix.real_space_refine on Tue Nov 18 12:49:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u2n_26316/11_2025/7u2n_26316_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u2n_26316/11_2025/7u2n_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_26316/11_2025/7u2n_26316_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u2n_26316/11_2025/7u2n_26316_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u2n_26316/11_2025/7u2n_26316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u2n_26316/11_2025/7u2n_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/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: 2.08, per 1000 atoms: 0.15 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: 1.19 Conformation dependent library (CDL) restraints added in 539.3 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: 0.51 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: 2.47 Time building geometry restraints manager: 1.57 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: 0.04 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.080 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:7.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.770 ------------------------------------------------------------------------------- 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 : 0.495 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 108 SER cc_start: 0.8729 (t) cc_final: 0.8529 (t) 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: 0.7614 (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: 0.7933 (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: 0.5073 time to fit residues: 269.4939 Evaluate side-chains 379 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.165163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116787 restraints weight = 16902.634| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.91 r_work: 0.3157 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2461 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 6.556 19655 Z= 0.385 Chirality : 0.048 0.163 2255 Planarity : 0.006 0.059 2420 Dihedral : 12.288 78.570 2190 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.64 % Allowed : 13.14 % Favored : 84.22 % 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: -2.68 (0.19), residues: 1705 helix: -1.25 (0.21), residues: 550 sheet: -2.59 (0.23), residues: 370 loop : -1.59 (0.21), residues: 785 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 0.026 0.002 PHE D 414 TRP 0.016 0.001 TRP C 259 HIS 0.004 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00338 (14425) covalent geometry : angle 0.73439 (19590) SS BOND : bond 0.00297 ( 10) SS BOND : angle 1.37832 ( 20) hydrogen bonds : bond 0.05424 ( 535) hydrogen bonds : angle 5.80604 ( 1590) link_BETA1-4 : bond 0.00862 ( 10) link_BETA1-4 : angle 3.06302 ( 30) link_NAG-ASN : bond 0.00296 ( 5) link_NAG-ASN : angle 0.31416 ( 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 443 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 403 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: A 25 PRO cc_start: 0.6795 (Cg_exo) cc_final: 0.6566 (Cg_endo) REVERT: A 104 SER cc_start: 0.8177 (t) cc_final: 0.7639 (p) REVERT: A 126 GLU cc_start: 0.7766 (mt-10) cc_final: 0.6924 (pm20) REVERT: A 132 LYS cc_start: 0.7859 (mttm) cc_final: 0.7648 (mtmp) REVERT: A 135 ARG cc_start: 0.7889 (ptp-170) cc_final: 0.7482 (ptp-170) REVERT: A 141 ASN cc_start: 0.8171 (m110) cc_final: 0.7849 (m110) REVERT: A 235 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7663 (mt0) REVERT: D 49 LYS cc_start: 0.8978 (mmmt) cc_final: 0.8766 (mmmm) REVERT: D 63 SER cc_start: 0.8396 (t) cc_final: 0.7833 (p) REVERT: D 75 ARG cc_start: 0.7877 (ttm-80) cc_final: 0.7567 (ttm-80) REVERT: D 96 ASP cc_start: 0.8020 (m-30) cc_final: 0.7544 (m-30) REVERT: D 97 ASP cc_start: 0.7965 (m-30) cc_final: 0.7593 (t0) REVERT: D 126 GLU cc_start: 0.7559 (mt-10) cc_final: 0.6452 (pm20) REVERT: D 130 ASP cc_start: 0.8437 (m-30) cc_final: 0.8138 (m-30) REVERT: D 132 LYS cc_start: 0.7830 (mttm) cc_final: 0.7502 (mtmm) REVERT: D 135 ARG cc_start: 0.7708 (ptp-170) cc_final: 0.7107 (ptp-170) REVERT: D 141 ASN cc_start: 0.8042 (m110) cc_final: 0.7661 (m110) REVERT: D 179 MET cc_start: 0.8067 (mmm) cc_final: 0.7768 (mmm) REVERT: D 189 LYS cc_start: 0.8251 (ptpt) cc_final: 0.8032 (ptpp) REVERT: D 206 LYS cc_start: 0.8213 (mtpt) cc_final: 0.7688 (mttm) REVERT: D 210 ASP cc_start: 0.8325 (m-30) cc_final: 0.8118 (m-30) REVERT: D 212 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6855 (ptt90) REVERT: D 235 GLN cc_start: 0.7950 (mm110) cc_final: 0.7626 (mt0) REVERT: D 262 MET cc_start: 0.8252 (mpp) cc_final: 0.7043 (tmt) REVERT: B 108 SER cc_start: 0.8706 (t) cc_final: 0.8421 (p) REVERT: B 126 GLU cc_start: 0.7795 (mt-10) cc_final: 0.6981 (pm20) REVERT: B 132 LYS cc_start: 0.7881 (mttm) cc_final: 0.7667 (mtmp) REVERT: B 135 ARG cc_start: 0.7774 (ptp-170) cc_final: 0.7478 (ptp-170) REVERT: B 179 MET cc_start: 0.8045 (mmm) cc_final: 0.7586 (mmm) REVERT: B 206 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7946 (mttt) REVERT: B 210 ASP cc_start: 0.8269 (m-30) cc_final: 0.7699 (m-30) REVERT: B 212 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7577 (pmm-80) REVERT: B 219 ASN cc_start: 0.8260 (p0) cc_final: 0.8034 (p0) REVERT: B 229 ARG cc_start: 0.8164 (mtt-85) cc_final: 0.7850 (mmm-85) REVERT: B 235 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7649 (mt0) REVERT: B 262 MET cc_start: 0.8068 (mpp) cc_final: 0.6929 (tmt) REVERT: C 94 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.7251 (t80) REVERT: C 96 ASP cc_start: 0.7945 (m-30) cc_final: 0.7705 (m-30) REVERT: C 100 ASP cc_start: 0.7966 (m-30) cc_final: 0.7311 (t70) REVERT: C 126 GLU cc_start: 0.7674 (mt-10) cc_final: 0.6759 (pm20) REVERT: C 130 ASP cc_start: 0.8501 (m-30) cc_final: 0.8188 (m-30) REVERT: C 135 ARG cc_start: 0.7861 (ptp-170) cc_final: 0.7353 (ptp-170) REVERT: C 156 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8532 (mmp) REVERT: C 179 MET cc_start: 0.8086 (mmm) cc_final: 0.7860 (mmm) REVERT: C 189 LYS cc_start: 0.8317 (ptpt) cc_final: 0.8093 (ptpp) REVERT: C 206 LYS cc_start: 0.8272 (mtpt) cc_final: 0.7928 (mttm) REVERT: C 235 GLN cc_start: 0.7933 (mm110) cc_final: 0.7610 (mt0) REVERT: C 401 ARG cc_start: 0.8727 (mmm160) cc_final: 0.8351 (mmm-85) REVERT: E 25 PRO cc_start: 0.6893 (Cg_exo) cc_final: 0.6683 (Cg_endo) REVERT: E 28 GLU cc_start: 0.8214 (tp30) cc_final: 0.7887 (tp30) REVERT: E 75 ARG cc_start: 0.7954 (ttm-80) cc_final: 0.7667 (ttm-80) REVERT: E 105 MET cc_start: 0.7309 (tpp) cc_final: 0.7039 (tpp) REVERT: E 126 GLU cc_start: 0.7831 (mt-10) cc_final: 0.6733 (pm20) REVERT: E 132 LYS cc_start: 0.7910 (mttm) cc_final: 0.7626 (mtmp) REVERT: E 135 ARG cc_start: 0.7707 (ptp-170) cc_final: 0.7216 (ttp-170) REVERT: E 141 ASN cc_start: 0.8138 (m110) cc_final: 0.7929 (m110) REVERT: E 189 LYS cc_start: 0.8099 (ptpt) cc_final: 0.7854 (ptpp) REVERT: E 210 ASP cc_start: 0.8264 (m-30) cc_final: 0.7884 (m-30) REVERT: E 235 GLN cc_start: 0.7996 (mm110) cc_final: 0.7492 (mt0) REVERT: E 262 MET cc_start: 0.8293 (mpp) cc_final: 0.7091 (tmt) outliers start: 40 outliers final: 14 residues processed: 411 average time/residue: 0.4991 time to fit residues: 226.5970 Evaluate side-chains 376 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 356 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 1 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.0670 chunk 58 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- 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 C 231 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.163728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114427 restraints weight = 16505.846| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.85 r_work: 0.3114 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14450 Z= 0.169 Angle : 0.690 7.049 19655 Z= 0.356 Chirality : 0.045 0.138 2255 Planarity : 0.005 0.061 2420 Dihedral : 11.364 68.597 2190 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.63 % Allowed : 16.44 % Favored : 79.93 % 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: -2.00 (0.20), residues: 1705 helix: -0.26 (0.22), residues: 555 sheet: -2.21 (0.24), residues: 370 loop : -1.55 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 212 TYR 0.018 0.002 TYR C 317 PHE 0.016 0.002 PHE E 29 TRP 0.014 0.002 TRP C 259 HIS 0.003 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00389 (14425) covalent geometry : angle 0.67858 (19590) SS BOND : bond 0.00383 ( 10) SS BOND : angle 1.83518 ( 20) hydrogen bonds : bond 0.04436 ( 535) hydrogen bonds : angle 5.24553 ( 1590) link_BETA1-4 : bond 0.00628 ( 10) link_BETA1-4 : angle 2.91608 ( 30) link_NAG-ASN : bond 0.00088 ( 5) link_NAG-ASN : angle 0.64116 ( 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 409 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 354 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 PRO cc_start: 0.6790 (Cg_exo) cc_final: 0.6545 (Cg_endo) REVERT: A 43 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.8287 (mtm180) REVERT: A 104 SER cc_start: 0.8248 (t) cc_final: 0.7682 (p) REVERT: A 126 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7201 (pm20) REVERT: A 130 ASP cc_start: 0.8533 (m-30) cc_final: 0.8305 (m-30) REVERT: A 135 ARG cc_start: 0.7955 (ptp-170) cc_final: 0.7472 (ptp-170) REVERT: A 141 ASN cc_start: 0.8404 (m110) cc_final: 0.8081 (m110) REVERT: D 43 ARG cc_start: 0.8524 (mtm-85) cc_final: 0.8265 (mtm180) REVERT: D 49 LYS cc_start: 0.9030 (mmmt) cc_final: 0.8775 (mmmm) REVERT: D 63 SER cc_start: 0.8716 (t) cc_final: 0.8193 (p) REVERT: D 75 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7802 (ttm-80) REVERT: D 126 GLU cc_start: 0.7792 (mt-10) cc_final: 0.6805 (pm20) REVERT: D 132 LYS cc_start: 0.8014 (mttm) cc_final: 0.7768 (mtmm) REVERT: D 135 ARG cc_start: 0.7883 (ptp-170) cc_final: 0.7376 (ptp-170) REVERT: D 189 LYS cc_start: 0.8385 (ptpt) cc_final: 0.8170 (ptpp) REVERT: D 206 LYS cc_start: 0.8425 (mtpt) cc_final: 0.7999 (mttm) REVERT: D 227 GLU cc_start: 0.8546 (pt0) cc_final: 0.8224 (pt0) REVERT: D 235 GLN cc_start: 0.8067 (mm110) cc_final: 0.7825 (mt0) REVERT: D 262 MET cc_start: 0.8279 (mpp) cc_final: 0.6765 (tmt) REVERT: B 32 LYS cc_start: 0.8201 (tmtt) cc_final: 0.7965 (tmtt) REVERT: B 126 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7185 (pm20) REVERT: B 135 ARG cc_start: 0.7888 (ptp-170) cc_final: 0.7644 (ptp-170) REVERT: B 179 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7767 (mmm) REVERT: B 206 LYS cc_start: 0.8491 (mtpt) cc_final: 0.8241 (mttp) REVERT: B 210 ASP cc_start: 0.8547 (m-30) cc_final: 0.8331 (m-30) REVERT: B 219 ASN cc_start: 0.8328 (p0) cc_final: 0.8084 (p0) REVERT: B 229 ARG cc_start: 0.8509 (mtt-85) cc_final: 0.7840 (mmm-85) REVERT: B 235 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: B 262 MET cc_start: 0.8085 (mpp) cc_final: 0.6744 (tmt) REVERT: C 94 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.7238 (t80) REVERT: C 96 ASP cc_start: 0.7990 (m-30) cc_final: 0.7391 (m-30) REVERT: C 97 ASP cc_start: 0.7804 (m-30) cc_final: 0.7521 (t0) REVERT: C 102 ASP cc_start: 0.7622 (t70) cc_final: 0.7198 (t0) REVERT: C 126 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7044 (pm20) REVERT: C 135 ARG cc_start: 0.8034 (ptp-170) cc_final: 0.7702 (ptp-170) REVERT: C 189 LYS cc_start: 0.8469 (ptpt) cc_final: 0.8263 (ptpp) REVERT: C 206 LYS cc_start: 0.8412 (mtpt) cc_final: 0.8123 (mttm) REVERT: C 227 GLU cc_start: 0.8562 (pt0) cc_final: 0.8329 (pt0) REVERT: C 235 GLN cc_start: 0.8122 (mm110) cc_final: 0.7886 (mt0) REVERT: C 243 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7504 (mtt) REVERT: C 401 ARG cc_start: 0.8708 (mmm160) cc_final: 0.8316 (mmm-85) REVERT: E 75 ARG cc_start: 0.8218 (ttm-80) cc_final: 0.7923 (ttm-80) REVERT: E 126 GLU cc_start: 0.7939 (mt-10) cc_final: 0.6933 (pm20) REVERT: E 132 LYS cc_start: 0.8096 (mttm) cc_final: 0.7855 (mtmp) REVERT: E 135 ARG cc_start: 0.7861 (ptp-170) cc_final: 0.7459 (ptp-170) REVERT: E 189 LYS cc_start: 0.8292 (ptpt) cc_final: 0.8067 (ptpp) REVERT: E 210 ASP cc_start: 0.8479 (m-30) cc_final: 0.8158 (m-30) REVERT: E 235 GLN cc_start: 0.8131 (mm110) cc_final: 0.7806 (mt0) REVERT: E 262 MET cc_start: 0.8177 (mpp) cc_final: 0.6842 (tmt) outliers start: 55 outliers final: 37 residues processed: 366 average time/residue: 0.5567 time to fit residues: 223.4433 Evaluate side-chains 357 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 316 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 208 GLU Chi-restraints excluded: chain A residue 312 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 92 SER Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 SER 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 208 GLU 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 63 SER Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 TYR 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 C residue 424 THR 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 312 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: 0.0870 chunk 156 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.165855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116384 restraints weight = 16250.232| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.86 r_work: 0.3140 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14450 Z= 0.131 Angle : 0.652 7.481 19655 Z= 0.332 Chirality : 0.044 0.145 2255 Planarity : 0.004 0.055 2420 Dihedral : 9.986 58.619 2190 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.55 % Allowed : 18.09 % Favored : 77.36 % 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: -1.50 (0.20), residues: 1705 helix: 0.36 (0.23), residues: 550 sheet: -1.84 (0.25), residues: 370 loop : -1.48 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 212 TYR 0.017 0.001 TYR C 317 PHE 0.017 0.001 PHE D 414 TRP 0.011 0.001 TRP A 259 HIS 0.002 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00293 (14425) covalent geometry : angle 0.64010 (19590) SS BOND : bond 0.00486 ( 10) SS BOND : angle 1.57202 ( 20) hydrogen bonds : bond 0.03808 ( 535) hydrogen bonds : angle 4.92096 ( 1590) link_BETA1-4 : bond 0.00454 ( 10) link_BETA1-4 : angle 3.06941 ( 30) link_NAG-ASN : bond 0.00057 ( 5) link_NAG-ASN : angle 0.41655 ( 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 403 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 334 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 PRO cc_start: 0.6715 (Cg_exo) cc_final: 0.6452 (Cg_endo) REVERT: A 104 SER cc_start: 0.8216 (t) cc_final: 0.7677 (p) REVERT: A 126 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7193 (pm20) REVERT: A 135 ARG cc_start: 0.7954 (ptp-170) cc_final: 0.7469 (ptp-170) REVERT: A 141 ASN cc_start: 0.8387 (m110) cc_final: 0.8088 (m110) REVERT: A 243 MET cc_start: 0.8319 (tpp) cc_final: 0.7864 (mtt) REVERT: A 391 MET cc_start: 0.4974 (pmm) cc_final: 0.4694 (pmm) REVERT: D 49 LYS cc_start: 0.9015 (mmmt) cc_final: 0.8814 (mmmm) REVERT: D 63 SER cc_start: 0.8726 (t) cc_final: 0.8241 (p) REVERT: D 75 ARG cc_start: 0.8083 (ttm-80) cc_final: 0.7735 (ttm-80) REVERT: D 126 GLU cc_start: 0.7801 (mt-10) cc_final: 0.6780 (pm20) REVERT: D 130 ASP cc_start: 0.8520 (m-30) cc_final: 0.8229 (m-30) REVERT: D 132 LYS cc_start: 0.7945 (mttm) cc_final: 0.7537 (mtmt) REVERT: D 135 ARG cc_start: 0.7858 (ptp-170) cc_final: 0.7359 (ptp-170) REVERT: D 206 LYS cc_start: 0.8415 (mtpt) cc_final: 0.8171 (mttt) REVERT: D 235 GLN cc_start: 0.8088 (mm110) cc_final: 0.7863 (mt0) REVERT: D 262 MET cc_start: 0.8158 (mpp) cc_final: 0.6715 (tmt) REVERT: B 126 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7150 (pm20) REVERT: B 130 ASP cc_start: 0.8619 (m-30) cc_final: 0.8414 (m-30) REVERT: B 135 ARG cc_start: 0.7923 (ptp-170) cc_final: 0.7679 (ptp-170) REVERT: B 163 MET cc_start: 0.8764 (mtm) cc_final: 0.8462 (mpp) REVERT: B 179 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7785 (mmm) REVERT: B 206 LYS cc_start: 0.8476 (mtpt) cc_final: 0.8249 (mttp) REVERT: B 210 ASP cc_start: 0.8500 (m-30) cc_final: 0.8221 (m-30) REVERT: B 229 ARG cc_start: 0.8520 (mtt-85) cc_final: 0.8222 (mmm-85) REVERT: B 235 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8018 (mt0) REVERT: B 262 MET cc_start: 0.8069 (mpp) cc_final: 0.6601 (tmt) REVERT: C 94 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.7218 (t80) REVERT: C 96 ASP cc_start: 0.7899 (m-30) cc_final: 0.7339 (m-30) REVERT: C 97 ASP cc_start: 0.7912 (m-30) cc_final: 0.7624 (t0) REVERT: C 102 ASP cc_start: 0.7719 (t70) cc_final: 0.7128 (t0) REVERT: C 126 GLU cc_start: 0.7801 (mt-10) cc_final: 0.6863 (pm20) REVERT: C 130 ASP cc_start: 0.8546 (m-30) cc_final: 0.8329 (m-30) REVERT: C 135 ARG cc_start: 0.7919 (ptp-170) cc_final: 0.7628 (ptp-170) REVERT: C 206 LYS cc_start: 0.8416 (mtpt) cc_final: 0.8161 (mttm) REVERT: C 235 GLN cc_start: 0.8117 (mm110) cc_final: 0.7903 (mt0) REVERT: C 243 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7669 (mtt) REVERT: C 279 MET cc_start: 0.8691 (tpp) cc_final: 0.7044 (mpp) REVERT: C 401 ARG cc_start: 0.8700 (mmm160) cc_final: 0.8294 (mmm-85) REVERT: E 71 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8987 (p) REVERT: E 75 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7881 (ttm-80) REVERT: E 126 GLU cc_start: 0.7905 (mt-10) cc_final: 0.6891 (pm20) REVERT: E 132 LYS cc_start: 0.8048 (mttm) cc_final: 0.7802 (mtmp) REVERT: E 135 ARG cc_start: 0.7818 (ptp-170) cc_final: 0.7328 (ttp-170) REVERT: E 138 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8718 (mtmt) REVERT: E 206 LYS cc_start: 0.8343 (mtpt) cc_final: 0.7918 (mttt) REVERT: E 210 ASP cc_start: 0.8454 (m-30) cc_final: 0.8153 (m-30) REVERT: E 219 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.8120 (p0) REVERT: E 235 GLN cc_start: 0.8075 (mm110) cc_final: 0.7769 (mt0) REVERT: E 262 MET cc_start: 0.8207 (mpp) cc_final: 0.6811 (tmt) outliers start: 69 outliers final: 29 residues processed: 357 average time/residue: 0.5370 time to fit residues: 210.9680 Evaluate side-chains 351 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 315 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 284 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 208 GLU 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 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 235 GLN Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 196 ASP 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 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: 0.4980 chunk 105 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 74 optimal weight: 4.9990 chunk 55 optimal weight: 0.0670 chunk 134 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.165829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.116182 restraints weight = 16389.212| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.90 r_work: 0.3134 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3547 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= 0.136 Angle : 0.651 8.563 19655 Z= 0.331 Chirality : 0.044 0.138 2255 Planarity : 0.004 0.051 2420 Dihedral : 8.732 49.557 2190 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.02 % Allowed : 18.28 % Favored : 76.70 % 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: -1.28 (0.20), residues: 1705 helix: 0.61 (0.23), residues: 565 sheet: -1.55 (0.25), residues: 370 loop : -1.55 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 212 TYR 0.016 0.001 TYR E 317 PHE 0.013 0.001 PHE B 29 TRP 0.010 0.001 TRP C 259 HIS 0.002 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00313 (14425) covalent geometry : angle 0.63898 (19590) SS BOND : bond 0.00397 ( 10) SS BOND : angle 1.69096 ( 20) hydrogen bonds : bond 0.03640 ( 535) hydrogen bonds : angle 4.71172 ( 1590) link_BETA1-4 : bond 0.00473 ( 10) link_BETA1-4 : angle 3.00599 ( 30) link_NAG-ASN : bond 0.00014 ( 5) link_NAG-ASN : angle 0.45461 ( 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 394 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 318 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8558 (mtm-85) cc_final: 0.8318 (mtm180) REVERT: A 94 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.7356 (t80) REVERT: A 104 SER cc_start: 0.8267 (t) cc_final: 0.7724 (p) REVERT: A 126 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7201 (pm20) REVERT: A 130 ASP cc_start: 0.8575 (m-30) cc_final: 0.8319 (m-30) REVERT: A 135 ARG cc_start: 0.7931 (ptp-170) cc_final: 0.7493 (ptp-170) REVERT: A 141 ASN cc_start: 0.8394 (m110) cc_final: 0.8086 (m110) REVERT: A 243 MET cc_start: 0.8365 (tpp) cc_final: 0.7800 (mtt) REVERT: A 391 MET cc_start: 0.4850 (pmm) cc_final: 0.4596 (pmm) REVERT: D 63 SER cc_start: 0.8728 (t) cc_final: 0.8264 (p) REVERT: D 75 ARG cc_start: 0.8098 (ttm-80) cc_final: 0.7729 (ttm-80) REVERT: D 126 GLU cc_start: 0.7823 (mt-10) cc_final: 0.6840 (pm20) REVERT: D 135 ARG cc_start: 0.7858 (ptp-170) cc_final: 0.7427 (ptp-170) REVERT: D 206 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8193 (mttp) REVERT: D 235 GLN cc_start: 0.8209 (mm110) cc_final: 0.7939 (mt0) REVERT: D 243 MET cc_start: 0.8309 (mpp) cc_final: 0.8075 (mtt) REVERT: D 262 MET cc_start: 0.8100 (mpp) cc_final: 0.6602 (tmt) REVERT: B 49 LYS cc_start: 0.9099 (mmmt) cc_final: 0.8735 (mmmt) REVERT: B 126 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7182 (pm20) REVERT: B 130 ASP cc_start: 0.8604 (m-30) cc_final: 0.8402 (m-30) REVERT: B 135 ARG cc_start: 0.7971 (ptp-170) cc_final: 0.7720 (ptp-170) REVERT: B 179 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7837 (mmm) REVERT: B 206 LYS cc_start: 0.8474 (mtpt) cc_final: 0.8167 (mttp) REVERT: B 210 ASP cc_start: 0.8532 (m-30) cc_final: 0.8293 (m-30) REVERT: B 229 ARG cc_start: 0.8555 (mtt-85) cc_final: 0.7627 (mmm-85) REVERT: B 235 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8087 (mt0) REVERT: B 262 MET cc_start: 0.7991 (mpp) cc_final: 0.6677 (tmt) REVERT: C 32 LYS cc_start: 0.8418 (ttpt) cc_final: 0.8174 (tmtt) REVERT: C 94 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.7161 (t80) REVERT: C 96 ASP cc_start: 0.7964 (m-30) cc_final: 0.7394 (m-30) REVERT: C 97 ASP cc_start: 0.7972 (m-30) cc_final: 0.7698 (t0) REVERT: C 102 ASP cc_start: 0.7744 (t70) cc_final: 0.7116 (t0) REVERT: C 126 GLU cc_start: 0.7778 (mt-10) cc_final: 0.6852 (pm20) REVERT: C 130 ASP cc_start: 0.8543 (m-30) cc_final: 0.8316 (m-30) REVERT: C 135 ARG cc_start: 0.7925 (ptp-170) cc_final: 0.7614 (ptp-170) REVERT: C 138 LYS cc_start: 0.8998 (ttpp) cc_final: 0.8794 (tttt) REVERT: C 206 LYS cc_start: 0.8437 (mtpt) cc_final: 0.8183 (mttm) REVERT: C 235 GLN cc_start: 0.8151 (mm110) cc_final: 0.7949 (mt0) REVERT: C 243 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7751 (mtt) REVERT: C 401 ARG cc_start: 0.8712 (mmm160) cc_final: 0.8290 (mmm-85) REVERT: E 63 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.8294 (p) REVERT: E 75 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7879 (ttm-80) REVERT: E 126 GLU cc_start: 0.7930 (mt-10) cc_final: 0.6924 (pm20) REVERT: E 132 LYS cc_start: 0.8052 (mttm) cc_final: 0.7792 (mtmp) REVERT: E 135 ARG cc_start: 0.7824 (ptp-170) cc_final: 0.7344 (ttp-170) REVERT: E 206 LYS cc_start: 0.8352 (mtpt) cc_final: 0.7917 (mttm) REVERT: E 210 ASP cc_start: 0.8477 (m-30) cc_final: 0.8182 (m-30) REVERT: E 219 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8041 (p0) REVERT: E 235 GLN cc_start: 0.8101 (mm110) cc_final: 0.7815 (mt0) REVERT: E 262 MET cc_start: 0.8178 (mpp) cc_final: 0.6831 (tmt) REVERT: E 312 SER cc_start: 0.8090 (m) cc_final: 0.7706 (p) outliers start: 76 outliers final: 41 residues processed: 347 average time/residue: 0.5402 time to fit residues: 207.1441 Evaluate side-chains 359 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 311 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 214 CYS Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 312 SER 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 207 GLU Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 THR 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 204 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 214 CYS 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 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 104 SER 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 423 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 293 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 96 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 124 optimal weight: 0.0970 chunk 169 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.163776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114340 restraints weight = 16396.561| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.88 r_work: 0.3103 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14450 Z= 0.175 Angle : 0.686 9.024 19655 Z= 0.347 Chirality : 0.045 0.140 2255 Planarity : 0.004 0.052 2420 Dihedral : 7.547 38.626 2190 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.16 % Allowed : 19.74 % 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: -1.04 (0.21), residues: 1705 helix: 0.84 (0.24), residues: 560 sheet: -1.48 (0.26), residues: 370 loop : -1.38 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 212 TYR 0.015 0.002 TYR B 317 PHE 0.013 0.001 PHE C 322 TRP 0.011 0.001 TRP C 259 HIS 0.002 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00412 (14425) covalent geometry : angle 0.67532 (19590) SS BOND : bond 0.00434 ( 10) SS BOND : angle 1.67098 ( 20) hydrogen bonds : bond 0.03701 ( 535) hydrogen bonds : angle 4.65436 ( 1590) link_BETA1-4 : bond 0.00480 ( 10) link_BETA1-4 : angle 2.91613 ( 30) link_NAG-ASN : bond 0.00058 ( 5) link_NAG-ASN : angle 0.55695 ( 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 384 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 321 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.7422 (t80) REVERT: A 104 SER cc_start: 0.8213 (t) cc_final: 0.7695 (p) REVERT: A 126 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7206 (pm20) REVERT: A 130 ASP cc_start: 0.8627 (m-30) cc_final: 0.8348 (m-30) REVERT: A 141 ASN cc_start: 0.8406 (m110) cc_final: 0.8120 (m110) REVERT: A 243 MET cc_start: 0.8442 (tpp) cc_final: 0.7835 (mtt) REVERT: D 63 SER cc_start: 0.8720 (t) cc_final: 0.8228 (p) REVERT: D 75 ARG cc_start: 0.8134 (ttm-80) cc_final: 0.7767 (ttm-80) REVERT: D 81 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8311 (mpp80) REVERT: D 126 GLU cc_start: 0.7829 (mt-10) cc_final: 0.6877 (pm20) REVERT: D 132 LYS cc_start: 0.7915 (mttm) cc_final: 0.7483 (mtmt) REVERT: D 135 ARG cc_start: 0.7939 (ptp-170) cc_final: 0.7459 (ptp-170) REVERT: D 206 LYS cc_start: 0.8459 (mtpt) cc_final: 0.8238 (mttp) REVERT: D 235 GLN cc_start: 0.8277 (mm110) cc_final: 0.8044 (mt0) REVERT: D 262 MET cc_start: 0.8099 (mpp) cc_final: 0.6667 (tmt) REVERT: B 126 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7198 (pm20) REVERT: B 179 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7872 (mmm) REVERT: B 206 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8218 (mttp) REVERT: B 210 ASP cc_start: 0.8550 (m-30) cc_final: 0.8299 (m-30) REVERT: B 219 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7937 (p0) REVERT: B 229 ARG cc_start: 0.8588 (mtt-85) cc_final: 0.7706 (mmm-85) REVERT: B 235 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8162 (mt0) REVERT: B 262 MET cc_start: 0.8001 (mpp) cc_final: 0.6697 (tmt) REVERT: C 32 LYS cc_start: 0.8389 (ttpt) cc_final: 0.8131 (tmtt) REVERT: C 94 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7376 (t80) REVERT: C 96 ASP cc_start: 0.7949 (m-30) cc_final: 0.7696 (m-30) REVERT: C 102 ASP cc_start: 0.7635 (t70) cc_final: 0.7057 (t0) REVERT: C 126 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7357 (mm-30) REVERT: C 135 ARG cc_start: 0.7929 (ptp-170) cc_final: 0.7691 (ptp-170) REVERT: C 206 LYS cc_start: 0.8461 (mtpt) cc_final: 0.8196 (mttm) REVERT: C 227 GLU cc_start: 0.8541 (pt0) cc_final: 0.8283 (pt0) REVERT: C 235 GLN cc_start: 0.8179 (mm110) cc_final: 0.7953 (mt0) REVERT: C 243 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7838 (mtt) REVERT: C 401 ARG cc_start: 0.8705 (mmm160) cc_final: 0.8290 (mmm-85) REVERT: E 75 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7829 (ttm-80) REVERT: E 94 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8175 (t80) REVERT: E 126 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7079 (pm20) REVERT: E 132 LYS cc_start: 0.8074 (mttm) cc_final: 0.7799 (mtmp) REVERT: E 210 ASP cc_start: 0.8479 (m-30) cc_final: 0.8164 (m-30) REVERT: E 219 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.7997 (p0) REVERT: E 235 GLN cc_start: 0.8162 (mm110) cc_final: 0.7849 (mt0) REVERT: E 262 MET cc_start: 0.8112 (mpp) cc_final: 0.6786 (tmt) REVERT: E 312 SER cc_start: 0.8118 (OUTLIER) cc_final: 0.7749 (p) REVERT: E 391 MET cc_start: 0.5070 (pmm) cc_final: 0.4729 (pmm) outliers start: 63 outliers final: 42 residues processed: 344 average time/residue: 0.5525 time to fit residues: 208.8438 Evaluate side-chains 359 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 307 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 214 CYS Chi-restraints excluded: chain A residue 312 SER 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 106 LEU 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 284 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 204 ILE 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 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 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 E residue 56 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 127 VAL 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 Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 38 optimal weight: 0.3980 chunk 132 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 chunk 78 optimal weight: 0.0570 chunk 49 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.164936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.113741 restraints weight = 16632.850| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.06 r_work: 0.3115 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14450 Z= 0.129 Angle : 0.661 9.239 19655 Z= 0.334 Chirality : 0.044 0.143 2255 Planarity : 0.004 0.042 2420 Dihedral : 5.960 24.192 2190 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.22 % Allowed : 20.20 % 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: -0.88 (0.21), residues: 1705 helix: 0.99 (0.23), residues: 560 sheet: -1.31 (0.26), residues: 370 loop : -1.34 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 135 TYR 0.014 0.001 TYR C 317 PHE 0.017 0.001 PHE A 29 TRP 0.010 0.001 TRP C 186 HIS 0.002 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00296 (14425) covalent geometry : angle 0.65176 (19590) SS BOND : bond 0.00357 ( 10) SS BOND : angle 1.85304 ( 20) hydrogen bonds : bond 0.03477 ( 535) hydrogen bonds : angle 4.51295 ( 1590) link_BETA1-4 : bond 0.00491 ( 10) link_BETA1-4 : angle 2.52640 ( 30) link_NAG-ASN : bond 0.00068 ( 5) link_NAG-ASN : angle 0.32771 ( 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 383 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 319 time to evaluate : 0.532 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: 0.8730 (OUTLIER) cc_final: 0.8318 (m-80) REVERT: A 104 SER cc_start: 0.8407 (t) cc_final: 0.8017 (p) REVERT: A 126 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7117 (pm20) REVERT: A 130 ASP cc_start: 0.8577 (m-30) cc_final: 0.8309 (m-30) REVERT: A 141 ASN cc_start: 0.8350 (m110) cc_final: 0.8081 (m110) REVERT: A 243 MET cc_start: 0.8425 (tpp) cc_final: 0.7867 (mtt) REVERT: D 63 SER cc_start: 0.8701 (t) cc_final: 0.8220 (p) REVERT: D 75 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7737 (ttm-80) REVERT: D 81 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8237 (mpp80) REVERT: D 105 MET cc_start: 0.7207 (mtp) cc_final: 0.6996 (ptp) REVERT: D 126 GLU cc_start: 0.7812 (mt-10) cc_final: 0.6800 (pm20) REVERT: D 132 LYS cc_start: 0.7898 (mttm) cc_final: 0.7510 (mtmt) REVERT: D 135 ARG cc_start: 0.7850 (ptp-170) cc_final: 0.7435 (ptp-170) REVERT: D 206 LYS cc_start: 0.8396 (mtpt) cc_final: 0.8184 (mttp) REVERT: D 235 GLN cc_start: 0.8249 (mm110) cc_final: 0.8017 (mt0) REVERT: D 262 MET cc_start: 0.8028 (mpp) cc_final: 0.6674 (tmt) REVERT: B 126 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7149 (pm20) REVERT: B 179 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7854 (mmm) REVERT: B 210 ASP cc_start: 0.8504 (m-30) cc_final: 0.8279 (m-30) REVERT: B 219 ASN cc_start: 0.8205 (OUTLIER) cc_final: 0.7897 (p0) REVERT: B 229 ARG cc_start: 0.8576 (mtt-85) cc_final: 0.7703 (mmm-85) REVERT: B 235 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8162 (mt0) REVERT: B 262 MET cc_start: 0.7923 (mpp) cc_final: 0.6637 (tmt) REVERT: C 32 LYS cc_start: 0.8413 (ttpt) cc_final: 0.8178 (tmtt) REVERT: C 94 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.7220 (t80) REVERT: C 96 ASP cc_start: 0.7929 (m-30) cc_final: 0.7610 (m-30) REVERT: C 97 ASP cc_start: 0.8025 (m-30) cc_final: 0.7771 (t0) REVERT: C 102 ASP cc_start: 0.7604 (t70) cc_final: 0.7063 (t0) REVERT: C 126 GLU cc_start: 0.7764 (mt-10) cc_final: 0.6878 (pm20) REVERT: C 130 ASP cc_start: 0.8557 (m-30) cc_final: 0.8343 (m-30) REVERT: C 135 ARG cc_start: 0.7866 (ptp-170) cc_final: 0.7551 (ptp-170) REVERT: C 156 MET cc_start: 0.8751 (mmp) cc_final: 0.7575 (mmt) REVERT: C 206 LYS cc_start: 0.8407 (mtpt) cc_final: 0.8127 (mttm) REVERT: C 401 ARG cc_start: 0.8707 (mmm160) cc_final: 0.8283 (mmm-85) REVERT: E 94 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7933 (t80) REVERT: E 126 GLU cc_start: 0.7970 (mt-10) cc_final: 0.6933 (pm20) REVERT: E 132 LYS cc_start: 0.8053 (mttm) cc_final: 0.7784 (mtmp) REVERT: E 135 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7258 (mtp180) REVERT: E 219 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.7923 (p0) REVERT: E 235 GLN cc_start: 0.8122 (mm110) cc_final: 0.7825 (mt0) REVERT: E 243 MET cc_start: 0.8153 (tpp) cc_final: 0.7952 (mtt) REVERT: E 262 MET cc_start: 0.8069 (mpp) cc_final: 0.6833 (tmt) REVERT: E 312 SER cc_start: 0.8120 (OUTLIER) cc_final: 0.7762 (p) REVERT: E 391 MET cc_start: 0.4898 (pmm) cc_final: 0.3972 (ppp) outliers start: 64 outliers final: 37 residues processed: 345 average time/residue: 0.5424 time to fit residues: 206.1550 Evaluate side-chains 356 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 309 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR 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 56 THR Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 146 ILE 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 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 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 214 CYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 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 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 Chi-restraints excluded: chain E residue 423 ILE 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: 0.9990 chunk 60 optimal weight: 0.0370 chunk 137 optimal weight: 0.0570 chunk 58 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.166367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.116903 restraints weight = 16514.582| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.86 r_work: 0.3154 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14450 Z= 0.128 Angle : 0.675 13.118 19655 Z= 0.337 Chirality : 0.044 0.152 2255 Planarity : 0.004 0.039 2420 Dihedral : 5.199 41.952 2190 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.43 % Allowed : 21.19 % 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: -0.85 (0.21), residues: 1705 helix: 1.16 (0.23), residues: 560 sheet: -1.43 (0.25), residues: 395 loop : -1.35 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 212 TYR 0.014 0.001 TYR E 317 PHE 0.017 0.001 PHE A 29 TRP 0.010 0.001 TRP C 186 HIS 0.002 0.001 HIS D 217 Details of bonding type rmsd covalent geometry : bond 0.00293 (14425) covalent geometry : angle 0.66667 (19590) SS BOND : bond 0.00383 ( 10) SS BOND : angle 2.25085 ( 20) hydrogen bonds : bond 0.03393 ( 535) hydrogen bonds : angle 4.42779 ( 1590) link_BETA1-4 : bond 0.00513 ( 10) link_BETA1-4 : angle 2.14863 ( 30) link_NAG-ASN : bond 0.00066 ( 5) link_NAG-ASN : angle 0.35287 ( 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 353 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 301 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.8293 (p) REVERT: A 94 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.7813 (t80) REVERT: A 126 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7211 (pm20) REVERT: A 141 ASN cc_start: 0.8346 (m110) cc_final: 0.8056 (m110) REVERT: A 243 MET cc_start: 0.8422 (tpp) cc_final: 0.7868 (mtt) REVERT: A 312 SER cc_start: 0.8023 (OUTLIER) cc_final: 0.7622 (p) REVERT: D 63 SER cc_start: 0.8722 (t) cc_final: 0.8255 (p) REVERT: D 75 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.7732 (ttm-80) REVERT: D 94 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7742 (t80) REVERT: D 132 LYS cc_start: 0.7823 (mttm) cc_final: 0.7462 (mtmt) REVERT: D 135 ARG cc_start: 0.7860 (ptp-170) cc_final: 0.7453 (ptp-170) REVERT: D 206 LYS cc_start: 0.8380 (mtpt) cc_final: 0.7958 (mttm) REVERT: D 262 MET cc_start: 0.7953 (mpp) cc_final: 0.6521 (tmt) REVERT: B 126 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7112 (pm20) REVERT: B 179 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7880 (mmm) REVERT: B 206 LYS cc_start: 0.8506 (mtpt) cc_final: 0.8134 (mttm) REVERT: B 210 ASP cc_start: 0.8505 (m-30) cc_final: 0.8235 (m-30) REVERT: B 219 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7857 (p0) REVERT: B 229 ARG cc_start: 0.8597 (mtt-85) cc_final: 0.7736 (mmm-85) REVERT: B 235 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8186 (mt0) REVERT: B 262 MET cc_start: 0.7861 (mpp) cc_final: 0.6607 (tmt) REVERT: B 391 MET cc_start: 0.4360 (pmm) cc_final: 0.3357 (ppp) REVERT: C 32 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8204 (tmtt) REVERT: C 94 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.7094 (t80) REVERT: C 96 ASP cc_start: 0.7984 (m-30) cc_final: 0.7579 (m-30) REVERT: C 97 ASP cc_start: 0.8058 (m-30) cc_final: 0.7824 (t0) REVERT: C 102 ASP cc_start: 0.7630 (t70) cc_final: 0.7129 (t0) REVERT: C 120 LYS cc_start: 0.8514 (ttmp) cc_final: 0.8103 (tttt) REVERT: C 126 GLU cc_start: 0.7777 (mt-10) cc_final: 0.6899 (pm20) REVERT: C 130 ASP cc_start: 0.8568 (m-30) cc_final: 0.8366 (m-30) REVERT: C 135 ARG cc_start: 0.7879 (ptp-170) cc_final: 0.7570 (ptp-170) REVERT: C 206 LYS cc_start: 0.8439 (mtpt) cc_final: 0.8177 (mttm) REVERT: E 63 SER cc_start: 0.8665 (OUTLIER) cc_final: 0.8317 (p) REVERT: E 94 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7732 (t80) REVERT: E 120 LYS cc_start: 0.8571 (tttp) cc_final: 0.8294 (tttt) REVERT: E 126 GLU cc_start: 0.7964 (mt-10) cc_final: 0.6969 (pm20) REVERT: E 132 LYS cc_start: 0.8062 (mttm) cc_final: 0.7829 (mtmp) REVERT: E 206 LYS cc_start: 0.8371 (mtpt) cc_final: 0.7986 (mttm) REVERT: E 219 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7934 (p0) REVERT: E 235 GLN cc_start: 0.8121 (mm110) cc_final: 0.7866 (mt0) REVERT: E 243 MET cc_start: 0.8279 (tpp) cc_final: 0.7870 (mtt) REVERT: E 262 MET cc_start: 0.7997 (mpp) cc_final: 0.6826 (tmt) REVERT: E 312 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7721 (p) REVERT: E 391 MET cc_start: 0.4871 (pmm) cc_final: 0.3967 (ppp) outliers start: 52 outliers final: 28 residues processed: 322 average time/residue: 0.5412 time to fit residues: 191.8368 Evaluate side-chains 332 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 292 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 204 ILE Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 106 LEU 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 71 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 146 ILE 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 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 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 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 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 Chi-restraints excluded: chain E residue 308 LEU 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: 0.7980 chunk 60 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 120 optimal weight: 0.1980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.165753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116300 restraints weight = 16640.261| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.88 r_work: 0.3138 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14450 Z= 0.135 Angle : 0.666 9.641 19655 Z= 0.334 Chirality : 0.044 0.140 2255 Planarity : 0.004 0.039 2420 Dihedral : 4.845 47.440 2190 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.97 % Allowed : 21.78 % Favored : 75.25 % 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: -0.78 (0.21), residues: 1705 helix: 1.34 (0.23), residues: 560 sheet: -1.40 (0.26), residues: 395 loop : -1.42 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 212 TYR 0.014 0.001 TYR E 317 PHE 0.016 0.001 PHE C 322 TRP 0.009 0.001 TRP C 259 HIS 0.001 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00313 (14425) covalent geometry : angle 0.65986 (19590) SS BOND : bond 0.00362 ( 10) SS BOND : angle 2.19199 ( 20) hydrogen bonds : bond 0.03320 ( 535) hydrogen bonds : angle 4.38089 ( 1590) link_BETA1-4 : bond 0.00511 ( 10) link_BETA1-4 : angle 1.74664 ( 30) link_NAG-ASN : bond 0.00052 ( 5) link_NAG-ASN : angle 0.38004 ( 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 341 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 296 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 SER cc_start: 0.8617 (OUTLIER) cc_final: 0.8241 (p) REVERT: A 94 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.7661 (t80) REVERT: A 126 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7106 (pm20) REVERT: A 141 ASN cc_start: 0.8312 (m110) cc_final: 0.8047 (m110) REVERT: A 243 MET cc_start: 0.8436 (tpp) cc_final: 0.7852 (mtt) REVERT: A 312 SER cc_start: 0.8014 (OUTLIER) cc_final: 0.7590 (p) REVERT: D 63 SER cc_start: 0.8702 (t) cc_final: 0.8213 (p) REVERT: D 71 THR cc_start: 0.8824 (p) cc_final: 0.8503 (p) REVERT: D 75 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7701 (ttm-80) REVERT: D 94 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7648 (t80) REVERT: D 132 LYS cc_start: 0.7836 (mttm) cc_final: 0.7466 (mtmt) REVERT: D 135 ARG cc_start: 0.7857 (ptp-170) cc_final: 0.7411 (ptp-170) REVERT: D 206 LYS cc_start: 0.8361 (mtpt) cc_final: 0.8021 (mttp) REVERT: D 219 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7786 (p0) REVERT: D 243 MET cc_start: 0.8406 (tpp) cc_final: 0.7990 (mtt) REVERT: D 262 MET cc_start: 0.8013 (mpp) cc_final: 0.6707 (tmt) REVERT: B 126 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7002 (pm20) REVERT: B 179 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7854 (mmm) REVERT: B 206 LYS cc_start: 0.8483 (mtpt) cc_final: 0.8108 (mttm) REVERT: B 210 ASP cc_start: 0.8487 (m-30) cc_final: 0.8228 (m-30) REVERT: B 219 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7867 (p0) REVERT: B 229 ARG cc_start: 0.8591 (mtt-85) cc_final: 0.7718 (mmm-85) REVERT: B 235 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8227 (mt0) REVERT: B 262 MET cc_start: 0.7907 (mpp) cc_final: 0.6698 (tmt) REVERT: B 391 MET cc_start: 0.4349 (pmm) cc_final: 0.3390 (ppp) REVERT: C 94 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.6971 (t80) REVERT: C 96 ASP cc_start: 0.7999 (m-30) cc_final: 0.7618 (m-30) REVERT: C 102 ASP cc_start: 0.7580 (t70) cc_final: 0.7070 (t0) REVERT: C 126 GLU cc_start: 0.7745 (mt-10) cc_final: 0.6847 (pm20) REVERT: C 135 ARG cc_start: 0.7859 (ptp-170) cc_final: 0.7544 (ptp-170) REVERT: C 206 LYS cc_start: 0.8430 (mtpt) cc_final: 0.8163 (mttm) REVERT: C 391 MET cc_start: 0.5678 (pmm) cc_final: 0.4927 (ppp) REVERT: E 63 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8296 (p) REVERT: E 94 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.7615 (t80) REVERT: E 120 LYS cc_start: 0.8475 (tttp) cc_final: 0.8186 (tttt) REVERT: E 126 GLU cc_start: 0.7970 (mt-10) cc_final: 0.6940 (pm20) REVERT: E 132 LYS cc_start: 0.8051 (mttm) cc_final: 0.7788 (mtmp) REVERT: E 206 LYS cc_start: 0.8342 (mtpt) cc_final: 0.7954 (mttm) REVERT: E 219 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.7919 (p0) REVERT: E 235 GLN cc_start: 0.8116 (mm110) cc_final: 0.7851 (mt0) REVERT: E 243 MET cc_start: 0.8260 (tpp) cc_final: 0.7917 (mtt) REVERT: E 262 MET cc_start: 0.8087 (mpp) cc_final: 0.6880 (tmt) REVERT: E 312 SER cc_start: 0.8063 (OUTLIER) cc_final: 0.7690 (p) REVERT: E 391 MET cc_start: 0.4815 (pmm) cc_final: 0.3935 (ppp) outliers start: 45 outliers final: 26 residues processed: 315 average time/residue: 0.5372 time to fit residues: 186.4695 Evaluate side-chains 325 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 286 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 204 ILE Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 219 ASN 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 71 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 146 ILE 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 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 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 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 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 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 125 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 129 optimal weight: 0.0770 chunk 39 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 106 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.166590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117238 restraints weight = 16725.594| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.92 r_work: 0.3150 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14450 Z= 0.130 Angle : 0.674 9.499 19655 Z= 0.339 Chirality : 0.044 0.140 2255 Planarity : 0.004 0.038 2420 Dihedral : 4.752 46.310 2190 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.17 % Allowed : 21.78 % Favored : 75.05 % 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 (0.20), residues: 1705 helix: 1.34 (0.23), residues: 570 sheet: -1.35 (0.25), residues: 395 loop : -1.63 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 212 TYR 0.014 0.001 TYR E 317 PHE 0.017 0.001 PHE C 322 TRP 0.009 0.001 TRP E 186 HIS 0.002 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00299 (14425) covalent geometry : angle 0.66922 (19590) SS BOND : bond 0.00332 ( 10) SS BOND : angle 2.08589 ( 20) hydrogen bonds : bond 0.03303 ( 535) hydrogen bonds : angle 4.38638 ( 1590) link_BETA1-4 : bond 0.00471 ( 10) link_BETA1-4 : angle 1.58770 ( 30) link_NAG-ASN : bond 0.00082 ( 5) link_NAG-ASN : angle 0.33626 ( 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 341 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 293 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 SER cc_start: 0.8631 (OUTLIER) cc_final: 0.8258 (p) REVERT: A 94 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7649 (t80) REVERT: A 126 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7092 (pm20) REVERT: A 141 ASN cc_start: 0.8289 (m110) cc_final: 0.8008 (m110) REVERT: A 243 MET cc_start: 0.8446 (tpp) cc_final: 0.7809 (mtt) REVERT: A 260 ILE cc_start: 0.4819 (OUTLIER) cc_final: 0.4589 (pt) REVERT: A 312 SER cc_start: 0.8015 (OUTLIER) cc_final: 0.7587 (p) REVERT: D 63 SER cc_start: 0.8708 (t) cc_final: 0.8220 (p) REVERT: D 71 THR cc_start: 0.8825 (p) cc_final: 0.8493 (p) REVERT: D 75 ARG cc_start: 0.8095 (ttm-80) cc_final: 0.7705 (ttm-80) REVERT: D 94 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7538 (t80) REVERT: D 132 LYS cc_start: 0.7837 (mttm) cc_final: 0.7462 (mtmt) REVERT: D 135 ARG cc_start: 0.7881 (ptp-170) cc_final: 0.7433 (ptp-170) REVERT: D 206 LYS cc_start: 0.8363 (mtpt) cc_final: 0.8036 (mttp) REVERT: D 219 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7771 (p0) REVERT: D 262 MET cc_start: 0.8011 (mpp) cc_final: 0.6689 (tmt) REVERT: B 126 GLU cc_start: 0.7904 (mt-10) cc_final: 0.6980 (pm20) REVERT: B 179 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7869 (mmm) REVERT: B 206 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8107 (mttm) REVERT: B 210 ASP cc_start: 0.8493 (m-30) cc_final: 0.8264 (m-30) REVERT: B 219 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7835 (p0) REVERT: B 229 ARG cc_start: 0.8588 (mtt-85) cc_final: 0.7722 (mmm-85) REVERT: B 235 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8240 (mt0) REVERT: B 262 MET cc_start: 0.7927 (mpp) cc_final: 0.6667 (tmt) REVERT: B 391 MET cc_start: 0.4398 (pmm) cc_final: 0.3428 (ppp) REVERT: C 94 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.6831 (t80) REVERT: C 96 ASP cc_start: 0.7871 (m-30) cc_final: 0.7648 (m-30) REVERT: C 126 GLU cc_start: 0.7719 (mt-10) cc_final: 0.6807 (pm20) REVERT: C 135 ARG cc_start: 0.7858 (ptp-170) cc_final: 0.7568 (ptp-170) REVERT: C 206 LYS cc_start: 0.8414 (mtpt) cc_final: 0.8146 (mttm) REVERT: C 219 ASN cc_start: 0.8355 (p0) cc_final: 0.8104 (p0) REVERT: C 279 MET cc_start: 0.8615 (tpp) cc_final: 0.6970 (mpp) REVERT: E 63 SER cc_start: 0.8638 (OUTLIER) cc_final: 0.8301 (p) REVERT: E 94 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.7297 (t80) REVERT: E 120 LYS cc_start: 0.8455 (tttp) cc_final: 0.8155 (tttt) REVERT: E 126 GLU cc_start: 0.7957 (mt-10) cc_final: 0.6923 (pm20) REVERT: E 132 LYS cc_start: 0.8067 (mttm) cc_final: 0.7795 (mtmp) REVERT: E 219 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7909 (p0) REVERT: E 235 GLN cc_start: 0.8090 (mm110) cc_final: 0.7866 (mt0) REVERT: E 243 MET cc_start: 0.8285 (tpp) cc_final: 0.7970 (mtt) REVERT: E 262 MET cc_start: 0.8143 (mpp) cc_final: 0.6900 (tmt) REVERT: E 312 SER cc_start: 0.8058 (OUTLIER) cc_final: 0.7677 (p) REVERT: E 391 MET cc_start: 0.4883 (pmm) cc_final: 0.4084 (ppp) outliers start: 48 outliers final: 31 residues processed: 314 average time/residue: 0.5205 time to fit residues: 180.9364 Evaluate side-chains 323 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 278 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR 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 204 ILE Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 219 ASN 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 71 THR Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 146 ILE 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 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 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 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 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: 2.9990 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 89 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 165 optimal weight: 0.0980 chunk 66 optimal weight: 0.1980 chunk 151 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN D 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.167005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.117871 restraints weight = 16683.634| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.88 r_work: 0.3284 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14450 Z= 0.125 Angle : 0.664 9.226 19655 Z= 0.333 Chirality : 0.044 0.138 2255 Planarity : 0.004 0.037 2420 Dihedral : 4.654 46.794 2190 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.90 % Allowed : 21.91 % Favored : 75.18 % 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: -0.79 (0.21), residues: 1705 helix: 1.49 (0.23), residues: 570 sheet: -1.33 (0.25), residues: 395 loop : -1.66 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 212 TYR 0.015 0.001 TYR C 317 PHE 0.017 0.001 PHE C 322 TRP 0.009 0.001 TRP C 186 HIS 0.001 0.001 HIS E 217 Details of bonding type rmsd covalent geometry : bond 0.00287 (14425) covalent geometry : angle 0.65719 (19590) SS BOND : bond 0.00319 ( 10) SS BOND : angle 2.52072 ( 20) hydrogen bonds : bond 0.03203 ( 535) hydrogen bonds : angle 4.33149 ( 1590) link_BETA1-4 : bond 0.00493 ( 10) link_BETA1-4 : angle 1.47780 ( 30) link_NAG-ASN : bond 0.00081 ( 5) link_NAG-ASN : angle 0.34666 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5769.67 seconds wall clock time: 98 minutes 56.89 seconds (5936.89 seconds total)