Starting phenix.real_space_refine on Thu Oct 29 00:03:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7spc_24770/10_2026/7spc_24770.cif Found real_map, /net/cci-nas-00/data/ceres_data/7spc_24770/10_2026/7spc_24770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7spc_24770/10_2026/7spc_24770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7spc_24770/10_2026/7spc_24770.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7spc_24770/10_2026/7spc_24770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7spc_24770/10_2026/7spc_24770.map" } resolution = 2.95 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= 0.008 sd= 0.122 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 187 5.16 5 C 18411 2.51 5 N 5219 2.21 5 O 5899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29716 Number of models: 1 Model: "" Number of chains: 2 Chain: "AB1" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 261 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "EF1" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1487 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain breaks: 1 Restraints were copied for chains: AB2, AB3, AB4, AB5, AB6, AB7, AB8, AB9, AB10, AB11, AB12, AB13, AB14, AB15, AB16, AB17, EF2, EF3, EF4, EF5, EF6, EF7, EF8, EF9, EF10, EF11, EF12, EF13, EF14, EF15, EF16, EF17 Time building chain proxies: 3.34, per 1000 atoms: 0.11 Number of scatterers: 29716 At special positions: 0 Unit cell: (185.345, 186.41, 112.911, 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 187 16.00 O 5899 8.00 N 5219 7.00 C 18411 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYSAB1 27 " - pdb=" SG CYSAB17 35 " distance=2.35 Simple disulfide: pdb=" SG CYSAB1 35 " - pdb=" SG CYSAB2 27 " distance=2.35 Simple disulfide: pdb=" SG CYSAB2 35 " - pdb=" SG CYSAB3 27 " distance=2.35 Simple disulfide: pdb=" SG CYSAB3 35 " - pdb=" SG CYSAB4 27 " distance=2.35 Simple disulfide: pdb=" SG CYSAB4 35 " - pdb=" SG CYSAB5 27 " distance=2.35 Simple disulfide: pdb=" SG CYSAB5 35 " - pdb=" SG CYSAB6 27 " distance=2.35 Simple disulfide: pdb=" SG CYSAB6 35 " - pdb=" SG CYSAB7 27 " distance=2.35 Simple disulfide: pdb=" SG CYSAB7 35 " - pdb=" SG CYSAB8 27 " distance=2.35 Simple disulfide: pdb=" SG CYSAB8 35 " - pdb=" SG CYSAB9 27 " distance=2.35 Simple disulfide: pdb=" SG CYSAB9 35 " - pdb=" SG CYSAB10 27 " distance=2.35 Simple disulfide: pdb=" SG CYSAB10 35 " - pdb=" SG CYSAB11 27 " distance=2.35 Simple disulfide: pdb=" SG CYSAB11 35 " - pdb=" SG CYSAB12 27 " distance=2.35 Simple disulfide: pdb=" SG CYSAB12 35 " - pdb=" SG CYSAB13 27 " distance=2.35 Simple disulfide: pdb=" SG CYSAB13 35 " - pdb=" SG CYSAB14 27 " distance=2.35 Simple disulfide: pdb=" SG CYSAB14 35 " - pdb=" SG CYSAB15 27 " distance=2.35 Simple disulfide: pdb=" SG CYSAB15 35 " - pdb=" SG CYSAB16 27 " distance=2.35 Simple disulfide: pdb=" SG CYSAB16 35 " - pdb=" SG CYSAB17 27 " distance=2.35 Simple disulfide: pdb=" SG CYSEF1 250 " - pdb=" SG CYSEF1 274 " distance=2.03 Simple disulfide: pdb=" SG CYSEF2 250 " - pdb=" SG CYSEF2 274 " distance=2.03 Simple disulfide: pdb=" SG CYSEF3 250 " - pdb=" SG CYSEF3 274 " distance=2.03 Simple disulfide: pdb=" SG CYSEF4 250 " - pdb=" SG CYSEF4 274 " distance=2.03 Simple disulfide: pdb=" SG CYSEF5 250 " - pdb=" SG CYSEF5 274 " distance=2.03 Simple disulfide: pdb=" SG CYSEF6 250 " - pdb=" SG CYSEF6 274 " distance=2.03 Simple disulfide: pdb=" SG CYSEF7 250 " - pdb=" SG CYSEF7 274 " distance=2.03 Simple disulfide: pdb=" SG CYSEF8 250 " - pdb=" SG CYSEF8 274 " distance=2.03 Simple disulfide: pdb=" SG CYSEF9 250 " - pdb=" SG CYSEF9 274 " distance=2.03 Simple disulfide: pdb=" SG CYSEF10 250 " - pdb=" SG CYSEF10 274 " distance=2.03 Simple disulfide: pdb=" SG CYSEF11 250 " - pdb=" SG CYSEF11 274 " distance=2.03 Simple disulfide: pdb=" SG CYSEF12 250 " - pdb=" SG CYSEF12 274 " distance=2.03 Simple disulfide: pdb=" SG CYSEF13 250 " - pdb=" SG CYSEF13 274 " distance=2.03 Simple disulfide: pdb=" SG CYSEF14 250 " - pdb=" SG CYSEF14 274 " distance=2.03 Simple disulfide: pdb=" SG CYSEF15 250 " - pdb=" SG CYSEF15 274 " distance=2.03 Simple disulfide: pdb=" SG CYSEF16 250 " - pdb=" SG CYSEF16 274 " distance=2.03 Simple disulfide: pdb=" SG CYSEF17 250 " - pdb=" SG CYSEF17 274 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.3 seconds 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7174 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 68 sheets defined 27.4% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'AB1' and resid 38 through 52 Processing helix chain 'AB2' and resid 38 through 52 Processing helix chain 'AB3' and resid 38 through 52 Processing helix chain 'AB4' and resid 38 through 52 Processing helix chain 'AB5' and resid 38 through 52 Processing helix chain 'AB6' and resid 38 through 52 Processing helix chain 'AB7' and resid 38 through 52 Processing helix chain 'AB8' and resid 38 through 52 Processing helix chain 'AB9' and resid 38 through 52 Processing helix chain 'AB10' and resid 38 through 52 Processing helix chain 'AB11' and resid 38 through 52 Processing helix chain 'AB12' and resid 38 through 52 Processing helix chain 'AB13' and resid 38 through 52 Processing helix chain 'AB14' and resid 38 through 52 Processing helix chain 'AB15' and resid 38 through 52 Processing helix chain 'AB16' and resid 38 through 52 Processing helix chain 'AB17' and resid 38 through 52 Processing helix chain 'EF1' and resid 306 through 326 Processing helix chain 'EF1' and resid 357 through 371 Processing helix chain 'EF1' and resid 398 through 410 Processing helix chain 'EF2' and resid 306 through 326 Processing helix chain 'EF2' and resid 357 through 371 Processing helix chain 'EF2' and resid 398 through 410 Processing helix chain 'EF3' and resid 306 through 326 Processing helix chain 'EF3' and resid 357 through 371 Processing helix chain 'EF3' and resid 398 through 410 Processing helix chain 'EF4' and resid 306 through 326 Processing helix chain 'EF4' and resid 357 through 371 Processing helix chain 'EF4' and resid 398 through 410 Processing helix chain 'EF5' and resid 306 through 326 Processing helix chain 'EF5' and resid 357 through 371 Processing helix chain 'EF5' and resid 398 through 410 Processing helix chain 'EF6' and resid 306 through 326 Processing helix chain 'EF6' and resid 357 through 371 Processing helix chain 'EF6' and resid 398 through 410 Processing helix chain 'EF7' and resid 306 through 326 Processing helix chain 'EF7' and resid 357 through 371 Processing helix chain 'EF7' and resid 398 through 410 Processing helix chain 'EF8' and resid 306 through 326 Processing helix chain 'EF8' and resid 357 through 371 Processing helix chain 'EF8' and resid 398 through 410 Processing helix chain 'EF9' and resid 306 through 326 Processing helix chain 'EF9' and resid 357 through 371 Processing helix chain 'EF9' and resid 398 through 410 Processing helix chain 'EF10' and resid 306 through 326 Processing helix chain 'EF10' and resid 357 through 371 Processing helix chain 'EF10' and resid 398 through 410 Processing helix chain 'EF11' and resid 306 through 326 Processing helix chain 'EF11' and resid 357 through 371 Processing helix chain 'EF11' and resid 398 through 410 Processing helix chain 'EF12' and resid 306 through 326 Processing helix chain 'EF12' and resid 357 through 371 Processing helix chain 'EF12' and resid 398 through 410 Processing helix chain 'EF13' and resid 306 through 326 Processing helix chain 'EF13' and resid 357 through 371 Processing helix chain 'EF13' and resid 398 through 410 Processing helix chain 'EF14' and resid 306 through 326 Processing helix chain 'EF14' and resid 357 through 371 Processing helix chain 'EF14' and resid 398 through 410 Processing helix chain 'EF15' and resid 306 through 326 Processing helix chain 'EF15' and resid 357 through 371 Processing helix chain 'EF15' and resid 398 through 410 Processing helix chain 'EF16' and resid 306 through 326 Processing helix chain 'EF16' and resid 357 through 371 Processing helix chain 'EF16' and resid 398 through 410 Processing helix chain 'EF17' and resid 306 through 326 Processing helix chain 'EF17' and resid 357 through 371 Processing helix chain 'EF17' and resid 398 through 410 Processing sheet with id=AA1, first strand: chain 'EF1' and resid 199 through 200 Processing sheet with id=AA2, first strand: chain 'EF1' and resid 204 through 210 WARNING: can't find start of bonding for strands! previous: chain 'EF1' and resid 204 through 210 current: chain 'EF1' and resid 251 through 259 removed outlier: 6.691A pdb=" N PHEEF1 251 " --> pdb=" O ILEEF1 272 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILEEF1 272 " --> pdb=" O PHEEF1 251 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THREF1 253 " --> pdb=" O ARGEF1 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'EF1' and resid 279 through 284 current: chain 'EF1' and resid 294 through 295 Processing sheet with id=AA3, first strand: chain 'EF1' and resid 214 through 215 Processing sheet with id=AA4, first strand: chain 'EF1' and resid 237 through 239 removed outlier: 3.777A pdb=" N GLUEF1 243 " --> pdb=" O METEF1 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'EF2' and resid 199 through 200 Processing sheet with id=AA6, first strand: chain 'EF2' and resid 204 through 210 WARNING: can't find start of bonding for strands! previous: chain 'EF2' and resid 204 through 210 current: chain 'EF2' and resid 251 through 259 removed outlier: 6.691A pdb=" N PHEEF2 251 " --> pdb=" O ILEEF2 272 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILEEF2 272 " --> pdb=" O PHEEF2 251 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THREF2 253 " --> pdb=" O ARGEF2 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'EF2' and resid 279 through 284 current: chain 'EF2' and resid 294 through 295 Processing sheet with id=AA7, first strand: chain 'EF2' and resid 214 through 215 Processing sheet with id=AA8, first strand: chain 'EF2' and resid 237 through 239 removed outlier: 3.777A pdb=" N GLUEF2 243 " --> pdb=" O METEF2 239 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'EF3' and resid 199 through 200 Processing sheet with id=AB1, first strand: chain 'EF3' and resid 204 through 210 WARNING: can't find start of bonding for strands! previous: chain 'EF3' and resid 204 through 210 current: chain 'EF3' and resid 251 through 259 removed outlier: 6.691A pdb=" N PHEEF3 251 " --> pdb=" O ILEEF3 272 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILEEF3 272 " --> pdb=" O PHEEF3 251 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THREF3 253 " --> pdb=" O ARGEF3 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'EF3' and resid 279 through 284 current: chain 'EF3' and resid 294 through 295 Processing sheet with id=AB2, first strand: chain 'EF3' and resid 214 through 215 Processing sheet with id=AB3, first strand: chain 'EF3' and resid 237 through 239 removed outlier: 3.778A pdb=" N GLUEF3 243 " --> pdb=" O METEF3 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'EF4' and resid 199 through 200 Processing sheet with id=AB5, first strand: chain 'EF4' and resid 204 through 210 WARNING: can't find start of bonding for strands! previous: chain 'EF4' and resid 204 through 210 current: chain 'EF4' and resid 251 through 259 removed outlier: 6.691A pdb=" N PHEEF4 251 " --> pdb=" O ILEEF4 272 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILEEF4 272 " --> pdb=" O PHEEF4 251 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THREF4 253 " --> pdb=" O ARGEF4 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'EF4' and resid 279 through 284 current: chain 'EF4' and resid 294 through 295 Processing sheet with id=AB6, first strand: chain 'EF4' and resid 214 through 215 Processing sheet with id=AB7, first strand: chain 'EF4' and resid 237 through 239 removed outlier: 3.777A pdb=" N GLUEF4 243 " --> pdb=" O METEF4 239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'EF5' and resid 199 through 200 Processing sheet with id=AB9, first strand: chain 'EF5' and resid 204 through 210 WARNING: can't find start of bonding for strands! previous: chain 'EF5' and resid 204 through 210 current: chain 'EF5' and resid 251 through 259 removed outlier: 6.690A pdb=" N PHEEF5 251 " --> pdb=" O ILEEF5 272 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILEEF5 272 " --> pdb=" O PHEEF5 251 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THREF5 253 " --> pdb=" O ARGEF5 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'EF5' and resid 279 through 284 current: chain 'EF5' and resid 294 through 295 Processing sheet with id=AC1, first strand: chain 'EF5' and resid 214 through 215 Processing sheet with id=AC2, first strand: chain 'EF5' and resid 237 through 239 removed outlier: 3.777A pdb=" N GLUEF5 243 " --> pdb=" O METEF5 239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'EF6' and resid 199 through 200 Processing sheet with id=AC4, first strand: chain 'EF6' and resid 204 through 210 WARNING: can't find start of bonding for strands! previous: chain 'EF6' and resid 204 through 210 current: chain 'EF6' and resid 251 through 259 removed outlier: 6.690A pdb=" N PHEEF6 251 " --> pdb=" O ILEEF6 272 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILEEF6 272 " --> pdb=" O PHEEF6 251 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THREF6 253 " --> pdb=" O ARGEF6 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'EF6' and resid 279 through 284 current: chain 'EF6' and resid 294 through 295 Processing sheet with id=AC5, first strand: chain 'EF6' and resid 214 through 215 Processing sheet with id=AC6, first strand: chain 'EF6' and resid 237 through 239 removed outlier: 3.778A pdb=" N GLUEF6 243 " --> pdb=" O METEF6 239 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'EF7' and resid 199 through 200 Processing sheet with id=AC8, first strand: chain 'EF7' and resid 204 through 210 WARNING: can't find start of bonding for strands! previous: chain 'EF7' and resid 204 through 210 current: chain 'EF7' and resid 251 through 259 removed outlier: 6.691A pdb=" N PHEEF7 251 " --> pdb=" O ILEEF7 272 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILEEF7 272 " --> pdb=" O PHEEF7 251 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THREF7 253 " --> pdb=" O ARGEF7 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'EF7' and resid 279 through 284 current: chain 'EF7' and resid 294 through 295 Processing sheet with id=AC9, first strand: chain 'EF7' and resid 214 through 215 Processing sheet with id=AD1, first strand: chain 'EF7' and resid 237 through 239 removed outlier: 3.778A pdb=" N GLUEF7 243 " --> pdb=" O METEF7 239 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'EF8' and resid 199 through 200 Processing sheet with id=AD3, first strand: chain 'EF8' and resid 204 through 210 WARNING: can't find start of bonding for strands! previous: chain 'EF8' and resid 204 through 210 current: chain 'EF8' and resid 251 through 259 removed outlier: 6.690A pdb=" N PHEEF8 251 " --> pdb=" O ILEEF8 272 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILEEF8 272 " --> pdb=" O PHEEF8 251 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THREF8 253 " --> pdb=" O ARGEF8 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'EF8' and resid 279 through 284 current: chain 'EF8' and resid 294 through 295 Processing sheet with id=AD4, first strand: chain 'EF8' and resid 214 through 215 Processing sheet with id=AD5, first strand: chain 'EF8' and resid 237 through 239 removed outlier: 3.777A pdb=" N GLUEF8 243 " --> pdb=" O METEF8 239 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'EF9' and resid 199 through 200 Processing sheet with id=AD7, first strand: chain 'EF9' and resid 204 through 210 WARNING: can't find start of bonding for strands! previous: chain 'EF9' and resid 204 through 210 current: chain 'EF9' and resid 251 through 259 removed outlier: 6.690A pdb=" N PHEEF9 251 " --> pdb=" O ILEEF9 272 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILEEF9 272 " --> pdb=" O PHEEF9 251 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THREF9 253 " --> pdb=" O ARGEF9 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'EF9' and resid 279 through 284 current: chain 'EF9' and resid 294 through 295 Processing sheet with id=AD8, first strand: chain 'EF9' and resid 214 through 215 Processing sheet with id=AD9, first strand: chain 'EF9' and resid 237 through 239 removed outlier: 3.777A pdb=" N GLUEF9 243 " --> pdb=" O METEF9 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'EF10' and resid 199 through 200 Processing sheet with id=AE2, first strand: chain 'EF10' and resid 204 through 210 WARNING: can't find start of bonding for strands! previous: chain 'EF10' and resid 204 through 210 current: chain 'EF10' and resid 251 through 259 removed outlier: 6.691A pdb=" N PHEEF10 251 " --> pdb=" O ILEEF10 272 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILEEF10 272 " --> pdb=" O PHEEF10 251 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THREF10 253 " --> pdb=" O ARGEF10 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'EF10' and resid 279 through 284 current: chain 'EF10' and resid 294 through 295 Processing sheet with id=AE3, first strand: chain 'EF10' and resid 214 through 215 Processing sheet with id=AE4, first strand: chain 'EF10' and resid 237 through 239 removed outlier: 3.778A pdb=" N GLUEF10 243 " --> pdb=" O METEF10 239 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'EF11' and resid 199 through 200 Processing sheet with id=AE6, first strand: chain 'EF11' and resid 204 through 210 WARNING: can't find start of bonding for strands! previous: chain 'EF11' and resid 204 through 210 current: chain 'EF11' and resid 251 through 259 removed outlier: 6.691A pdb=" N PHEEF11 251 " --> pdb=" O ILEEF11 272 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILEEF11 272 " --> pdb=" O PHEEF11 251 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THREF11 253 " --> pdb=" O ARGEF11 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'EF11' and resid 279 through 284 current: chain 'EF11' and resid 294 through 295 Processing sheet with id=AE7, first strand: chain 'EF11' and resid 214 through 215 Processing sheet with id=AE8, first strand: chain 'EF11' and resid 237 through 239 removed outlier: 3.777A pdb=" N GLUEF11 243 " --> pdb=" O METEF11 239 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'EF12' and resid 199 through 200 Processing sheet with id=AF1, first strand: chain 'EF12' and resid 204 through 210 WARNING: can't find start of bonding for strands! previous: chain 'EF12' and resid 204 through 210 current: chain 'EF12' and resid 251 through 259 removed outlier: 6.691A pdb=" N PHEEF12 251 " --> pdb=" O ILEEF12 272 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILEEF12 272 " --> pdb=" O PHEEF12 251 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THREF12 253 " --> pdb=" O ARGEF12 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'EF12' and resid 279 through 284 current: chain 'EF12' and resid 294 through 295 Processing sheet with id=AF2, first strand: chain 'EF12' and resid 214 through 215 Processing sheet with id=AF3, first strand: chain 'EF12' and resid 237 through 239 removed outlier: 3.777A pdb=" N GLUEF12 243 " --> pdb=" O METEF12 239 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'EF13' and resid 199 through 200 Processing sheet with id=AF5, first strand: chain 'EF13' and resid 204 through 210 WARNING: can't find start of bonding for strands! previous: chain 'EF13' and resid 204 through 210 current: chain 'EF13' and resid 251 through 259 removed outlier: 6.691A pdb=" N PHEEF13 251 " --> pdb=" O ILEEF13 272 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILEEF13 272 " --> pdb=" O PHEEF13 251 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THREF13 253 " --> pdb=" O ARGEF13 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'EF13' and resid 279 through 284 current: chain 'EF13' and resid 294 through 295 Processing sheet with id=AF6, first strand: chain 'EF13' and resid 214 through 215 Processing sheet with id=AF7, first strand: chain 'EF13' and resid 237 through 239 removed outlier: 3.777A pdb=" N GLUEF13 243 " --> pdb=" O METEF13 239 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'EF14' and resid 199 through 200 Processing sheet with id=AF9, first strand: chain 'EF14' and resid 204 through 210 WARNING: can't find start of bonding for strands! previous: chain 'EF14' and resid 204 through 210 current: chain 'EF14' and resid 251 through 259 removed outlier: 6.690A pdb=" N PHEEF14 251 " --> pdb=" O ILEEF14 272 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILEEF14 272 " --> pdb=" O PHEEF14 251 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THREF14 253 " --> pdb=" O ARGEF14 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'EF14' and resid 279 through 284 current: chain 'EF14' and resid 294 through 295 Processing sheet with id=AG1, first strand: chain 'EF14' and resid 214 through 215 Processing sheet with id=AG2, first strand: chain 'EF14' and resid 237 through 239 removed outlier: 3.777A pdb=" N GLUEF14 243 " --> pdb=" O METEF14 239 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'EF15' and resid 199 through 200 Processing sheet with id=AG4, first strand: chain 'EF15' and resid 204 through 210 WARNING: can't find start of bonding for strands! previous: chain 'EF15' and resid 204 through 210 current: chain 'EF15' and resid 251 through 259 removed outlier: 6.691A pdb=" N PHEEF15 251 " --> pdb=" O ILEEF15 272 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILEEF15 272 " --> pdb=" O PHEEF15 251 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THREF15 253 " --> pdb=" O ARGEF15 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'EF15' and resid 279 through 284 current: chain 'EF15' and resid 294 through 295 Processing sheet with id=AG5, first strand: chain 'EF15' and resid 214 through 215 Processing sheet with id=AG6, first strand: chain 'EF15' and resid 237 through 239 removed outlier: 3.777A pdb=" N GLUEF15 243 " --> pdb=" O METEF15 239 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'EF16' and resid 199 through 200 Processing sheet with id=AG8, first strand: chain 'EF16' and resid 204 through 210 WARNING: can't find start of bonding for strands! previous: chain 'EF16' and resid 204 through 210 current: chain 'EF16' and resid 251 through 259 removed outlier: 6.691A pdb=" N PHEEF16 251 " --> pdb=" O ILEEF16 272 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILEEF16 272 " --> pdb=" O PHEEF16 251 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THREF16 253 " --> pdb=" O ARGEF16 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'EF16' and resid 279 through 284 current: chain 'EF16' and resid 294 through 295 Processing sheet with id=AG9, first strand: chain 'EF16' and resid 214 through 215 Processing sheet with id=AH1, first strand: chain 'EF16' and resid 237 through 239 removed outlier: 3.777A pdb=" N GLUEF16 243 " --> pdb=" O METEF16 239 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'EF17' and resid 199 through 200 Processing sheet with id=AH3, first strand: chain 'EF17' and resid 204 through 210 WARNING: can't find start of bonding for strands! previous: chain 'EF17' and resid 204 through 210 current: chain 'EF17' and resid 251 through 259 removed outlier: 6.691A pdb=" N PHEEF17 251 " --> pdb=" O ILEEF17 272 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILEEF17 272 " --> pdb=" O PHEEF17 251 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THREF17 253 " --> pdb=" O ARGEF17 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'EF17' and resid 279 through 284 current: chain 'EF17' and resid 294 through 295 Processing sheet with id=AH4, first strand: chain 'EF17' and resid 214 through 215 Processing sheet with id=AH5, first strand: chain 'EF17' and resid 237 through 239 removed outlier: 3.777A pdb=" N GLUEF17 243 " --> pdb=" O METEF17 239 " (cutoff:3.500A) 1156 hydrogen bonds defined for protein. 3213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5355 1.31 - 1.44: 7293 1.44 - 1.57: 17153 1.57 - 1.70: 0 1.70 - 1.82: 289 Bond restraints: 30090 Sorted by residual: bond pdb=" CA VALEF12 237 " pdb=" C VALEF12 237 " ideal model delta sigma weight residual 1.521 1.456 0.065 1.21e-02 6.83e+03 2.87e+01 bond pdb=" CA VALEF16 237 " pdb=" C VALEF16 237 " ideal model delta sigma weight residual 1.521 1.456 0.065 1.21e-02 6.83e+03 2.86e+01 bond pdb=" CA VALEF8 237 " pdb=" C VALEF8 237 " ideal model delta sigma weight residual 1.521 1.456 0.065 1.21e-02 6.83e+03 2.86e+01 bond pdb=" CA VALEF7 237 " pdb=" C VALEF7 237 " ideal model delta sigma weight residual 1.521 1.457 0.064 1.21e-02 6.83e+03 2.84e+01 bond pdb=" CA VALEF17 237 " pdb=" C VALEF17 237 " ideal model delta sigma weight residual 1.521 1.457 0.064 1.21e-02 6.83e+03 2.83e+01 ... (remaining 30085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 36837 1.93 - 3.85: 2966 3.85 - 5.78: 453 5.78 - 7.70: 119 7.70 - 9.63: 68 Bond angle restraints: 40443 Sorted by residual: angle pdb=" N ILEEF10 325 " pdb=" CA ILEEF10 325 " pdb=" C ILEEF10 325 " ideal model delta sigma weight residual 111.90 103.88 8.02 8.10e-01 1.52e+00 9.81e+01 angle pdb=" N ILEEF14 325 " pdb=" CA ILEEF14 325 " pdb=" C ILEEF14 325 " ideal model delta sigma weight residual 111.90 103.89 8.01 8.10e-01 1.52e+00 9.79e+01 angle pdb=" N ILEEF4 325 " pdb=" CA ILEEF4 325 " pdb=" C ILEEF4 325 " ideal model delta sigma weight residual 111.90 103.89 8.01 8.10e-01 1.52e+00 9.78e+01 angle pdb=" N ILEEF17 325 " pdb=" CA ILEEF17 325 " pdb=" C ILEEF17 325 " ideal model delta sigma weight residual 111.90 103.89 8.01 8.10e-01 1.52e+00 9.78e+01 angle pdb=" N ILEEF7 325 " pdb=" CA ILEEF7 325 " pdb=" C ILEEF7 325 " ideal model delta sigma weight residual 111.90 103.89 8.01 8.10e-01 1.52e+00 9.78e+01 ... (remaining 40438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 15593 15.87 - 31.74: 1900 31.74 - 47.60: 544 47.60 - 63.47: 273 63.47 - 79.34: 50 Dihedral angle restraints: 18360 sinusoidal: 7191 harmonic: 11169 Sorted by residual: dihedral pdb=" CB CYSAB15 35 " pdb=" SG CYSAB15 35 " pdb=" SG CYSAB16 27 " pdb=" CB CYSAB16 27 " ideal model delta sinusoidal sigma weight residual 93.00 162.47 -69.47 1 1.00e+01 1.00e-02 6.23e+01 dihedral pdb=" CB CYSAB5 35 " pdb=" SG CYSAB5 35 " pdb=" SG CYSAB6 27 " pdb=" CB CYSAB6 27 " ideal model delta sinusoidal sigma weight residual 93.00 162.46 -69.46 1 1.00e+01 1.00e-02 6.23e+01 dihedral pdb=" CB CYSAB7 35 " pdb=" SG CYSAB7 35 " pdb=" SG CYSAB8 27 " pdb=" CB CYSAB8 27 " ideal model delta sinusoidal sigma weight residual 93.00 162.46 -69.46 1 1.00e+01 1.00e-02 6.23e+01 ... (remaining 18357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3442 0.070 - 0.140: 752 0.140 - 0.210: 243 0.210 - 0.280: 68 0.280 - 0.350: 34 Chirality restraints: 4539 Sorted by residual: chirality pdb=" CA ASNEF10 241 " pdb=" N ASNEF10 241 " pdb=" C ASNEF10 241 " pdb=" CB ASNEF10 241 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA ASNEF16 241 " pdb=" N ASNEF16 241 " pdb=" C ASNEF16 241 " pdb=" CB ASNEF16 241 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA ASNEF12 241 " pdb=" N ASNEF12 241 " pdb=" C ASNEF12 241 " pdb=" CB ASNEF12 241 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 4536 not shown) Planarity restraints: 5304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLYEF8 316 " 0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C GLYEF8 316 " -0.057 2.00e-02 2.50e+03 pdb=" O GLYEF8 316 " 0.021 2.00e-02 2.50e+03 pdb=" N PHEEF8 317 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLYEF7 316 " 0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C GLYEF7 316 " -0.057 2.00e-02 2.50e+03 pdb=" O GLYEF7 316 " 0.021 2.00e-02 2.50e+03 pdb=" N PHEEF7 317 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLYEF3 316 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C GLYEF3 316 " 0.057 2.00e-02 2.50e+03 pdb=" O GLYEF3 316 " -0.021 2.00e-02 2.50e+03 pdb=" N PHEEF3 317 " -0.020 2.00e-02 2.50e+03 ... (remaining 5301 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3643 2.75 - 3.29: 28777 3.29 - 3.83: 49342 3.83 - 4.36: 60237 4.36 - 4.90: 102755 Nonbonded interactions: 244754 Sorted by model distance: nonbonded pdb=" OG SEREF9 330 " pdb=" O SEREF10 329 " model vdw 2.217 3.040 nonbonded pdb=" OG SEREF13 330 " pdb=" O SEREF14 329 " model vdw 2.217 3.040 nonbonded pdb=" OG SEREF11 330 " pdb=" O SEREF12 329 " model vdw 2.217 3.040 nonbonded pdb=" OG SEREF5 330 " pdb=" O SEREF6 329 " model vdw 2.217 3.040 nonbonded pdb=" OG SEREF1 330 " pdb=" O SEREF2 329 " model vdw 2.217 3.040 ... (remaining 244749 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: 0.12 Found NCS groups: ncs_group { reference = chain 'AB1' selection = chain 'AB2' selection = chain 'AB3' selection = chain 'AB4' selection = chain 'AB5' selection = chain 'AB6' selection = chain 'AB7' selection = chain 'AB8' selection = chain 'AB9' selection = chain 'AB10' selection = chain 'AB11' selection = chain 'AB12' selection = chain 'AB13' selection = chain 'AB14' selection = chain 'AB15' selection = chain 'AB16' selection = chain 'AB17' } ncs_group { reference = chain 'EF1' selection = chain 'EF2' selection = chain 'EF3' selection = chain 'EF4' selection = chain 'EF5' selection = chain 'EF6' selection = chain 'EF7' selection = chain 'EF8' selection = chain 'EF9' selection = chain 'EF10' selection = chain 'EF11' selection = chain 'EF12' selection = chain 'EF13' selection = chain 'EF14' selection = chain 'EF15' selection = chain 'EF16' selection = chain 'EF17' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.970 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.300 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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 : 0.012 0.318 30124 Z= 0.782 Angle : 1.130 9.629 40511 Z= 0.820 Chirality : 0.073 0.350 4539 Planarity : 0.006 0.053 5304 Dihedral : 16.548 79.340 11084 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.26 % Allowed : 27.65 % Favored : 69.09 % 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: -0.98 (0.13), residues: 3876 helix: 0.64 (0.14), residues: 1292 sheet: -0.40 (0.19), residues: 782 loop : -1.74 (0.13), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGEF12 268 TYR 0.006 0.002 TYREF5 373 PHE 0.015 0.002 PHEEF17 317 TRP 0.004 0.001 TRPEF12 257 HIS 0.002 0.001 HISEF2 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00967 / 0.69 (30090) covalent geometry : angle 1.13094 / 0.82 (40443) SS BOND : bond 0.22473 / 14.73 ( 34) SS BOND : angle 0.17609 / 0.11 ( 68) hydrogen bonds : bond 0.13887 / 9.13 ( 1156) hydrogen bonds : angle 6.93169 / 4.66 ( 3213) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 857 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: AB2 52 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.7136 (mm-40) REVERT: AB3 40 LYS cc_start: 0.6827 (mmmt) cc_final: 0.6626 (mttt) REVERT: AB3 52 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6720 (mm-40) REVERT: AB4 52 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6665 (mm-40) REVERT: AB6 48 LYS cc_start: 0.6238 (tttp) cc_final: 0.5655 (tptt) REVERT: AB6 51 LYS cc_start: 0.7209 (tppp) cc_final: 0.6982 (mmmt) REVERT: AB6 52 GLN cc_start: 0.6549 (OUTLIER) cc_final: 0.5427 (mp-120) REVERT: AB7 52 GLN cc_start: 0.6362 (OUTLIER) cc_final: 0.5478 (mp-120) REVERT: AB8 40 LYS cc_start: 0.7084 (mmmt) cc_final: 0.6328 (mttp) REVERT: AB9 40 LYS cc_start: 0.6974 (mmmt) cc_final: 0.6538 (mmtt) REVERT: AB9 52 GLN cc_start: 0.6366 (OUTLIER) cc_final: 0.5933 (mp-120) REVERT: AB11 51 LYS cc_start: 0.7986 (tppp) cc_final: 0.7678 (tppt) REVERT: EF3 229 MET cc_start: 0.7775 (ttm) cc_final: 0.7377 (ttp) REVERT: EF5 371 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6710 (mm-30) REVERT: EF6 364 ASP cc_start: 0.7473 (t70) cc_final: 0.7171 (t0) REVERT: EF6 371 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6779 (mm-30) REVERT: EF7 217 ASN cc_start: 0.8306 (t0) cc_final: 0.8028 (t0) REVERT: EF7 279 ASP cc_start: 0.7757 (m-30) cc_final: 0.7530 (m-30) REVERT: EF8 217 ASN cc_start: 0.8263 (t0) cc_final: 0.8037 (t0) REVERT: EF8 225 ASN cc_start: 0.8841 (m-40) cc_final: 0.8481 (m110) REVERT: EF9 225 ASN cc_start: 0.8872 (m-40) cc_final: 0.8564 (m110) REVERT: EF9 364 ASP cc_start: 0.7431 (t70) cc_final: 0.7196 (t0) REVERT: EF12 217 ASN cc_start: 0.8471 (t0) cc_final: 0.8245 (t0) REVERT: EF12 259 ASP cc_start: 0.7329 (t70) cc_final: 0.6925 (t0) REVERT: EF13 259 ASP cc_start: 0.7722 (t70) cc_final: 0.7108 (t0) REVERT: EF14 243 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7526 (mm-30) REVERT: EF14 292 MET cc_start: 0.8246 (mmm) cc_final: 0.8024 (mmt) REVERT: EF14 319 ASP cc_start: 0.6299 (t0) cc_final: 0.6049 (t70) REVERT: EF14 364 ASP cc_start: 0.7438 (t70) cc_final: 0.7215 (t0) REVERT: EF15 239 MET cc_start: 0.8842 (mtm) cc_final: 0.8439 (mtp) REVERT: EF15 259 ASP cc_start: 0.8102 (t70) cc_final: 0.7886 (t0) REVERT: EF15 290 SER cc_start: 0.9046 (m) cc_final: 0.8713 (p) REVERT: EF16 290 SER cc_start: 0.9031 (m) cc_final: 0.8683 (p) REVERT: EF17 303 MET cc_start: 0.8697 (tpt) cc_final: 0.8474 (tpp) REVERT: EF17 364 ASP cc_start: 0.7538 (t70) cc_final: 0.7297 (t0) REVERT: EF17 391 ASP cc_start: 0.8440 (m-30) cc_final: 0.8182 (m-30) outliers start: 102 outliers final: 31 residues processed: 952 average time/residue: 0.6251 time to fit residues: 697.3630 Evaluate side-chains 562 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 525 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB2 residue 52 GLN Chi-restraints excluded: chain AB3 residue 52 GLN Chi-restraints excluded: chain AB4 residue 52 GLN Chi-restraints excluded: chain AB6 residue 52 GLN Chi-restraints excluded: chain AB7 residue 52 GLN Chi-restraints excluded: chain AB9 residue 52 GLN Chi-restraints excluded: chain AB10 residue 44 LEU Chi-restraints excluded: chain AB12 residue 44 LEU Chi-restraints excluded: chain EF1 residue 206 VAL Chi-restraints excluded: chain EF1 residue 261 SER Chi-restraints excluded: chain EF2 residue 206 VAL Chi-restraints excluded: chain EF2 residue 261 SER Chi-restraints excluded: chain EF3 residue 261 SER Chi-restraints excluded: chain EF3 residue 355 VAL Chi-restraints excluded: chain EF4 residue 261 SER Chi-restraints excluded: chain EF4 residue 355 VAL Chi-restraints excluded: chain EF5 residue 261 SER Chi-restraints excluded: chain EF6 residue 355 VAL Chi-restraints excluded: chain EF7 residue 206 VAL Chi-restraints excluded: chain EF9 residue 355 VAL Chi-restraints excluded: chain EF10 residue 271 SER Chi-restraints excluded: chain EF11 residue 261 SER Chi-restraints excluded: chain EF12 residue 206 VAL Chi-restraints excluded: chain EF12 residue 261 SER Chi-restraints excluded: chain EF12 residue 271 SER Chi-restraints excluded: chain EF13 residue 271 SER Chi-restraints excluded: chain EF13 residue 355 VAL Chi-restraints excluded: chain EF14 residue 206 VAL Chi-restraints excluded: chain EF14 residue 261 SER Chi-restraints excluded: chain EF15 residue 206 VAL Chi-restraints excluded: chain EF15 residue 261 SER Chi-restraints excluded: chain EF15 residue 355 VAL Chi-restraints excluded: chain EF16 residue 206 VAL Chi-restraints excluded: chain EF16 residue 261 SER Chi-restraints excluded: chain EF17 residue 206 VAL Chi-restraints excluded: chain EF17 residue 209 ILE Chi-restraints excluded: chain EF17 residue 261 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.138696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.109084 restraints weight = 37867.410| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.55 r_work: 0.3159 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30124 Z= 0.149 Angle : 0.510 8.540 40511 Z= 0.280 Chirality : 0.040 0.135 4539 Planarity : 0.004 0.048 5304 Dihedral : 5.264 56.721 4217 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 6.65 % Allowed : 27.85 % Favored : 65.51 % 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: 0.10 (0.13), residues: 3876 helix: 1.99 (0.14), residues: 1292 sheet: -0.04 (0.17), residues: 986 loop : -1.51 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAB13 46 TYR 0.009 0.001 TYREF9 366 PHE 0.015 0.001 PHEEF10 197 TRP 0.010 0.001 TRPEF13 199 HIS 0.003 0.001 HISEF10 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (30090) covalent geometry : angle 0.51021 / 0.28 (40443) SS BOND : bond 0.00513 / 0.34 ( 34) SS BOND : angle 0.52876 / 0.34 ( 68) hydrogen bonds : bond 0.03367 / 2.23 ( 1156) hydrogen bonds : angle 5.14704 / 3.44 ( 3213) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 527 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: AB3 51 LYS cc_start: 0.7681 (tptt) cc_final: 0.7358 (tppt) REVERT: AB6 48 LYS cc_start: 0.7155 (tttp) cc_final: 0.6434 (tttt) REVERT: AB6 51 LYS cc_start: 0.7482 (tppp) cc_final: 0.7175 (tppt) REVERT: AB6 52 GLN cc_start: 0.6750 (OUTLIER) cc_final: 0.5532 (mp-120) REVERT: AB7 46 ARG cc_start: 0.7442 (ttm170) cc_final: 0.7213 (ttm-80) REVERT: AB7 48 LYS cc_start: 0.7218 (tttp) cc_final: 0.6983 (tttm) REVERT: AB7 52 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.5914 (mp-120) REVERT: AB8 36 MET cc_start: 0.8426 (ttm) cc_final: 0.8081 (ttm) REVERT: AB9 43 GLN cc_start: 0.7415 (tp-100) cc_final: 0.7172 (tp40) REVERT: AB9 48 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6931 (tttt) REVERT: AB9 52 GLN cc_start: 0.6608 (OUTLIER) cc_final: 0.5657 (mp-120) REVERT: AB11 51 LYS cc_start: 0.8206 (tppp) cc_final: 0.7976 (tppt) REVERT: AB12 47 ASP cc_start: 0.7796 (m-30) cc_final: 0.7589 (m-30) REVERT: AB12 51 LYS cc_start: 0.8032 (tptt) cc_final: 0.7743 (tppt) REVERT: AB13 51 LYS cc_start: 0.8034 (tptt) cc_final: 0.7766 (tppt) REVERT: AB14 51 LYS cc_start: 0.8043 (tptt) cc_final: 0.7796 (tppt) REVERT: AB15 51 LYS cc_start: 0.8164 (tppp) cc_final: 0.7754 (tppt) REVERT: EF1 223 ASP cc_start: 0.8222 (t0) cc_final: 0.7688 (m-30) REVERT: EF1 268 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7546 (ttp-110) REVERT: EF2 207 GLU cc_start: 0.7785 (mp0) cc_final: 0.7473 (mt-10) REVERT: EF2 223 ASP cc_start: 0.8334 (t0) cc_final: 0.7786 (m-30) REVERT: EF2 243 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7482 (mm-30) REVERT: EF3 229 MET cc_start: 0.8258 (ttm) cc_final: 0.7854 (ttp) REVERT: EF3 384 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8115 (mt-10) REVERT: EF4 221 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8560 (p) REVERT: EF4 244 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8302 (mt-10) REVERT: EF5 243 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7683 (mm-30) REVERT: EF5 284 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8589 (mmmt) REVERT: EF5 384 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7990 (mt-10) REVERT: EF6 221 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8299 (t) REVERT: EF6 259 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7828 (t0) REVERT: EF6 284 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8659 (mmmt) REVERT: EF6 363 SER cc_start: 0.7547 (m) cc_final: 0.7293 (m) REVERT: EF6 364 ASP cc_start: 0.7869 (t70) cc_final: 0.7551 (t0) REVERT: EF8 221 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.7952 (p) REVERT: EF8 225 ASN cc_start: 0.8751 (m-40) cc_final: 0.8547 (m110) REVERT: EF8 239 MET cc_start: 0.8378 (mtm) cc_final: 0.8117 (mtm) REVERT: EF9 364 ASP cc_start: 0.7927 (t70) cc_final: 0.7476 (t0) REVERT: EF10 364 ASP cc_start: 0.7952 (t70) cc_final: 0.7642 (t0) REVERT: EF12 237 VAL cc_start: 0.8638 (t) cc_final: 0.8406 (p) REVERT: EF12 243 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7571 (mm-30) REVERT: EF13 197 PHE cc_start: 0.9229 (m-80) cc_final: 0.8879 (m-80) REVERT: EF13 239 MET cc_start: 0.8812 (mtm) cc_final: 0.8537 (mtp) REVERT: EF13 259 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7946 (t0) REVERT: EF13 268 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7472 (ttp-110) REVERT: EF13 384 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: EF14 238 GLN cc_start: 0.8398 (mt0) cc_final: 0.8095 (mm-40) REVERT: EF14 244 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8417 (mt-10) REVERT: EF14 268 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7544 (ttp-110) REVERT: EF14 384 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: EF15 239 MET cc_start: 0.8902 (mtm) cc_final: 0.8686 (mtp) REVERT: EF15 259 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8116 (t0) REVERT: EF16 223 ASP cc_start: 0.8337 (t0) cc_final: 0.7871 (m-30) REVERT: EF16 237 VAL cc_start: 0.8630 (t) cc_final: 0.8400 (p) REVERT: EF16 244 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8303 (mt-10) REVERT: EF16 391 ASP cc_start: 0.8920 (m-30) cc_final: 0.8705 (m-30) REVERT: EF17 244 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8397 (mt-10) outliers start: 208 outliers final: 75 residues processed: 705 average time/residue: 0.5886 time to fit residues: 491.4630 Evaluate side-chains 563 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 466 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB3 residue 18 CYS Chi-restraints excluded: chain AB4 residue 52 GLN Chi-restraints excluded: chain AB6 residue 27 CYS Chi-restraints excluded: chain AB6 residue 52 GLN Chi-restraints excluded: chain AB7 residue 27 CYS Chi-restraints excluded: chain AB7 residue 52 GLN Chi-restraints excluded: chain AB8 residue 18 CYS Chi-restraints excluded: chain AB8 residue 27 CYS Chi-restraints excluded: chain AB8 residue 37 THR Chi-restraints excluded: chain AB9 residue 18 CYS Chi-restraints excluded: chain AB9 residue 27 CYS Chi-restraints excluded: chain AB9 residue 48 LYS Chi-restraints excluded: chain AB9 residue 52 GLN Chi-restraints excluded: chain AB10 residue 18 CYS Chi-restraints excluded: chain EF1 residue 206 VAL Chi-restraints excluded: chain EF1 residue 221 THR Chi-restraints excluded: chain EF1 residue 260 VAL Chi-restraints excluded: chain EF1 residue 261 SER Chi-restraints excluded: chain EF1 residue 268 ARG Chi-restraints excluded: chain EF1 residue 271 SER Chi-restraints excluded: chain EF1 residue 284 LYS Chi-restraints excluded: chain EF2 residue 206 VAL Chi-restraints excluded: chain EF2 residue 209 ILE Chi-restraints excluded: chain EF2 residue 221 THR Chi-restraints excluded: chain EF2 residue 261 SER Chi-restraints excluded: chain EF3 residue 261 SER Chi-restraints excluded: chain EF3 residue 355 VAL Chi-restraints excluded: chain EF4 residue 209 ILE Chi-restraints excluded: chain EF4 residue 221 THR Chi-restraints excluded: chain EF4 residue 244 GLU Chi-restraints excluded: chain EF4 residue 260 VAL Chi-restraints excluded: chain EF4 residue 261 SER Chi-restraints excluded: chain EF4 residue 271 SER Chi-restraints excluded: chain EF4 residue 355 VAL Chi-restraints excluded: chain EF5 residue 260 VAL Chi-restraints excluded: chain EF5 residue 261 SER Chi-restraints excluded: chain EF5 residue 271 SER Chi-restraints excluded: chain EF5 residue 284 LYS Chi-restraints excluded: chain EF5 residue 355 VAL Chi-restraints excluded: chain EF6 residue 209 ILE Chi-restraints excluded: chain EF6 residue 221 THR Chi-restraints excluded: chain EF6 residue 259 ASP Chi-restraints excluded: chain EF6 residue 260 VAL Chi-restraints excluded: chain EF6 residue 261 SER Chi-restraints excluded: chain EF6 residue 284 LYS Chi-restraints excluded: chain EF6 residue 355 VAL Chi-restraints excluded: chain EF7 residue 206 VAL Chi-restraints excluded: chain EF7 residue 221 THR Chi-restraints excluded: chain EF7 residue 237 VAL Chi-restraints excluded: chain EF7 residue 261 SER Chi-restraints excluded: chain EF7 residue 292 MET Chi-restraints excluded: chain EF8 residue 206 VAL Chi-restraints excluded: chain EF8 residue 221 THR Chi-restraints excluded: chain EF8 residue 237 VAL Chi-restraints excluded: chain EF8 residue 261 SER Chi-restraints excluded: chain EF9 residue 221 THR Chi-restraints excluded: chain EF9 residue 244 GLU Chi-restraints excluded: chain EF9 residue 267 VAL Chi-restraints excluded: chain EF9 residue 355 VAL Chi-restraints excluded: chain EF10 residue 221 THR Chi-restraints excluded: chain EF10 residue 234 THR Chi-restraints excluded: chain EF10 residue 237 VAL Chi-restraints excluded: chain EF10 residue 261 SER Chi-restraints excluded: chain EF10 residue 267 VAL Chi-restraints excluded: chain EF11 residue 221 THR Chi-restraints excluded: chain EF11 residue 267 VAL Chi-restraints excluded: chain EF12 residue 206 VAL Chi-restraints excluded: chain EF12 residue 221 THR Chi-restraints excluded: chain EF12 residue 243 GLU Chi-restraints excluded: chain EF12 residue 261 SER Chi-restraints excluded: chain EF12 residue 267 VAL Chi-restraints excluded: chain EF13 residue 206 VAL Chi-restraints excluded: chain EF13 residue 221 THR Chi-restraints excluded: chain EF13 residue 259 ASP Chi-restraints excluded: chain EF13 residue 268 ARG Chi-restraints excluded: chain EF13 residue 355 VAL Chi-restraints excluded: chain EF13 residue 384 GLU Chi-restraints excluded: chain EF14 residue 206 VAL Chi-restraints excluded: chain EF14 residue 221 THR Chi-restraints excluded: chain EF14 residue 244 GLU Chi-restraints excluded: chain EF14 residue 268 ARG Chi-restraints excluded: chain EF14 residue 278 ASP Chi-restraints excluded: chain EF14 residue 384 GLU Chi-restraints excluded: chain EF15 residue 206 VAL Chi-restraints excluded: chain EF15 residue 221 THR Chi-restraints excluded: chain EF15 residue 259 ASP Chi-restraints excluded: chain EF15 residue 278 ASP Chi-restraints excluded: chain EF15 residue 355 VAL Chi-restraints excluded: chain EF16 residue 206 VAL Chi-restraints excluded: chain EF16 residue 244 GLU Chi-restraints excluded: chain EF16 residue 261 SER Chi-restraints excluded: chain EF17 residue 206 VAL Chi-restraints excluded: chain EF17 residue 221 THR Chi-restraints excluded: chain EF17 residue 244 GLU Chi-restraints excluded: chain EF17 residue 260 VAL Chi-restraints excluded: chain EF17 residue 267 VAL Chi-restraints excluded: chain EF17 residue 278 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [335, 157, 17, 180, 272, 118, 69, 6, 65, 303, 30] chunk 335 optimal weight: 0.0770 chunk 157 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 272 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 303 optimal weight: 2.9990 chunk 30 optimal weight: 0.0370 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.131477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.101793 restraints weight = 38105.503| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.53 r_work: 0.3061 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30124 Z= 0.171 Angle : 0.496 6.210 40511 Z= 0.268 Chirality : 0.040 0.130 4539 Planarity : 0.004 0.043 5304 Dihedral : 4.911 58.427 4198 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.56 % Allowed : 27.62 % Favored : 66.82 % 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: 0.30 (0.14), residues: 3876 helix: 2.23 (0.15), residues: 1292 sheet: -0.36 (0.19), residues: 765 loop : -1.07 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAB16 46 TYR 0.009 0.001 TYREF8 373 PHE 0.010 0.001 PHEEF12 317 TRP 0.009 0.001 TRPEF13 199 HIS 0.004 0.001 HISEF13 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (30090) covalent geometry : angle 0.49574 / 0.27 (40443) SS BOND : bond 0.00153 / 0.09 ( 34) SS BOND : angle 0.42920 / 0.28 ( 68) hydrogen bonds : bond 0.03373 / 2.22 ( 1156) hydrogen bonds : angle 4.91009 / 3.28 ( 3213) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 468 time to evaluate : 1.031 Fit side-chains REVERT: AB3 51 LYS cc_start: 0.7777 (tptt) cc_final: 0.7428 (tppt) REVERT: AB4 52 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.5937 (mp-120) REVERT: AB6 51 LYS cc_start: 0.7699 (tppp) cc_final: 0.7364 (tppt) REVERT: AB6 52 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.5801 (mp-120) REVERT: AB7 48 LYS cc_start: 0.7195 (tttp) cc_final: 0.6483 (tttt) REVERT: AB7 52 GLN cc_start: 0.7155 (OUTLIER) cc_final: 0.5866 (mp-120) REVERT: AB8 36 MET cc_start: 0.8431 (ttm) cc_final: 0.8019 (ttm) REVERT: AB9 48 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6809 (tttt) REVERT: AB9 52 GLN cc_start: 0.7001 (OUTLIER) cc_final: 0.5839 (mp-120) REVERT: AB10 38 MET cc_start: 0.8551 (ttt) cc_final: 0.8155 (ttp) REVERT: AB11 51 LYS cc_start: 0.8128 (tppp) cc_final: 0.7857 (tppt) REVERT: AB12 51 LYS cc_start: 0.8146 (tptt) cc_final: 0.7719 (tppt) REVERT: AB13 51 LYS cc_start: 0.8100 (tptt) cc_final: 0.7781 (tppt) REVERT: AB14 51 LYS cc_start: 0.8063 (tptt) cc_final: 0.7749 (tppt) REVERT: AB15 51 LYS cc_start: 0.8149 (tppp) cc_final: 0.7735 (tppt) REVERT: AB17 51 LYS cc_start: 0.7948 (tptt) cc_final: 0.7727 (tppt) REVERT: EF1 268 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7612 (ttp-110) REVERT: EF1 364 ASP cc_start: 0.7891 (t70) cc_final: 0.7458 (t0) REVERT: EF2 207 GLU cc_start: 0.8066 (mp0) cc_final: 0.7784 (mt-10) REVERT: EF3 229 MET cc_start: 0.8123 (ttm) cc_final: 0.7648 (ttp) REVERT: EF3 244 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8378 (mt-10) REVERT: EF3 390 GLN cc_start: 0.8187 (tt0) cc_final: 0.7979 (tt0) REVERT: EF4 221 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8490 (p) REVERT: EF4 244 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8438 (mt-10) REVERT: EF6 259 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.7897 (t70) REVERT: EF6 284 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8778 (mmmt) REVERT: EF7 207 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: EF8 221 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8313 (p) REVERT: EF8 239 MET cc_start: 0.8628 (mtm) cc_final: 0.8301 (mtp) REVERT: EF8 391 ASP cc_start: 0.8940 (m-30) cc_final: 0.8717 (m-30) REVERT: EF9 221 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8127 (p) REVERT: EF9 223 ASP cc_start: 0.8212 (t0) cc_final: 0.7614 (m-30) REVERT: EF9 364 ASP cc_start: 0.7917 (t70) cc_final: 0.7474 (t0) REVERT: EF10 239 MET cc_start: 0.8747 (mtm) cc_final: 0.8506 (mtp) REVERT: EF10 241 ASN cc_start: 0.8832 (m-40) cc_final: 0.8074 (m-40) REVERT: EF10 268 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7429 (ttm170) REVERT: EF10 364 ASP cc_start: 0.7996 (t70) cc_final: 0.7640 (t0) REVERT: EF11 268 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7455 (ttp-110) REVERT: EF12 243 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7532 (mm-30) REVERT: EF13 239 MET cc_start: 0.8899 (mtm) cc_final: 0.8650 (mtp) REVERT: EF13 384 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7909 (mt-10) REVERT: EF14 223 ASP cc_start: 0.8423 (t0) cc_final: 0.7900 (m-30) REVERT: EF14 384 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: EF15 259 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8258 (t0) REVERT: EF15 278 ASP cc_start: 0.8826 (m-30) cc_final: 0.8556 (m-30) REVERT: EF15 384 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8296 (mp0) REVERT: EF16 223 ASP cc_start: 0.8301 (t0) cc_final: 0.7864 (m-30) REVERT: EF16 268 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7887 (ttp-110) REVERT: EF16 391 ASP cc_start: 0.8933 (m-30) cc_final: 0.8706 (m-30) REVERT: EF17 244 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8364 (mt-10) REVERT: EF17 305 ASN cc_start: 0.8137 (m-40) cc_final: 0.7914 (m-40) outliers start: 174 outliers final: 82 residues processed: 619 average time/residue: 0.5780 time to fit residues: 424.8417 Evaluate side-chains 535 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 431 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB1 residue 23 SER Chi-restraints excluded: chain AB1 residue 27 CYS Chi-restraints excluded: chain AB2 residue 27 CYS Chi-restraints excluded: chain AB4 residue 52 GLN Chi-restraints excluded: chain AB6 residue 52 GLN Chi-restraints excluded: chain AB7 residue 27 CYS Chi-restraints excluded: chain AB7 residue 52 GLN Chi-restraints excluded: chain AB9 residue 48 LYS Chi-restraints excluded: chain AB9 residue 52 GLN Chi-restraints excluded: chain AB10 residue 23 SER Chi-restraints excluded: chain AB10 residue 27 CYS Chi-restraints excluded: chain AB11 residue 27 CYS Chi-restraints excluded: chain AB12 residue 27 CYS Chi-restraints excluded: chain AB15 residue 27 CYS Chi-restraints excluded: chain AB16 residue 27 CYS Chi-restraints excluded: chain EF1 residue 202 SER Chi-restraints excluded: chain EF1 residue 206 VAL Chi-restraints excluded: chain EF1 residue 209 ILE Chi-restraints excluded: chain EF1 residue 221 THR Chi-restraints excluded: chain EF1 residue 260 VAL Chi-restraints excluded: chain EF1 residue 261 SER Chi-restraints excluded: chain EF1 residue 268 ARG Chi-restraints excluded: chain EF2 residue 206 VAL Chi-restraints excluded: chain EF2 residue 209 ILE Chi-restraints excluded: chain EF2 residue 221 THR Chi-restraints excluded: chain EF2 residue 260 VAL Chi-restraints excluded: chain EF3 residue 209 ILE Chi-restraints excluded: chain EF3 residue 244 GLU Chi-restraints excluded: chain EF3 residue 260 VAL Chi-restraints excluded: chain EF4 residue 209 ILE Chi-restraints excluded: chain EF4 residue 221 THR Chi-restraints excluded: chain EF4 residue 244 GLU Chi-restraints excluded: chain EF4 residue 260 VAL Chi-restraints excluded: chain EF4 residue 261 SER Chi-restraints excluded: chain EF5 residue 206 VAL Chi-restraints excluded: chain EF5 residue 260 VAL Chi-restraints excluded: chain EF5 residue 261 SER Chi-restraints excluded: chain EF6 residue 221 THR Chi-restraints excluded: chain EF6 residue 259 ASP Chi-restraints excluded: chain EF6 residue 260 VAL Chi-restraints excluded: chain EF6 residue 261 SER Chi-restraints excluded: chain EF6 residue 267 VAL Chi-restraints excluded: chain EF6 residue 284 LYS Chi-restraints excluded: chain EF7 residue 202 SER Chi-restraints excluded: chain EF7 residue 207 GLU Chi-restraints excluded: chain EF7 residue 209 ILE Chi-restraints excluded: chain EF7 residue 221 THR Chi-restraints excluded: chain EF7 residue 237 VAL Chi-restraints excluded: chain EF7 residue 260 VAL Chi-restraints excluded: chain EF7 residue 261 SER Chi-restraints excluded: chain EF7 residue 267 VAL Chi-restraints excluded: chain EF8 residue 206 VAL Chi-restraints excluded: chain EF8 residue 221 THR Chi-restraints excluded: chain EF8 residue 237 VAL Chi-restraints excluded: chain EF8 residue 260 VAL Chi-restraints excluded: chain EF8 residue 261 SER Chi-restraints excluded: chain EF9 residue 221 THR Chi-restraints excluded: chain EF9 residue 237 VAL Chi-restraints excluded: chain EF9 residue 260 VAL Chi-restraints excluded: chain EF9 residue 261 SER Chi-restraints excluded: chain EF9 residue 267 VAL Chi-restraints excluded: chain EF10 residue 209 ILE Chi-restraints excluded: chain EF10 residue 221 THR Chi-restraints excluded: chain EF10 residue 234 THR Chi-restraints excluded: chain EF10 residue 237 VAL Chi-restraints excluded: chain EF10 residue 261 SER Chi-restraints excluded: chain EF10 residue 267 VAL Chi-restraints excluded: chain EF10 residue 268 ARG Chi-restraints excluded: chain EF10 residue 278 ASP Chi-restraints excluded: chain EF11 residue 221 THR Chi-restraints excluded: chain EF11 residue 267 VAL Chi-restraints excluded: chain EF11 residue 268 ARG Chi-restraints excluded: chain EF11 residue 278 ASP Chi-restraints excluded: chain EF11 residue 292 MET Chi-restraints excluded: chain EF12 residue 206 VAL Chi-restraints excluded: chain EF12 residue 209 ILE Chi-restraints excluded: chain EF12 residue 221 THR Chi-restraints excluded: chain EF12 residue 243 GLU Chi-restraints excluded: chain EF12 residue 267 VAL Chi-restraints excluded: chain EF12 residue 278 ASP Chi-restraints excluded: chain EF13 residue 206 VAL Chi-restraints excluded: chain EF13 residue 221 THR Chi-restraints excluded: chain EF13 residue 261 SER Chi-restraints excluded: chain EF13 residue 267 VAL Chi-restraints excluded: chain EF13 residue 278 ASP Chi-restraints excluded: chain EF13 residue 384 GLU Chi-restraints excluded: chain EF14 residue 206 VAL Chi-restraints excluded: chain EF14 residue 221 THR Chi-restraints excluded: chain EF14 residue 244 GLU Chi-restraints excluded: chain EF14 residue 384 GLU Chi-restraints excluded: chain EF15 residue 206 VAL Chi-restraints excluded: chain EF15 residue 209 ILE Chi-restraints excluded: chain EF15 residue 221 THR Chi-restraints excluded: chain EF15 residue 259 ASP Chi-restraints excluded: chain EF15 residue 273 SER Chi-restraints excluded: chain EF16 residue 206 VAL Chi-restraints excluded: chain EF16 residue 209 ILE Chi-restraints excluded: chain EF16 residue 261 SER Chi-restraints excluded: chain EF16 residue 268 ARG Chi-restraints excluded: chain EF17 residue 206 VAL Chi-restraints excluded: chain EF17 residue 221 THR Chi-restraints excluded: chain EF17 residue 244 GLU Chi-restraints excluded: chain EF17 residue 260 VAL Chi-restraints excluded: chain EF17 residue 267 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [263, 228, 244, 54, 214, 365, 113, 198, 112, 105, 118] chunk 263 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 365 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.132018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102366 restraints weight = 37921.999| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.53 r_work: 0.3073 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30124 Z= 0.137 Angle : 0.462 6.398 40511 Z= 0.248 Chirality : 0.039 0.149 4539 Planarity : 0.004 0.041 5304 Dihedral : 4.604 59.325 4188 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.15 % Allowed : 28.01 % Favored : 66.85 % 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: 0.47 (0.14), residues: 3876 helix: 2.37 (0.15), residues: 1292 sheet: -0.41 (0.19), residues: 765 loop : -0.90 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAB2 46 TYR 0.011 0.001 TYREF11 373 PHE 0.009 0.001 PHEEF12 317 TRP 0.007 0.001 TRPEF13 199 HIS 0.004 0.001 HISEF4 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (30090) covalent geometry : angle 0.46259 / 0.25 (40443) SS BOND : bond 0.00214 / 0.15 ( 34) SS BOND : angle 0.34948 / 0.23 ( 68) hydrogen bonds : bond 0.02927 / 1.94 ( 1156) hydrogen bonds : angle 4.68050 / 3.13 ( 3213) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 453 time to evaluate : 1.197 Fit side-chains REVERT: AB3 51 LYS cc_start: 0.7688 (tptt) cc_final: 0.7340 (tppt) REVERT: AB4 52 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.5908 (mp-120) REVERT: AB6 51 LYS cc_start: 0.7737 (tppp) cc_final: 0.7452 (tppt) REVERT: AB6 52 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.5896 (mp-120) REVERT: AB7 48 LYS cc_start: 0.7279 (tttp) cc_final: 0.6574 (tttt) REVERT: AB7 52 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.5902 (mp-120) REVERT: AB9 48 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6764 (tttt) REVERT: AB9 52 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.5896 (mp-120) REVERT: AB10 38 MET cc_start: 0.8559 (ttt) cc_final: 0.8173 (ttp) REVERT: AB10 51 LYS cc_start: 0.8306 (tppt) cc_final: 0.8075 (tppt) REVERT: AB11 51 LYS cc_start: 0.8135 (tppp) cc_final: 0.7868 (tppt) REVERT: AB12 51 LYS cc_start: 0.8141 (tptt) cc_final: 0.7765 (tppt) REVERT: AB13 51 LYS cc_start: 0.8106 (tptt) cc_final: 0.7782 (tppt) REVERT: AB14 51 LYS cc_start: 0.8067 (tptt) cc_final: 0.7772 (tppt) REVERT: AB15 51 LYS cc_start: 0.8154 (tppp) cc_final: 0.7749 (tppt) REVERT: AB17 51 LYS cc_start: 0.7960 (tptt) cc_final: 0.7755 (tppt) REVERT: EF2 207 GLU cc_start: 0.8094 (mp0) cc_final: 0.7818 (mt-10) REVERT: EF4 221 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8545 (p) REVERT: EF4 243 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7551 (mm-30) REVERT: EF4 244 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8560 (mt-10) REVERT: EF5 196 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6701 (ttm-80) REVERT: EF6 196 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6743 (ttm-80) REVERT: EF6 259 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.7976 (t70) REVERT: EF8 221 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8367 (p) REVERT: EF8 239 MET cc_start: 0.8662 (mtm) cc_final: 0.8324 (mtp) REVERT: EF8 268 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7481 (ttm170) REVERT: EF8 391 ASP cc_start: 0.8938 (m-30) cc_final: 0.8737 (m-30) REVERT: EF9 221 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8165 (p) REVERT: EF9 223 ASP cc_start: 0.8272 (t0) cc_final: 0.7610 (m-30) REVERT: EF9 241 ASN cc_start: 0.8772 (m-40) cc_final: 0.7950 (m-40) REVERT: EF10 223 ASP cc_start: 0.8277 (t0) cc_final: 0.7631 (m-30) REVERT: EF10 241 ASN cc_start: 0.8922 (m-40) cc_final: 0.8236 (m-40) REVERT: EF10 268 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7432 (ttm170) REVERT: EF11 223 ASP cc_start: 0.8153 (t0) cc_final: 0.7583 (m-30) REVERT: EF11 268 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7359 (ttp-110) REVERT: EF12 223 ASP cc_start: 0.8088 (t0) cc_final: 0.7685 (m-30) REVERT: EF12 279 ASP cc_start: 0.7859 (m-30) cc_final: 0.7655 (m-30) REVERT: EF13 223 ASP cc_start: 0.8205 (t0) cc_final: 0.7861 (m-30) REVERT: EF13 268 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7546 (ttm170) REVERT: EF13 279 ASP cc_start: 0.7866 (m-30) cc_final: 0.7645 (m-30) REVERT: EF13 384 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7889 (mt-10) REVERT: EF14 223 ASP cc_start: 0.8383 (t0) cc_final: 0.7875 (m-30) REVERT: EF14 244 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8548 (mt-10) REVERT: EF14 268 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7639 (ttp-110) REVERT: EF14 278 ASP cc_start: 0.8759 (m-30) cc_final: 0.8482 (m-30) REVERT: EF14 384 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: EF15 223 ASP cc_start: 0.8286 (t0) cc_final: 0.7839 (m-30) REVERT: EF15 259 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8241 (t0) REVERT: EF15 384 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8262 (mp0) REVERT: EF16 221 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8427 (p) REVERT: EF16 223 ASP cc_start: 0.8270 (t0) cc_final: 0.7918 (m-30) REVERT: EF16 268 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7907 (ttp-110) REVERT: EF16 391 ASP cc_start: 0.8923 (m-30) cc_final: 0.8701 (m-30) REVERT: EF17 305 ASN cc_start: 0.8336 (m-40) cc_final: 0.8133 (m-40) outliers start: 161 outliers final: 80 residues processed: 588 average time/residue: 0.5692 time to fit residues: 397.2817 Evaluate side-chains 496 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 393 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB3 residue 36 MET Chi-restraints excluded: chain AB3 residue 48 LYS Chi-restraints excluded: chain AB4 residue 52 GLN Chi-restraints excluded: chain AB6 residue 52 GLN Chi-restraints excluded: chain AB7 residue 27 CYS Chi-restraints excluded: chain AB7 residue 52 GLN Chi-restraints excluded: chain AB8 residue 37 THR Chi-restraints excluded: chain AB9 residue 27 CYS Chi-restraints excluded: chain AB9 residue 48 LYS Chi-restraints excluded: chain AB9 residue 52 GLN Chi-restraints excluded: chain AB10 residue 27 CYS Chi-restraints excluded: chain AB11 residue 27 CYS Chi-restraints excluded: chain AB11 residue 44 LEU Chi-restraints excluded: chain AB12 residue 27 CYS Chi-restraints excluded: chain AB15 residue 27 CYS Chi-restraints excluded: chain AB16 residue 27 CYS Chi-restraints excluded: chain EF1 residue 206 VAL Chi-restraints excluded: chain EF1 residue 209 ILE Chi-restraints excluded: chain EF1 residue 221 THR Chi-restraints excluded: chain EF1 residue 260 VAL Chi-restraints excluded: chain EF2 residue 206 VAL Chi-restraints excluded: chain EF2 residue 221 THR Chi-restraints excluded: chain EF2 residue 260 VAL Chi-restraints excluded: chain EF2 residue 261 SER Chi-restraints excluded: chain EF3 residue 206 VAL Chi-restraints excluded: chain EF3 residue 209 ILE Chi-restraints excluded: chain EF3 residue 260 VAL Chi-restraints excluded: chain EF4 residue 209 ILE Chi-restraints excluded: chain EF4 residue 221 THR Chi-restraints excluded: chain EF4 residue 244 GLU Chi-restraints excluded: chain EF4 residue 254 LEU Chi-restraints excluded: chain EF4 residue 260 VAL Chi-restraints excluded: chain EF4 residue 271 SER Chi-restraints excluded: chain EF5 residue 196 ARG Chi-restraints excluded: chain EF5 residue 260 VAL Chi-restraints excluded: chain EF6 residue 196 ARG Chi-restraints excluded: chain EF6 residue 209 ILE Chi-restraints excluded: chain EF6 residue 221 THR Chi-restraints excluded: chain EF6 residue 259 ASP Chi-restraints excluded: chain EF6 residue 260 VAL Chi-restraints excluded: chain EF6 residue 261 SER Chi-restraints excluded: chain EF6 residue 267 VAL Chi-restraints excluded: chain EF6 residue 355 VAL Chi-restraints excluded: chain EF7 residue 209 ILE Chi-restraints excluded: chain EF7 residue 221 THR Chi-restraints excluded: chain EF7 residue 237 VAL Chi-restraints excluded: chain EF7 residue 260 VAL Chi-restraints excluded: chain EF7 residue 261 SER Chi-restraints excluded: chain EF7 residue 267 VAL Chi-restraints excluded: chain EF7 residue 273 SER Chi-restraints excluded: chain EF8 residue 206 VAL Chi-restraints excluded: chain EF8 residue 221 THR Chi-restraints excluded: chain EF8 residue 237 VAL Chi-restraints excluded: chain EF8 residue 260 VAL Chi-restraints excluded: chain EF8 residue 261 SER Chi-restraints excluded: chain EF8 residue 268 ARG Chi-restraints excluded: chain EF9 residue 221 THR Chi-restraints excluded: chain EF9 residue 237 VAL Chi-restraints excluded: chain EF9 residue 260 VAL Chi-restraints excluded: chain EF9 residue 261 SER Chi-restraints excluded: chain EF9 residue 267 VAL Chi-restraints excluded: chain EF9 residue 355 VAL Chi-restraints excluded: chain EF10 residue 209 ILE Chi-restraints excluded: chain EF10 residue 221 THR Chi-restraints excluded: chain EF10 residue 237 VAL Chi-restraints excluded: chain EF10 residue 261 SER Chi-restraints excluded: chain EF10 residue 267 VAL Chi-restraints excluded: chain EF10 residue 268 ARG Chi-restraints excluded: chain EF10 residue 271 SER Chi-restraints excluded: chain EF10 residue 273 SER Chi-restraints excluded: chain EF11 residue 206 VAL Chi-restraints excluded: chain EF11 residue 221 THR Chi-restraints excluded: chain EF11 residue 261 SER Chi-restraints excluded: chain EF11 residue 267 VAL Chi-restraints excluded: chain EF11 residue 268 ARG Chi-restraints excluded: chain EF12 residue 206 VAL Chi-restraints excluded: chain EF12 residue 209 ILE Chi-restraints excluded: chain EF12 residue 221 THR Chi-restraints excluded: chain EF12 residue 267 VAL Chi-restraints excluded: chain EF12 residue 271 SER Chi-restraints excluded: chain EF13 residue 206 VAL Chi-restraints excluded: chain EF13 residue 221 THR Chi-restraints excluded: chain EF13 residue 261 SER Chi-restraints excluded: chain EF13 residue 267 VAL Chi-restraints excluded: chain EF13 residue 268 ARG Chi-restraints excluded: chain EF13 residue 355 VAL Chi-restraints excluded: chain EF13 residue 384 GLU Chi-restraints excluded: chain EF14 residue 209 ILE Chi-restraints excluded: chain EF14 residue 221 THR Chi-restraints excluded: chain EF14 residue 244 GLU Chi-restraints excluded: chain EF14 residue 268 ARG Chi-restraints excluded: chain EF14 residue 384 GLU Chi-restraints excluded: chain EF15 residue 206 VAL Chi-restraints excluded: chain EF15 residue 221 THR Chi-restraints excluded: chain EF15 residue 259 ASP Chi-restraints excluded: chain EF15 residue 355 VAL Chi-restraints excluded: chain EF16 residue 206 VAL Chi-restraints excluded: chain EF16 residue 221 THR Chi-restraints excluded: chain EF16 residue 268 ARG Chi-restraints excluded: chain EF17 residue 206 VAL Chi-restraints excluded: chain EF17 residue 221 THR Chi-restraints excluded: chain EF17 residue 260 VAL Chi-restraints excluded: chain EF17 residue 267 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [56, 154, 86, 71, 244, 257, 24, 273, 348, 136, 146] chunk 56 optimal weight: 3.9990 chunk 154 optimal weight: 0.3980 chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 24 optimal weight: 0.0030 chunk 273 optimal weight: 9.9990 chunk 348 optimal weight: 9.9990 chunk 136 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.133481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104163 restraints weight = 37974.543| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.52 r_work: 0.3094 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30124 Z= 0.109 Angle : 0.435 5.891 40511 Z= 0.233 Chirality : 0.039 0.141 4539 Planarity : 0.003 0.037 5304 Dihedral : 4.351 59.804 4183 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.73 % Allowed : 28.58 % Favored : 66.69 % 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: 0.58 (0.14), residues: 3876 helix: 2.51 (0.15), residues: 1292 sheet: -0.43 (0.19), residues: 765 loop : -0.81 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGEF11 304 TYR 0.008 0.001 TYREF11 373 PHE 0.008 0.001 PHEEF12 317 TRP 0.007 0.001 TRPEF3 257 HIS 0.004 0.001 HISEF12 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (30090) covalent geometry : angle 0.43538 / 0.23 (40443) SS BOND : bond 0.00121 / 0.08 ( 34) SS BOND : angle 0.28770 / 0.19 ( 68) hydrogen bonds : bond 0.02611 / 1.73 ( 1156) hydrogen bonds : angle 4.43386 / 2.96 ( 3213) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 414 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AB3 51 LYS cc_start: 0.7832 (tptt) cc_final: 0.7466 (tppt) REVERT: AB4 52 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.5926 (mp-120) REVERT: AB5 51 LYS cc_start: 0.7765 (tppt) cc_final: 0.7314 (tptt) REVERT: AB6 51 LYS cc_start: 0.7766 (tppp) cc_final: 0.7484 (tppt) REVERT: AB6 52 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.5914 (mp-120) REVERT: AB7 48 LYS cc_start: 0.7308 (tttp) cc_final: 0.6568 (tttt) REVERT: AB7 52 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6026 (mp-120) REVERT: AB9 48 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6724 (tptt) REVERT: AB9 52 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.5883 (mp-120) REVERT: AB11 51 LYS cc_start: 0.8159 (tppp) cc_final: 0.7888 (tppt) REVERT: AB12 51 LYS cc_start: 0.8141 (tptt) cc_final: 0.7785 (tppt) REVERT: AB13 51 LYS cc_start: 0.8120 (tptt) cc_final: 0.7791 (tppt) REVERT: AB14 51 LYS cc_start: 0.8050 (tptt) cc_final: 0.7826 (tppt) REVERT: AB15 51 LYS cc_start: 0.8182 (tppp) cc_final: 0.7767 (tppt) REVERT: AB16 51 LYS cc_start: 0.8203 (tppt) cc_final: 0.7885 (tppt) REVERT: EF1 268 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7666 (ttp-110) REVERT: EF1 384 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7727 (mt-10) REVERT: EF2 196 ARG cc_start: 0.7717 (ttm-80) cc_final: 0.7388 (mtm180) REVERT: EF2 207 GLU cc_start: 0.8095 (mp0) cc_final: 0.7831 (mt-10) REVERT: EF4 221 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8561 (p) REVERT: EF4 243 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7551 (mm-30) REVERT: EF5 196 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6800 (ttm-80) REVERT: EF5 239 MET cc_start: 0.8889 (mtm) cc_final: 0.8682 (mtp) REVERT: EF5 241 ASN cc_start: 0.8952 (m-40) cc_final: 0.8676 (m110) REVERT: EF6 196 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.6730 (ttm-80) REVERT: EF6 259 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.7902 (t70) REVERT: EF8 221 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8380 (p) REVERT: EF8 239 MET cc_start: 0.8653 (mtm) cc_final: 0.8333 (mtp) REVERT: EF8 244 GLU cc_start: 0.8513 (pt0) cc_final: 0.8005 (mt-10) REVERT: EF8 259 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7679 (t0) REVERT: EF8 268 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7463 (ttm170) REVERT: EF8 391 ASP cc_start: 0.8913 (m-30) cc_final: 0.8681 (m-30) REVERT: EF9 221 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8191 (p) REVERT: EF9 241 ASN cc_start: 0.8843 (m-40) cc_final: 0.8090 (m-40) REVERT: EF9 244 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8264 (mt-10) REVERT: EF10 241 ASN cc_start: 0.8836 (m-40) cc_final: 0.8138 (m110) REVERT: EF10 268 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7468 (ttm170) REVERT: EF10 384 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7566 (tt0) REVERT: EF11 268 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7429 (ttp-110) REVERT: EF12 279 ASP cc_start: 0.7854 (m-30) cc_final: 0.7542 (m-30) REVERT: EF13 207 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7395 (mp0) REVERT: EF14 223 ASP cc_start: 0.8333 (t0) cc_final: 0.7848 (m-30) REVERT: EF14 241 ASN cc_start: 0.8941 (m110) cc_final: 0.8557 (m-40) REVERT: EF14 244 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8509 (mt-10) REVERT: EF14 384 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7767 (mt-10) REVERT: EF15 259 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8058 (t0) REVERT: EF16 221 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8389 (p) REVERT: EF17 280 ASP cc_start: 0.7905 (m-30) cc_final: 0.7664 (m-30) outliers start: 148 outliers final: 84 residues processed: 540 average time/residue: 0.6175 time to fit residues: 391.7270 Evaluate side-chains 528 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 422 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB1 residue 23 SER Chi-restraints excluded: chain AB1 residue 27 CYS Chi-restraints excluded: chain AB2 residue 27 CYS Chi-restraints excluded: chain AB3 residue 48 LYS Chi-restraints excluded: chain AB4 residue 52 GLN Chi-restraints excluded: chain AB6 residue 27 CYS Chi-restraints excluded: chain AB6 residue 52 GLN Chi-restraints excluded: chain AB7 residue 27 CYS Chi-restraints excluded: chain AB7 residue 52 GLN Chi-restraints excluded: chain AB8 residue 37 THR Chi-restraints excluded: chain AB9 residue 27 CYS Chi-restraints excluded: chain AB9 residue 48 LYS Chi-restraints excluded: chain AB9 residue 52 GLN Chi-restraints excluded: chain AB10 residue 27 CYS Chi-restraints excluded: chain AB11 residue 27 CYS Chi-restraints excluded: chain EF1 residue 202 SER Chi-restraints excluded: chain EF1 residue 206 VAL Chi-restraints excluded: chain EF1 residue 209 ILE Chi-restraints excluded: chain EF1 residue 221 THR Chi-restraints excluded: chain EF1 residue 260 VAL Chi-restraints excluded: chain EF1 residue 268 ARG Chi-restraints excluded: chain EF2 residue 202 SER Chi-restraints excluded: chain EF2 residue 206 VAL Chi-restraints excluded: chain EF2 residue 209 ILE Chi-restraints excluded: chain EF2 residue 221 THR Chi-restraints excluded: chain EF2 residue 260 VAL Chi-restraints excluded: chain EF3 residue 206 VAL Chi-restraints excluded: chain EF3 residue 209 ILE Chi-restraints excluded: chain EF3 residue 260 VAL Chi-restraints excluded: chain EF3 residue 261 SER Chi-restraints excluded: chain EF4 residue 209 ILE Chi-restraints excluded: chain EF4 residue 221 THR Chi-restraints excluded: chain EF4 residue 254 LEU Chi-restraints excluded: chain EF4 residue 260 VAL Chi-restraints excluded: chain EF4 residue 355 VAL Chi-restraints excluded: chain EF5 residue 196 ARG Chi-restraints excluded: chain EF5 residue 260 VAL Chi-restraints excluded: chain EF6 residue 196 ARG Chi-restraints excluded: chain EF6 residue 209 ILE Chi-restraints excluded: chain EF6 residue 221 THR Chi-restraints excluded: chain EF6 residue 259 ASP Chi-restraints excluded: chain EF6 residue 260 VAL Chi-restraints excluded: chain EF6 residue 261 SER Chi-restraints excluded: chain EF6 residue 267 VAL Chi-restraints excluded: chain EF6 residue 355 VAL Chi-restraints excluded: chain EF7 residue 202 SER Chi-restraints excluded: chain EF7 residue 221 THR Chi-restraints excluded: chain EF7 residue 237 VAL Chi-restraints excluded: chain EF7 residue 260 VAL Chi-restraints excluded: chain EF7 residue 261 SER Chi-restraints excluded: chain EF7 residue 267 VAL Chi-restraints excluded: chain EF7 residue 273 SER Chi-restraints excluded: chain EF8 residue 206 VAL Chi-restraints excluded: chain EF8 residue 221 THR Chi-restraints excluded: chain EF8 residue 237 VAL Chi-restraints excluded: chain EF8 residue 259 ASP Chi-restraints excluded: chain EF8 residue 260 VAL Chi-restraints excluded: chain EF8 residue 261 SER Chi-restraints excluded: chain EF8 residue 268 ARG Chi-restraints excluded: chain EF9 residue 206 VAL Chi-restraints excluded: chain EF9 residue 221 THR Chi-restraints excluded: chain EF9 residue 230 GLN Chi-restraints excluded: chain EF9 residue 237 VAL Chi-restraints excluded: chain EF9 residue 244 GLU Chi-restraints excluded: chain EF9 residue 260 VAL Chi-restraints excluded: chain EF9 residue 261 SER Chi-restraints excluded: chain EF9 residue 267 VAL Chi-restraints excluded: chain EF9 residue 355 VAL Chi-restraints excluded: chain EF10 residue 209 ILE Chi-restraints excluded: chain EF10 residue 221 THR Chi-restraints excluded: chain EF10 residue 237 VAL Chi-restraints excluded: chain EF10 residue 261 SER Chi-restraints excluded: chain EF10 residue 267 VAL Chi-restraints excluded: chain EF10 residue 268 ARG Chi-restraints excluded: chain EF10 residue 292 MET Chi-restraints excluded: chain EF10 residue 384 GLU Chi-restraints excluded: chain EF11 residue 206 VAL Chi-restraints excluded: chain EF11 residue 221 THR Chi-restraints excluded: chain EF11 residue 267 VAL Chi-restraints excluded: chain EF11 residue 268 ARG Chi-restraints excluded: chain EF11 residue 292 MET Chi-restraints excluded: chain EF11 residue 384 GLU Chi-restraints excluded: chain EF12 residue 206 VAL Chi-restraints excluded: chain EF12 residue 209 ILE Chi-restraints excluded: chain EF12 residue 221 THR Chi-restraints excluded: chain EF12 residue 267 VAL Chi-restraints excluded: chain EF13 residue 200 ILE Chi-restraints excluded: chain EF13 residue 206 VAL Chi-restraints excluded: chain EF13 residue 221 THR Chi-restraints excluded: chain EF13 residue 267 VAL Chi-restraints excluded: chain EF13 residue 355 VAL Chi-restraints excluded: chain EF13 residue 384 GLU Chi-restraints excluded: chain EF14 residue 209 ILE Chi-restraints excluded: chain EF14 residue 221 THR Chi-restraints excluded: chain EF14 residue 244 GLU Chi-restraints excluded: chain EF14 residue 384 GLU Chi-restraints excluded: chain EF15 residue 206 VAL Chi-restraints excluded: chain EF15 residue 221 THR Chi-restraints excluded: chain EF15 residue 259 ASP Chi-restraints excluded: chain EF16 residue 206 VAL Chi-restraints excluded: chain EF16 residue 221 THR Chi-restraints excluded: chain EF17 residue 206 VAL Chi-restraints excluded: chain EF17 residue 221 THR Chi-restraints excluded: chain EF17 residue 260 VAL Chi-restraints excluded: chain EF17 residue 261 SER Chi-restraints excluded: chain EF17 residue 267 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [296, 20, 354, 6, 32, 116, 50, 7, 224, 332, 122] chunk 296 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 354 optimal weight: 5.9990 chunk 6 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 332 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.131023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.101784 restraints weight = 38170.008| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.50 r_work: 0.3039 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30124 Z= 0.178 Angle : 0.491 7.883 40511 Z= 0.261 Chirality : 0.040 0.142 4539 Planarity : 0.004 0.037 5304 Dihedral : 4.588 59.794 4183 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.08 % Allowed : 28.01 % Favored : 66.91 % 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: 0.49 (0.14), residues: 3876 helix: 2.36 (0.15), residues: 1292 sheet: -0.46 (0.19), residues: 765 loop : -0.82 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAB17 46 TYR 0.012 0.001 TYREF11 373 PHE 0.008 0.001 PHEEF8 317 TRP 0.007 0.001 TRPEF13 199 HIS 0.003 0.001 HISEF12 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (30090) covalent geometry : angle 0.49131 / 0.26 (40443) SS BOND : bond 0.00228 / 0.14 ( 34) SS BOND : angle 0.34395 / 0.23 ( 68) hydrogen bonds : bond 0.03191 / 2.11 ( 1156) hydrogen bonds : angle 4.54092 / 3.03 ( 3213) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 421 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AB3 51 LYS cc_start: 0.7865 (tptt) cc_final: 0.7470 (tppt) REVERT: AB6 51 LYS cc_start: 0.7815 (tppp) cc_final: 0.7564 (tppt) REVERT: AB6 52 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.7015 (mm110) REVERT: AB7 48 LYS cc_start: 0.7459 (tttp) cc_final: 0.6625 (tttt) REVERT: AB7 52 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6170 (mp-120) REVERT: AB9 48 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6742 (tttt) REVERT: AB9 52 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6059 (mp-120) REVERT: AB10 38 MET cc_start: 0.8620 (ttt) cc_final: 0.8224 (ttp) REVERT: AB11 51 LYS cc_start: 0.8120 (tppp) cc_final: 0.7838 (tppt) REVERT: AB12 51 LYS cc_start: 0.8138 (tptt) cc_final: 0.7781 (tppt) REVERT: AB13 51 LYS cc_start: 0.8134 (tptt) cc_final: 0.7792 (tppt) REVERT: AB14 51 LYS cc_start: 0.8083 (tptt) cc_final: 0.7811 (tppt) REVERT: AB15 51 LYS cc_start: 0.8204 (tppp) cc_final: 0.7776 (tppt) REVERT: EF1 268 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7715 (ttp-110) REVERT: EF1 364 ASP cc_start: 0.7977 (t70) cc_final: 0.7545 (t0) REVERT: EF2 207 GLU cc_start: 0.8140 (mp0) cc_final: 0.7861 (mt-10) REVERT: EF4 221 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8507 (p) REVERT: EF4 259 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.7937 (t0) REVERT: EF4 305 ASN cc_start: 0.8391 (m-40) cc_final: 0.8108 (m-40) REVERT: EF5 196 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6716 (ttm-80) REVERT: EF5 241 ASN cc_start: 0.8988 (m-40) cc_final: 0.8759 (m110) REVERT: EF6 196 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6776 (ttm-80) REVERT: EF6 207 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7289 (mp0) REVERT: EF6 259 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8006 (t70) REVERT: EF8 221 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8440 (p) REVERT: EF8 239 MET cc_start: 0.8801 (mtm) cc_final: 0.8447 (mtp) REVERT: EF8 259 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7703 (t0) REVERT: EF8 268 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7591 (ttm170) REVERT: EF8 391 ASP cc_start: 0.8932 (m-30) cc_final: 0.8710 (m-30) REVERT: EF9 207 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7273 (mp0) REVERT: EF9 221 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8207 (p) REVERT: EF9 241 ASN cc_start: 0.8870 (m-40) cc_final: 0.8170 (m-40) REVERT: EF10 223 ASP cc_start: 0.8271 (t0) cc_final: 0.7553 (m-30) REVERT: EF10 241 ASN cc_start: 0.8785 (m-40) cc_final: 0.8098 (m110) REVERT: EF10 268 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7549 (ttm170) REVERT: EF10 384 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7813 (mt-10) REVERT: EF11 268 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7555 (ttp-110) REVERT: EF12 279 ASP cc_start: 0.8048 (m-30) cc_final: 0.7725 (m-30) REVERT: EF14 223 ASP cc_start: 0.8394 (t0) cc_final: 0.7984 (m-30) REVERT: EF14 241 ASN cc_start: 0.9005 (m110) cc_final: 0.8628 (m-40) REVERT: EF14 268 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7801 (ttp-110) REVERT: EF14 278 ASP cc_start: 0.8694 (m-30) cc_final: 0.8485 (m-30) REVERT: EF14 384 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: EF15 196 ARG cc_start: 0.8141 (mtt90) cc_final: 0.7914 (mpp80) REVERT: EF16 221 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8465 (p) REVERT: EF16 223 ASP cc_start: 0.8335 (t0) cc_final: 0.8075 (m-30) outliers start: 159 outliers final: 107 residues processed: 562 average time/residue: 0.5910 time to fit residues: 392.3220 Evaluate side-chains 541 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 414 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB1 residue 23 SER Chi-restraints excluded: chain AB1 residue 27 CYS Chi-restraints excluded: chain AB2 residue 27 CYS Chi-restraints excluded: chain AB3 residue 48 LYS Chi-restraints excluded: chain AB4 residue 52 GLN Chi-restraints excluded: chain AB6 residue 52 GLN Chi-restraints excluded: chain AB7 residue 27 CYS Chi-restraints excluded: chain AB7 residue 52 GLN Chi-restraints excluded: chain AB8 residue 37 THR Chi-restraints excluded: chain AB9 residue 27 CYS Chi-restraints excluded: chain AB9 residue 48 LYS Chi-restraints excluded: chain AB9 residue 52 GLN Chi-restraints excluded: chain AB10 residue 27 CYS Chi-restraints excluded: chain AB11 residue 27 CYS Chi-restraints excluded: chain AB12 residue 27 CYS Chi-restraints excluded: chain AB14 residue 34 THR Chi-restraints excluded: chain AB15 residue 27 CYS Chi-restraints excluded: chain AB16 residue 27 CYS Chi-restraints excluded: chain AB17 residue 23 SER Chi-restraints excluded: chain EF1 residue 202 SER Chi-restraints excluded: chain EF1 residue 206 VAL Chi-restraints excluded: chain EF1 residue 209 ILE Chi-restraints excluded: chain EF1 residue 221 THR Chi-restraints excluded: chain EF1 residue 260 VAL Chi-restraints excluded: chain EF1 residue 268 ARG Chi-restraints excluded: chain EF1 residue 355 VAL Chi-restraints excluded: chain EF2 residue 202 SER Chi-restraints excluded: chain EF2 residue 206 VAL Chi-restraints excluded: chain EF2 residue 209 ILE Chi-restraints excluded: chain EF2 residue 221 THR Chi-restraints excluded: chain EF2 residue 260 VAL Chi-restraints excluded: chain EF2 residue 261 SER Chi-restraints excluded: chain EF3 residue 206 VAL Chi-restraints excluded: chain EF3 residue 209 ILE Chi-restraints excluded: chain EF3 residue 260 VAL Chi-restraints excluded: chain EF3 residue 261 SER Chi-restraints excluded: chain EF4 residue 209 ILE Chi-restraints excluded: chain EF4 residue 221 THR Chi-restraints excluded: chain EF4 residue 259 ASP Chi-restraints excluded: chain EF4 residue 260 VAL Chi-restraints excluded: chain EF5 residue 196 ARG Chi-restraints excluded: chain EF5 residue 260 VAL Chi-restraints excluded: chain EF6 residue 196 ARG Chi-restraints excluded: chain EF6 residue 209 ILE Chi-restraints excluded: chain EF6 residue 221 THR Chi-restraints excluded: chain EF6 residue 259 ASP Chi-restraints excluded: chain EF6 residue 260 VAL Chi-restraints excluded: chain EF6 residue 261 SER Chi-restraints excluded: chain EF6 residue 267 VAL Chi-restraints excluded: chain EF6 residue 271 SER Chi-restraints excluded: chain EF6 residue 355 VAL Chi-restraints excluded: chain EF7 residue 202 SER Chi-restraints excluded: chain EF7 residue 221 THR Chi-restraints excluded: chain EF7 residue 237 VAL Chi-restraints excluded: chain EF7 residue 260 VAL Chi-restraints excluded: chain EF7 residue 261 SER Chi-restraints excluded: chain EF7 residue 267 VAL Chi-restraints excluded: chain EF7 residue 271 SER Chi-restraints excluded: chain EF7 residue 273 SER Chi-restraints excluded: chain EF8 residue 206 VAL Chi-restraints excluded: chain EF8 residue 209 ILE Chi-restraints excluded: chain EF8 residue 221 THR Chi-restraints excluded: chain EF8 residue 237 VAL Chi-restraints excluded: chain EF8 residue 259 ASP Chi-restraints excluded: chain EF8 residue 260 VAL Chi-restraints excluded: chain EF8 residue 261 SER Chi-restraints excluded: chain EF8 residue 268 ARG Chi-restraints excluded: chain EF9 residue 206 VAL Chi-restraints excluded: chain EF9 residue 221 THR Chi-restraints excluded: chain EF9 residue 234 THR Chi-restraints excluded: chain EF9 residue 237 VAL Chi-restraints excluded: chain EF9 residue 260 VAL Chi-restraints excluded: chain EF9 residue 261 SER Chi-restraints excluded: chain EF9 residue 267 VAL Chi-restraints excluded: chain EF9 residue 355 VAL Chi-restraints excluded: chain EF10 residue 209 ILE Chi-restraints excluded: chain EF10 residue 221 THR Chi-restraints excluded: chain EF10 residue 237 VAL Chi-restraints excluded: chain EF10 residue 261 SER Chi-restraints excluded: chain EF10 residue 267 VAL Chi-restraints excluded: chain EF10 residue 268 ARG Chi-restraints excluded: chain EF10 residue 273 SER Chi-restraints excluded: chain EF10 residue 292 MET Chi-restraints excluded: chain EF10 residue 384 GLU Chi-restraints excluded: chain EF11 residue 206 VAL Chi-restraints excluded: chain EF11 residue 221 THR Chi-restraints excluded: chain EF11 residue 261 SER Chi-restraints excluded: chain EF11 residue 267 VAL Chi-restraints excluded: chain EF11 residue 268 ARG Chi-restraints excluded: chain EF11 residue 292 MET Chi-restraints excluded: chain EF11 residue 384 GLU Chi-restraints excluded: chain EF12 residue 206 VAL Chi-restraints excluded: chain EF12 residue 209 ILE Chi-restraints excluded: chain EF12 residue 221 THR Chi-restraints excluded: chain EF12 residue 267 VAL Chi-restraints excluded: chain EF12 residue 271 SER Chi-restraints excluded: chain EF13 residue 200 ILE Chi-restraints excluded: chain EF13 residue 206 VAL Chi-restraints excluded: chain EF13 residue 209 ILE Chi-restraints excluded: chain EF13 residue 221 THR Chi-restraints excluded: chain EF13 residue 234 THR Chi-restraints excluded: chain EF13 residue 261 SER Chi-restraints excluded: chain EF13 residue 267 VAL Chi-restraints excluded: chain EF13 residue 355 VAL Chi-restraints excluded: chain EF13 residue 384 GLU Chi-restraints excluded: chain EF14 residue 206 VAL Chi-restraints excluded: chain EF14 residue 209 ILE Chi-restraints excluded: chain EF14 residue 221 THR Chi-restraints excluded: chain EF14 residue 237 VAL Chi-restraints excluded: chain EF14 residue 261 SER Chi-restraints excluded: chain EF14 residue 268 ARG Chi-restraints excluded: chain EF14 residue 384 GLU Chi-restraints excluded: chain EF15 residue 206 VAL Chi-restraints excluded: chain EF15 residue 209 ILE Chi-restraints excluded: chain EF15 residue 221 THR Chi-restraints excluded: chain EF15 residue 261 SER Chi-restraints excluded: chain EF15 residue 355 VAL Chi-restraints excluded: chain EF16 residue 206 VAL Chi-restraints excluded: chain EF16 residue 221 THR Chi-restraints excluded: chain EF16 residue 253 THR Chi-restraints excluded: chain EF16 residue 278 ASP Chi-restraints excluded: chain EF17 residue 206 VAL Chi-restraints excluded: chain EF17 residue 209 ILE Chi-restraints excluded: chain EF17 residue 221 THR Chi-restraints excluded: chain EF17 residue 260 VAL Chi-restraints excluded: chain EF17 residue 261 SER Chi-restraints excluded: chain EF17 residue 267 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [271, 118, 305, 113, 333, 65, 44, 193, 5, 213, 251] chunk 271 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 305 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 333 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.132161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103086 restraints weight = 38083.037| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.51 r_work: 0.3055 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30124 Z= 0.144 Angle : 0.474 6.981 40511 Z= 0.252 Chirality : 0.039 0.150 4539 Planarity : 0.004 0.037 5304 Dihedral : 4.450 59.313 4183 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.57 % Allowed : 28.84 % Favored : 66.59 % 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: 0.50 (0.14), residues: 3876 helix: 2.38 (0.15), residues: 1292 sheet: -0.47 (0.19), residues: 765 loop : -0.81 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAB17 46 TYR 0.013 0.001 TYREF17 373 PHE 0.009 0.001 PHEEF12 317 TRP 0.006 0.001 TRPEF13 199 HIS 0.003 0.001 HISEF12 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (30090) covalent geometry : angle 0.47421 / 0.25 (40443) SS BOND : bond 0.00154 / 0.10 ( 34) SS BOND : angle 0.30380 / 0.20 ( 68) hydrogen bonds : bond 0.02880 / 1.91 ( 1156) hydrogen bonds : angle 4.44158 / 2.97 ( 3213) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 421 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AB5 51 LYS cc_start: 0.7809 (tppt) cc_final: 0.7392 (tptt) REVERT: AB6 51 LYS cc_start: 0.7824 (tppp) cc_final: 0.7428 (tppt) REVERT: AB7 48 LYS cc_start: 0.7464 (tttp) cc_final: 0.6617 (tttt) REVERT: AB7 52 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6113 (mp-120) REVERT: AB9 48 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6687 (tttt) REVERT: AB9 52 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6047 (mp-120) REVERT: AB10 38 MET cc_start: 0.8571 (ttt) cc_final: 0.8145 (ttp) REVERT: AB11 51 LYS cc_start: 0.8120 (tppp) cc_final: 0.7838 (tppt) REVERT: AB12 51 LYS cc_start: 0.8149 (tptt) cc_final: 0.7737 (tppt) REVERT: AB13 51 LYS cc_start: 0.8124 (tptt) cc_final: 0.7873 (tppt) REVERT: AB14 51 LYS cc_start: 0.8075 (tptt) cc_final: 0.7804 (tppt) REVERT: AB15 51 LYS cc_start: 0.8204 (tppp) cc_final: 0.7777 (tppt) REVERT: EF1 364 ASP cc_start: 0.7931 (t70) cc_final: 0.7495 (t0) REVERT: EF2 207 GLU cc_start: 0.8146 (mp0) cc_final: 0.7868 (mt-10) REVERT: EF4 221 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8488 (p) REVERT: EF4 259 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.7990 (t0) REVERT: EF4 305 ASN cc_start: 0.8380 (m-40) cc_final: 0.8109 (m-40) REVERT: EF5 196 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.6783 (ttm-80) REVERT: EF5 241 ASN cc_start: 0.8907 (m-40) cc_final: 0.8679 (m110) REVERT: EF6 196 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6757 (ttm-80) REVERT: EF6 259 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8005 (t70) REVERT: EF8 221 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8473 (p) REVERT: EF8 239 MET cc_start: 0.8803 (mtm) cc_final: 0.8458 (mtp) REVERT: EF8 244 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8284 (mt-10) REVERT: EF8 259 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7716 (t0) REVERT: EF8 268 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7524 (ttm170) REVERT: EF9 207 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7276 (mp0) REVERT: EF9 221 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8197 (p) REVERT: EF9 241 ASN cc_start: 0.8877 (m-40) cc_final: 0.8199 (m-40) REVERT: EF9 384 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: EF10 241 ASN cc_start: 0.8652 (m-40) cc_final: 0.7972 (m110) REVERT: EF10 259 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.7743 (t0) REVERT: EF10 268 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7543 (ttm170) REVERT: EF10 384 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7504 (tt0) REVERT: EF11 223 ASP cc_start: 0.8086 (t0) cc_final: 0.7638 (m-30) REVERT: EF11 268 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7522 (ttp-110) REVERT: EF12 223 ASP cc_start: 0.8108 (t0) cc_final: 0.7839 (m-30) REVERT: EF12 242 ASP cc_start: 0.8959 (m-30) cc_final: 0.8644 (m-30) REVERT: EF12 279 ASP cc_start: 0.8084 (m-30) cc_final: 0.7734 (m-30) REVERT: EF13 223 ASP cc_start: 0.8154 (t0) cc_final: 0.7891 (m-30) REVERT: EF14 223 ASP cc_start: 0.8347 (t0) cc_final: 0.7959 (m-30) REVERT: EF14 241 ASN cc_start: 0.8954 (m110) cc_final: 0.8553 (m-40) REVERT: EF14 268 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7827 (ttp-110) REVERT: EF14 384 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: EF16 221 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8438 (p) REVERT: EF16 223 ASP cc_start: 0.8316 (t0) cc_final: 0.8079 (m-30) REVERT: EF17 280 ASP cc_start: 0.7973 (m-30) cc_final: 0.7743 (m-30) outliers start: 143 outliers final: 104 residues processed: 546 average time/residue: 0.5926 time to fit residues: 382.4923 Evaluate side-chains 534 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 409 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB1 residue 23 SER Chi-restraints excluded: chain AB1 residue 27 CYS Chi-restraints excluded: chain AB2 residue 27 CYS Chi-restraints excluded: chain AB3 residue 37 THR Chi-restraints excluded: chain AB3 residue 48 LYS Chi-restraints excluded: chain AB4 residue 52 GLN Chi-restraints excluded: chain AB6 residue 52 GLN Chi-restraints excluded: chain AB7 residue 27 CYS Chi-restraints excluded: chain AB7 residue 52 GLN Chi-restraints excluded: chain AB8 residue 37 THR Chi-restraints excluded: chain AB9 residue 27 CYS Chi-restraints excluded: chain AB9 residue 48 LYS Chi-restraints excluded: chain AB9 residue 52 GLN Chi-restraints excluded: chain AB10 residue 27 CYS Chi-restraints excluded: chain AB11 residue 27 CYS Chi-restraints excluded: chain AB12 residue 27 CYS Chi-restraints excluded: chain AB15 residue 27 CYS Chi-restraints excluded: chain AB16 residue 27 CYS Chi-restraints excluded: chain EF1 residue 202 SER Chi-restraints excluded: chain EF1 residue 206 VAL Chi-restraints excluded: chain EF1 residue 209 ILE Chi-restraints excluded: chain EF1 residue 221 THR Chi-restraints excluded: chain EF1 residue 260 VAL Chi-restraints excluded: chain EF1 residue 355 VAL Chi-restraints excluded: chain EF2 residue 202 SER Chi-restraints excluded: chain EF2 residue 206 VAL Chi-restraints excluded: chain EF2 residue 209 ILE Chi-restraints excluded: chain EF2 residue 221 THR Chi-restraints excluded: chain EF2 residue 260 VAL Chi-restraints excluded: chain EF2 residue 261 SER Chi-restraints excluded: chain EF3 residue 206 VAL Chi-restraints excluded: chain EF3 residue 209 ILE Chi-restraints excluded: chain EF3 residue 260 VAL Chi-restraints excluded: chain EF3 residue 261 SER Chi-restraints excluded: chain EF4 residue 209 ILE Chi-restraints excluded: chain EF4 residue 221 THR Chi-restraints excluded: chain EF4 residue 259 ASP Chi-restraints excluded: chain EF4 residue 260 VAL Chi-restraints excluded: chain EF5 residue 196 ARG Chi-restraints excluded: chain EF5 residue 206 VAL Chi-restraints excluded: chain EF5 residue 260 VAL Chi-restraints excluded: chain EF6 residue 196 ARG Chi-restraints excluded: chain EF6 residue 209 ILE Chi-restraints excluded: chain EF6 residue 221 THR Chi-restraints excluded: chain EF6 residue 259 ASP Chi-restraints excluded: chain EF6 residue 260 VAL Chi-restraints excluded: chain EF6 residue 261 SER Chi-restraints excluded: chain EF6 residue 267 VAL Chi-restraints excluded: chain EF6 residue 271 SER Chi-restraints excluded: chain EF6 residue 355 VAL Chi-restraints excluded: chain EF7 residue 202 SER Chi-restraints excluded: chain EF7 residue 221 THR Chi-restraints excluded: chain EF7 residue 237 VAL Chi-restraints excluded: chain EF7 residue 260 VAL Chi-restraints excluded: chain EF7 residue 261 SER Chi-restraints excluded: chain EF7 residue 267 VAL Chi-restraints excluded: chain EF7 residue 271 SER Chi-restraints excluded: chain EF7 residue 273 SER Chi-restraints excluded: chain EF8 residue 206 VAL Chi-restraints excluded: chain EF8 residue 209 ILE Chi-restraints excluded: chain EF8 residue 221 THR Chi-restraints excluded: chain EF8 residue 237 VAL Chi-restraints excluded: chain EF8 residue 244 GLU Chi-restraints excluded: chain EF8 residue 259 ASP Chi-restraints excluded: chain EF8 residue 260 VAL Chi-restraints excluded: chain EF8 residue 261 SER Chi-restraints excluded: chain EF8 residue 268 ARG Chi-restraints excluded: chain EF9 residue 206 VAL Chi-restraints excluded: chain EF9 residue 221 THR Chi-restraints excluded: chain EF9 residue 237 VAL Chi-restraints excluded: chain EF9 residue 260 VAL Chi-restraints excluded: chain EF9 residue 261 SER Chi-restraints excluded: chain EF9 residue 267 VAL Chi-restraints excluded: chain EF9 residue 355 VAL Chi-restraints excluded: chain EF9 residue 384 GLU Chi-restraints excluded: chain EF10 residue 209 ILE Chi-restraints excluded: chain EF10 residue 221 THR Chi-restraints excluded: chain EF10 residue 237 VAL Chi-restraints excluded: chain EF10 residue 259 ASP Chi-restraints excluded: chain EF10 residue 261 SER Chi-restraints excluded: chain EF10 residue 267 VAL Chi-restraints excluded: chain EF10 residue 268 ARG Chi-restraints excluded: chain EF10 residue 271 SER Chi-restraints excluded: chain EF10 residue 292 MET Chi-restraints excluded: chain EF10 residue 384 GLU Chi-restraints excluded: chain EF11 residue 206 VAL Chi-restraints excluded: chain EF11 residue 221 THR Chi-restraints excluded: chain EF11 residue 261 SER Chi-restraints excluded: chain EF11 residue 267 VAL Chi-restraints excluded: chain EF11 residue 268 ARG Chi-restraints excluded: chain EF11 residue 292 MET Chi-restraints excluded: chain EF11 residue 384 GLU Chi-restraints excluded: chain EF12 residue 206 VAL Chi-restraints excluded: chain EF12 residue 209 ILE Chi-restraints excluded: chain EF12 residue 221 THR Chi-restraints excluded: chain EF12 residue 267 VAL Chi-restraints excluded: chain EF12 residue 271 SER Chi-restraints excluded: chain EF13 residue 200 ILE Chi-restraints excluded: chain EF13 residue 206 VAL Chi-restraints excluded: chain EF13 residue 221 THR Chi-restraints excluded: chain EF13 residue 261 SER Chi-restraints excluded: chain EF13 residue 267 VAL Chi-restraints excluded: chain EF13 residue 303 MET Chi-restraints excluded: chain EF13 residue 355 VAL Chi-restraints excluded: chain EF13 residue 384 GLU Chi-restraints excluded: chain EF14 residue 206 VAL Chi-restraints excluded: chain EF14 residue 209 ILE Chi-restraints excluded: chain EF14 residue 221 THR Chi-restraints excluded: chain EF14 residue 237 VAL Chi-restraints excluded: chain EF14 residue 268 ARG Chi-restraints excluded: chain EF14 residue 384 GLU Chi-restraints excluded: chain EF15 residue 206 VAL Chi-restraints excluded: chain EF15 residue 209 ILE Chi-restraints excluded: chain EF15 residue 221 THR Chi-restraints excluded: chain EF15 residue 261 SER Chi-restraints excluded: chain EF15 residue 355 VAL Chi-restraints excluded: chain EF16 residue 206 VAL Chi-restraints excluded: chain EF16 residue 221 THR Chi-restraints excluded: chain EF16 residue 271 SER Chi-restraints excluded: chain EF17 residue 206 VAL Chi-restraints excluded: chain EF17 residue 209 ILE Chi-restraints excluded: chain EF17 residue 221 THR Chi-restraints excluded: chain EF17 residue 260 VAL Chi-restraints excluded: chain EF17 residue 261 SER Chi-restraints excluded: chain EF17 residue 267 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [40, 130, 34, 114, 15, 87, 51, 260, 268, 267, 321] chunk 40 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 260 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 chunk 321 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.130852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.101837 restraints weight = 38332.258| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.49 r_work: 0.3035 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30124 Z= 0.178 Angle : 0.501 7.212 40511 Z= 0.265 Chirality : 0.040 0.142 4539 Planarity : 0.004 0.041 5304 Dihedral : 4.573 59.474 4183 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.83 % Allowed : 29.06 % Favored : 66.11 % 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: 0.42 (0.14), residues: 3876 helix: 2.27 (0.15), residues: 1292 sheet: -0.52 (0.19), residues: 765 loop : -0.84 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAB2 46 TYR 0.019 0.001 TYREF17 373 PHE 0.008 0.001 PHEEF12 317 TRP 0.007 0.001 TRPEF16 199 HIS 0.004 0.001 HISEF12 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (30090) covalent geometry : angle 0.50110 / 0.27 (40443) SS BOND : bond 0.00211 / 0.13 ( 34) SS BOND : angle 0.29422 / 0.19 ( 68) hydrogen bonds : bond 0.03168 / 2.09 ( 1156) hydrogen bonds : angle 4.50914 / 3.01 ( 3213) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 409 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AB5 51 LYS cc_start: 0.7832 (tppt) cc_final: 0.7414 (tptt) REVERT: AB6 51 LYS cc_start: 0.7969 (tppp) cc_final: 0.7580 (tppt) REVERT: AB6 52 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.7092 (mm-40) REVERT: AB7 48 LYS cc_start: 0.7482 (tttp) cc_final: 0.6631 (tttt) REVERT: AB7 52 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6175 (mp-120) REVERT: AB9 48 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.6675 (tttt) REVERT: AB9 52 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6112 (mp-120) REVERT: AB10 38 MET cc_start: 0.8594 (ttt) cc_final: 0.8177 (ttp) REVERT: AB11 51 LYS cc_start: 0.8145 (tppp) cc_final: 0.7855 (tppt) REVERT: AB12 51 LYS cc_start: 0.8082 (tptt) cc_final: 0.7757 (tppt) REVERT: AB13 51 LYS cc_start: 0.8148 (tptt) cc_final: 0.7890 (tppt) REVERT: AB14 51 LYS cc_start: 0.8111 (tptt) cc_final: 0.7830 (tppt) REVERT: AB15 51 LYS cc_start: 0.8229 (tppp) cc_final: 0.7813 (tppt) REVERT: EF1 364 ASP cc_start: 0.8025 (t70) cc_final: 0.7608 (t0) REVERT: EF4 221 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8557 (p) REVERT: EF4 259 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.7956 (t0) REVERT: EF4 305 ASN cc_start: 0.8418 (m-40) cc_final: 0.8135 (m-40) REVERT: EF5 196 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6728 (ttm-80) REVERT: EF5 241 ASN cc_start: 0.8944 (m-40) cc_final: 0.8705 (m110) REVERT: EF6 196 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6790 (ttm-80) REVERT: EF6 207 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7361 (mp0) REVERT: EF6 259 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8023 (t70) REVERT: EF8 221 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8401 (p) REVERT: EF8 238 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7730 (mm-40) REVERT: EF8 239 MET cc_start: 0.8843 (mtm) cc_final: 0.8535 (mtp) REVERT: EF8 244 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8151 (mt-10) REVERT: EF8 259 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7732 (t0) REVERT: EF9 207 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7315 (mp0) REVERT: EF9 221 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8259 (p) REVERT: EF9 241 ASN cc_start: 0.8898 (m-40) cc_final: 0.8209 (m-40) REVERT: EF10 241 ASN cc_start: 0.8691 (m-40) cc_final: 0.8026 (m110) REVERT: EF10 268 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7601 (ttm170) REVERT: EF10 384 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7564 (tt0) REVERT: EF11 223 ASP cc_start: 0.8171 (t0) cc_final: 0.7756 (m-30) REVERT: EF11 268 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7591 (ttp-110) REVERT: EF12 223 ASP cc_start: 0.8122 (t0) cc_final: 0.7872 (m-30) REVERT: EF12 242 ASP cc_start: 0.8934 (m-30) cc_final: 0.8671 (m-30) REVERT: EF12 279 ASP cc_start: 0.8040 (m-30) cc_final: 0.7681 (m-30) REVERT: EF14 223 ASP cc_start: 0.8396 (t0) cc_final: 0.8057 (m-30) REVERT: EF14 241 ASN cc_start: 0.8969 (m110) cc_final: 0.8376 (m110) REVERT: EF14 384 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7811 (mt-10) REVERT: EF15 196 ARG cc_start: 0.7667 (ttm-80) cc_final: 0.7177 (mpp80) REVERT: EF16 221 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8525 (p) outliers start: 151 outliers final: 112 residues processed: 538 average time/residue: 0.5823 time to fit residues: 371.2322 Evaluate side-chains 534 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 403 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB1 residue 23 SER Chi-restraints excluded: chain AB1 residue 27 CYS Chi-restraints excluded: chain AB2 residue 27 CYS Chi-restraints excluded: chain AB3 residue 37 THR Chi-restraints excluded: chain AB3 residue 48 LYS Chi-restraints excluded: chain AB4 residue 52 GLN Chi-restraints excluded: chain AB6 residue 52 GLN Chi-restraints excluded: chain AB7 residue 23 SER Chi-restraints excluded: chain AB7 residue 27 CYS Chi-restraints excluded: chain AB7 residue 52 GLN Chi-restraints excluded: chain AB8 residue 37 THR Chi-restraints excluded: chain AB9 residue 27 CYS Chi-restraints excluded: chain AB9 residue 48 LYS Chi-restraints excluded: chain AB9 residue 52 GLN Chi-restraints excluded: chain AB10 residue 27 CYS Chi-restraints excluded: chain AB11 residue 27 CYS Chi-restraints excluded: chain AB12 residue 27 CYS Chi-restraints excluded: chain AB15 residue 27 CYS Chi-restraints excluded: chain AB16 residue 27 CYS Chi-restraints excluded: chain AB17 residue 23 SER Chi-restraints excluded: chain EF1 residue 202 SER Chi-restraints excluded: chain EF1 residue 206 VAL Chi-restraints excluded: chain EF1 residue 209 ILE Chi-restraints excluded: chain EF1 residue 221 THR Chi-restraints excluded: chain EF1 residue 260 VAL Chi-restraints excluded: chain EF1 residue 355 VAL Chi-restraints excluded: chain EF2 residue 202 SER Chi-restraints excluded: chain EF2 residue 206 VAL Chi-restraints excluded: chain EF2 residue 209 ILE Chi-restraints excluded: chain EF2 residue 221 THR Chi-restraints excluded: chain EF2 residue 260 VAL Chi-restraints excluded: chain EF2 residue 261 SER Chi-restraints excluded: chain EF3 residue 206 VAL Chi-restraints excluded: chain EF3 residue 209 ILE Chi-restraints excluded: chain EF3 residue 260 VAL Chi-restraints excluded: chain EF3 residue 261 SER Chi-restraints excluded: chain EF4 residue 209 ILE Chi-restraints excluded: chain EF4 residue 221 THR Chi-restraints excluded: chain EF4 residue 259 ASP Chi-restraints excluded: chain EF4 residue 260 VAL Chi-restraints excluded: chain EF5 residue 196 ARG Chi-restraints excluded: chain EF5 residue 206 VAL Chi-restraints excluded: chain EF5 residue 260 VAL Chi-restraints excluded: chain EF5 residue 292 MET Chi-restraints excluded: chain EF6 residue 196 ARG Chi-restraints excluded: chain EF6 residue 209 ILE Chi-restraints excluded: chain EF6 residue 221 THR Chi-restraints excluded: chain EF6 residue 259 ASP Chi-restraints excluded: chain EF6 residue 260 VAL Chi-restraints excluded: chain EF6 residue 261 SER Chi-restraints excluded: chain EF6 residue 267 VAL Chi-restraints excluded: chain EF6 residue 271 SER Chi-restraints excluded: chain EF6 residue 355 VAL Chi-restraints excluded: chain EF7 residue 202 SER Chi-restraints excluded: chain EF7 residue 221 THR Chi-restraints excluded: chain EF7 residue 237 VAL Chi-restraints excluded: chain EF7 residue 260 VAL Chi-restraints excluded: chain EF7 residue 261 SER Chi-restraints excluded: chain EF7 residue 267 VAL Chi-restraints excluded: chain EF7 residue 271 SER Chi-restraints excluded: chain EF7 residue 273 SER Chi-restraints excluded: chain EF8 residue 206 VAL Chi-restraints excluded: chain EF8 residue 209 ILE Chi-restraints excluded: chain EF8 residue 221 THR Chi-restraints excluded: chain EF8 residue 237 VAL Chi-restraints excluded: chain EF8 residue 238 GLN Chi-restraints excluded: chain EF8 residue 244 GLU Chi-restraints excluded: chain EF8 residue 259 ASP Chi-restraints excluded: chain EF8 residue 260 VAL Chi-restraints excluded: chain EF8 residue 261 SER Chi-restraints excluded: chain EF9 residue 206 VAL Chi-restraints excluded: chain EF9 residue 221 THR Chi-restraints excluded: chain EF9 residue 237 VAL Chi-restraints excluded: chain EF9 residue 260 VAL Chi-restraints excluded: chain EF9 residue 261 SER Chi-restraints excluded: chain EF9 residue 267 VAL Chi-restraints excluded: chain EF9 residue 355 VAL Chi-restraints excluded: chain EF10 residue 209 ILE Chi-restraints excluded: chain EF10 residue 221 THR Chi-restraints excluded: chain EF10 residue 237 VAL Chi-restraints excluded: chain EF10 residue 261 SER Chi-restraints excluded: chain EF10 residue 267 VAL Chi-restraints excluded: chain EF10 residue 268 ARG Chi-restraints excluded: chain EF10 residue 271 SER Chi-restraints excluded: chain EF10 residue 292 MET Chi-restraints excluded: chain EF10 residue 384 GLU Chi-restraints excluded: chain EF11 residue 206 VAL Chi-restraints excluded: chain EF11 residue 221 THR Chi-restraints excluded: chain EF11 residue 237 VAL Chi-restraints excluded: chain EF11 residue 261 SER Chi-restraints excluded: chain EF11 residue 267 VAL Chi-restraints excluded: chain EF11 residue 268 ARG Chi-restraints excluded: chain EF11 residue 292 MET Chi-restraints excluded: chain EF11 residue 384 GLU Chi-restraints excluded: chain EF12 residue 206 VAL Chi-restraints excluded: chain EF12 residue 209 ILE Chi-restraints excluded: chain EF12 residue 221 THR Chi-restraints excluded: chain EF12 residue 267 VAL Chi-restraints excluded: chain EF12 residue 271 SER Chi-restraints excluded: chain EF13 residue 200 ILE Chi-restraints excluded: chain EF13 residue 206 VAL Chi-restraints excluded: chain EF13 residue 209 ILE Chi-restraints excluded: chain EF13 residue 221 THR Chi-restraints excluded: chain EF13 residue 234 THR Chi-restraints excluded: chain EF13 residue 267 VAL Chi-restraints excluded: chain EF13 residue 303 MET Chi-restraints excluded: chain EF13 residue 355 VAL Chi-restraints excluded: chain EF13 residue 384 GLU Chi-restraints excluded: chain EF14 residue 206 VAL Chi-restraints excluded: chain EF14 residue 209 ILE Chi-restraints excluded: chain EF14 residue 221 THR Chi-restraints excluded: chain EF14 residue 237 VAL Chi-restraints excluded: chain EF14 residue 253 THR Chi-restraints excluded: chain EF14 residue 261 SER Chi-restraints excluded: chain EF14 residue 384 GLU Chi-restraints excluded: chain EF15 residue 206 VAL Chi-restraints excluded: chain EF15 residue 209 ILE Chi-restraints excluded: chain EF15 residue 221 THR Chi-restraints excluded: chain EF15 residue 261 SER Chi-restraints excluded: chain EF15 residue 355 VAL Chi-restraints excluded: chain EF16 residue 206 VAL Chi-restraints excluded: chain EF16 residue 209 ILE Chi-restraints excluded: chain EF16 residue 221 THR Chi-restraints excluded: chain EF16 residue 253 THR Chi-restraints excluded: chain EF16 residue 271 SER Chi-restraints excluded: chain EF17 residue 206 VAL Chi-restraints excluded: chain EF17 residue 209 ILE Chi-restraints excluded: chain EF17 residue 221 THR Chi-restraints excluded: chain EF17 residue 260 VAL Chi-restraints excluded: chain EF17 residue 261 SER Chi-restraints excluded: chain EF17 residue 267 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [67, 302, 303, 187, 77, 238, 150, 220, 252, 331, 35] chunk 67 optimal weight: 0.5980 chunk 302 optimal weight: 0.6980 chunk 303 optimal weight: 0.6980 chunk 187 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 238 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 220 optimal weight: 0.9990 chunk 252 optimal weight: 0.4980 chunk 331 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.100743 restraints weight = 39035.731| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.41 r_work: 0.3009 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30124 Z= 0.118 Angle : 0.464 7.410 40511 Z= 0.246 Chirality : 0.039 0.143 4539 Planarity : 0.003 0.036 5304 Dihedral : 4.342 58.183 4183 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.09 % Allowed : 29.86 % Favored : 66.05 % 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: 0.50 (0.14), residues: 3876 helix: 2.40 (0.15), residues: 1292 sheet: -0.54 (0.19), residues: 765 loop : -0.80 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAB13 46 TYR 0.012 0.001 TYREF17 373 PHE 0.008 0.001 PHEEF12 317 TRP 0.006 0.001 TRPEF4 257 HIS 0.004 0.001 HISEF12 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (30090) covalent geometry : angle 0.46447 / 0.25 (40443) SS BOND : bond 0.00106 / 0.07 ( 34) SS BOND : angle 0.22273 / 0.15 ( 68) hydrogen bonds : bond 0.02687 / 1.78 ( 1156) hydrogen bonds : angle 4.35562 / 2.91 ( 3213) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 408 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AB4 51 LYS cc_start: 0.7902 (tppt) cc_final: 0.7463 (tppt) REVERT: AB6 51 LYS cc_start: 0.7734 (tppp) cc_final: 0.7352 (tppt) REVERT: AB9 48 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6467 (tptt) REVERT: AB9 52 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.5941 (mp-120) REVERT: AB10 38 MET cc_start: 0.8444 (ttt) cc_final: 0.7960 (ttp) REVERT: AB10 51 LYS cc_start: 0.8232 (tppt) cc_final: 0.8031 (tppt) REVERT: AB11 51 LYS cc_start: 0.8084 (tppp) cc_final: 0.7802 (tppt) REVERT: AB12 51 LYS cc_start: 0.8018 (tptt) cc_final: 0.7623 (tppt) REVERT: AB13 51 LYS cc_start: 0.8069 (tptt) cc_final: 0.7792 (tppt) REVERT: AB14 51 LYS cc_start: 0.7974 (tptt) cc_final: 0.7686 (tppt) REVERT: AB15 51 LYS cc_start: 0.8131 (tppp) cc_final: 0.7723 (tppt) REVERT: EF1 384 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7680 (mt-10) REVERT: EF2 196 ARG cc_start: 0.7628 (ttm-80) cc_final: 0.7287 (mtm180) REVERT: EF2 280 ASP cc_start: 0.7815 (m-30) cc_final: 0.7532 (m-30) REVERT: EF4 221 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8502 (p) REVERT: EF4 259 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7822 (t0) REVERT: EF5 196 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.6782 (ttm-80) REVERT: EF5 241 ASN cc_start: 0.8812 (m-40) cc_final: 0.8552 (m110) REVERT: EF6 196 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6738 (ttm-80) REVERT: EF6 207 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7058 (mp0) REVERT: EF6 259 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7742 (t70) REVERT: EF8 221 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8291 (p) REVERT: EF8 238 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7465 (mm-40) REVERT: EF8 239 MET cc_start: 0.8604 (mtm) cc_final: 0.8327 (mtp) REVERT: EF8 244 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: EF8 259 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7575 (t0) REVERT: EF9 207 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7095 (mp0) REVERT: EF9 221 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.8049 (p) REVERT: EF9 241 ASN cc_start: 0.8840 (m-40) cc_final: 0.8126 (m-40) REVERT: EF9 384 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7966 (mt-10) REVERT: EF10 241 ASN cc_start: 0.8494 (m-40) cc_final: 0.7766 (m110) REVERT: EF10 268 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7286 (ttm170) REVERT: EF10 384 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: EF11 239 MET cc_start: 0.8800 (mtp) cc_final: 0.8542 (mtm) REVERT: EF11 268 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7366 (ttp-110) REVERT: EF12 279 ASP cc_start: 0.7938 (m-30) cc_final: 0.7559 (m-30) REVERT: EF13 223 ASP cc_start: 0.8111 (t0) cc_final: 0.7849 (m-30) REVERT: EF14 223 ASP cc_start: 0.8355 (t0) cc_final: 0.7978 (m-30) REVERT: EF14 238 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7521 (mm-40) REVERT: EF14 241 ASN cc_start: 0.8754 (m110) cc_final: 0.8128 (m110) REVERT: EF14 384 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7833 (mt-10) REVERT: EF16 221 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8301 (p) REVERT: EF16 223 ASP cc_start: 0.8239 (t0) cc_final: 0.7939 (m-30) REVERT: EF16 292 MET cc_start: 0.8467 (tpp) cc_final: 0.8234 (tpp) REVERT: EF16 391 ASP cc_start: 0.8831 (m-30) cc_final: 0.8617 (m-30) REVERT: EF17 280 ASP cc_start: 0.7833 (m-30) cc_final: 0.7610 (m-30) outliers start: 128 outliers final: 98 residues processed: 524 average time/residue: 0.6060 time to fit residues: 373.7681 Evaluate side-chains 517 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 401 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB1 residue 23 SER Chi-restraints excluded: chain AB2 residue 27 CYS Chi-restraints excluded: chain AB3 residue 37 THR Chi-restraints excluded: chain AB3 residue 48 LYS Chi-restraints excluded: chain AB4 residue 52 GLN Chi-restraints excluded: chain AB6 residue 27 CYS Chi-restraints excluded: chain AB6 residue 52 GLN Chi-restraints excluded: chain AB7 residue 52 GLN Chi-restraints excluded: chain AB8 residue 37 THR Chi-restraints excluded: chain AB9 residue 27 CYS Chi-restraints excluded: chain AB9 residue 48 LYS Chi-restraints excluded: chain AB9 residue 52 GLN Chi-restraints excluded: chain AB10 residue 27 CYS Chi-restraints excluded: chain AB12 residue 27 CYS Chi-restraints excluded: chain AB15 residue 27 CYS Chi-restraints excluded: chain AB16 residue 27 CYS Chi-restraints excluded: chain EF1 residue 202 SER Chi-restraints excluded: chain EF1 residue 206 VAL Chi-restraints excluded: chain EF1 residue 209 ILE Chi-restraints excluded: chain EF1 residue 221 THR Chi-restraints excluded: chain EF1 residue 260 VAL Chi-restraints excluded: chain EF1 residue 355 VAL Chi-restraints excluded: chain EF2 residue 202 SER Chi-restraints excluded: chain EF2 residue 206 VAL Chi-restraints excluded: chain EF2 residue 221 THR Chi-restraints excluded: chain EF2 residue 260 VAL Chi-restraints excluded: chain EF2 residue 261 SER Chi-restraints excluded: chain EF3 residue 209 ILE Chi-restraints excluded: chain EF3 residue 260 VAL Chi-restraints excluded: chain EF3 residue 261 SER Chi-restraints excluded: chain EF4 residue 209 ILE Chi-restraints excluded: chain EF4 residue 221 THR Chi-restraints excluded: chain EF4 residue 259 ASP Chi-restraints excluded: chain EF4 residue 260 VAL Chi-restraints excluded: chain EF4 residue 355 VAL Chi-restraints excluded: chain EF5 residue 196 ARG Chi-restraints excluded: chain EF5 residue 260 VAL Chi-restraints excluded: chain EF6 residue 196 ARG Chi-restraints excluded: chain EF6 residue 209 ILE Chi-restraints excluded: chain EF6 residue 221 THR Chi-restraints excluded: chain EF6 residue 259 ASP Chi-restraints excluded: chain EF6 residue 260 VAL Chi-restraints excluded: chain EF6 residue 261 SER Chi-restraints excluded: chain EF6 residue 267 VAL Chi-restraints excluded: chain EF6 residue 355 VAL Chi-restraints excluded: chain EF7 residue 202 SER Chi-restraints excluded: chain EF7 residue 221 THR Chi-restraints excluded: chain EF7 residue 237 VAL Chi-restraints excluded: chain EF7 residue 260 VAL Chi-restraints excluded: chain EF7 residue 261 SER Chi-restraints excluded: chain EF7 residue 267 VAL Chi-restraints excluded: chain EF7 residue 271 SER Chi-restraints excluded: chain EF8 residue 206 VAL Chi-restraints excluded: chain EF8 residue 221 THR Chi-restraints excluded: chain EF8 residue 230 GLN Chi-restraints excluded: chain EF8 residue 237 VAL Chi-restraints excluded: chain EF8 residue 238 GLN Chi-restraints excluded: chain EF8 residue 244 GLU Chi-restraints excluded: chain EF8 residue 259 ASP Chi-restraints excluded: chain EF8 residue 260 VAL Chi-restraints excluded: chain EF8 residue 261 SER Chi-restraints excluded: chain EF9 residue 206 VAL Chi-restraints excluded: chain EF9 residue 221 THR Chi-restraints excluded: chain EF9 residue 237 VAL Chi-restraints excluded: chain EF9 residue 260 VAL Chi-restraints excluded: chain EF9 residue 261 SER Chi-restraints excluded: chain EF9 residue 267 VAL Chi-restraints excluded: chain EF9 residue 280 ASP Chi-restraints excluded: chain EF9 residue 355 VAL Chi-restraints excluded: chain EF10 residue 209 ILE Chi-restraints excluded: chain EF10 residue 221 THR Chi-restraints excluded: chain EF10 residue 237 VAL Chi-restraints excluded: chain EF10 residue 261 SER Chi-restraints excluded: chain EF10 residue 267 VAL Chi-restraints excluded: chain EF10 residue 268 ARG Chi-restraints excluded: chain EF10 residue 273 SER Chi-restraints excluded: chain EF10 residue 292 MET Chi-restraints excluded: chain EF10 residue 384 GLU Chi-restraints excluded: chain EF11 residue 206 VAL Chi-restraints excluded: chain EF11 residue 221 THR Chi-restraints excluded: chain EF11 residue 261 SER Chi-restraints excluded: chain EF11 residue 267 VAL Chi-restraints excluded: chain EF11 residue 268 ARG Chi-restraints excluded: chain EF11 residue 292 MET Chi-restraints excluded: chain EF11 residue 384 GLU Chi-restraints excluded: chain EF12 residue 206 VAL Chi-restraints excluded: chain EF12 residue 209 ILE Chi-restraints excluded: chain EF12 residue 221 THR Chi-restraints excluded: chain EF12 residue 261 SER Chi-restraints excluded: chain EF12 residue 267 VAL Chi-restraints excluded: chain EF13 residue 200 ILE Chi-restraints excluded: chain EF13 residue 206 VAL Chi-restraints excluded: chain EF13 residue 221 THR Chi-restraints excluded: chain EF13 residue 267 VAL Chi-restraints excluded: chain EF13 residue 303 MET Chi-restraints excluded: chain EF13 residue 355 VAL Chi-restraints excluded: chain EF13 residue 384 GLU Chi-restraints excluded: chain EF14 residue 206 VAL Chi-restraints excluded: chain EF14 residue 209 ILE Chi-restraints excluded: chain EF14 residue 221 THR Chi-restraints excluded: chain EF14 residue 237 VAL Chi-restraints excluded: chain EF14 residue 238 GLN Chi-restraints excluded: chain EF14 residue 261 SER Chi-restraints excluded: chain EF14 residue 384 GLU Chi-restraints excluded: chain EF15 residue 206 VAL Chi-restraints excluded: chain EF15 residue 221 THR Chi-restraints excluded: chain EF15 residue 261 SER Chi-restraints excluded: chain EF15 residue 355 VAL Chi-restraints excluded: chain EF16 residue 206 VAL Chi-restraints excluded: chain EF16 residue 221 THR Chi-restraints excluded: chain EF16 residue 253 THR Chi-restraints excluded: chain EF17 residue 209 ILE Chi-restraints excluded: chain EF17 residue 221 THR Chi-restraints excluded: chain EF17 residue 260 VAL Chi-restraints excluded: chain EF17 residue 261 SER Chi-restraints excluded: chain EF17 residue 267 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [77, 103, 78, 56, 354, 306, 249, 184, 17, 338, 189] chunk 77 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 354 optimal weight: 0.7980 chunk 306 optimal weight: 0.0870 chunk 249 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 338 optimal weight: 8.9990 chunk 189 optimal weight: 2.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.096237 restraints weight = 39295.354| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.41 r_work: 0.2948 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 30124 Z= 0.240 Angle : 0.551 7.760 40511 Z= 0.292 Chirality : 0.041 0.144 4539 Planarity : 0.004 0.056 5304 Dihedral : 4.751 59.264 4182 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.12 % Allowed : 29.89 % Favored : 65.98 % 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: 0.53 (0.14), residues: 3876 helix: 2.67 (0.15), residues: 1190 sheet: -0.19 (0.17), residues: 935 loop : -1.00 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAB13 46 TYR 0.021 0.001 TYREF10 373 PHE 0.008 0.001 PHEEF12 317 TRP 0.011 0.001 TRPEF1 199 HIS 0.004 0.001 HISEF12 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.24 (30090) covalent geometry : angle 0.55104 / 0.29 (40443) SS BOND : bond 0.00315 / 0.20 ( 34) SS BOND : angle 0.33458 / 0.22 ( 68) hydrogen bonds : bond 0.03569 / 2.35 ( 1156) hydrogen bonds : angle 4.61446 / 3.08 ( 3213) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 404 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB4 51 LYS cc_start: 0.7902 (tppt) cc_final: 0.7449 (tppt) REVERT: AB6 51 LYS cc_start: 0.7882 (tppp) cc_final: 0.7475 (tppt) REVERT: AB6 52 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.7036 (mm-40) REVERT: AB9 48 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6294 (tptt) REVERT: AB9 52 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.6236 (mp-120) REVERT: AB10 38 MET cc_start: 0.8477 (ttt) cc_final: 0.8094 (ttp) REVERT: AB10 51 LYS cc_start: 0.8203 (tppt) cc_final: 0.7934 (tppt) REVERT: AB11 51 LYS cc_start: 0.8070 (tppp) cc_final: 0.7787 (tppt) REVERT: AB12 51 LYS cc_start: 0.7955 (tptt) cc_final: 0.7626 (tppt) REVERT: AB13 51 LYS cc_start: 0.8051 (tptt) cc_final: 0.7763 (tppt) REVERT: AB14 51 LYS cc_start: 0.8005 (tptt) cc_final: 0.7709 (tppt) REVERT: AB15 51 LYS cc_start: 0.8159 (tppp) cc_final: 0.7732 (tppt) REVERT: EF2 305 ASN cc_start: 0.8418 (m-40) cc_final: 0.7958 (m-40) REVERT: EF4 259 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.7822 (t0) REVERT: EF4 305 ASN cc_start: 0.8402 (m-40) cc_final: 0.8073 (m-40) REVERT: EF5 196 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6772 (ttm-80) REVERT: EF6 196 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6808 (ttm-80) REVERT: EF6 207 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7072 (mp0) REVERT: EF6 259 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.7755 (t70) REVERT: EF8 238 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7467 (mm-40) REVERT: EF8 239 MET cc_start: 0.8559 (mtm) cc_final: 0.8183 (mtp) REVERT: EF8 244 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: EF8 259 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7717 (t0) REVERT: EF9 207 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7138 (mp0) REVERT: EF9 221 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8134 (p) REVERT: EF9 241 ASN cc_start: 0.8817 (m-40) cc_final: 0.8086 (m-40) REVERT: EF10 241 ASN cc_start: 0.8776 (m-40) cc_final: 0.7962 (m110) REVERT: EF10 268 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7381 (ttm170) REVERT: EF10 384 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: EF11 268 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7470 (ttp-110) REVERT: EF12 279 ASP cc_start: 0.7972 (m-30) cc_final: 0.7608 (m-30) REVERT: EF12 305 ASN cc_start: 0.8632 (m-40) cc_final: 0.8406 (m-40) REVERT: EF13 223 ASP cc_start: 0.8086 (t0) cc_final: 0.7870 (m-30) REVERT: EF14 238 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7506 (mm-40) REVERT: EF16 223 ASP cc_start: 0.8216 (t0) cc_final: 0.7947 (m-30) REVERT: EF16 279 ASP cc_start: 0.7916 (m-30) cc_final: 0.7577 (m-30) outliers start: 129 outliers final: 96 residues processed: 524 average time/residue: 0.5979 time to fit residues: 371.3803 Evaluate side-chains 502 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 391 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB1 residue 23 SER Chi-restraints excluded: chain AB2 residue 23 SER Chi-restraints excluded: chain AB2 residue 27 CYS Chi-restraints excluded: chain AB3 residue 37 THR Chi-restraints excluded: chain AB3 residue 48 LYS Chi-restraints excluded: chain AB4 residue 52 GLN Chi-restraints excluded: chain AB6 residue 52 GLN Chi-restraints excluded: chain AB8 residue 37 THR Chi-restraints excluded: chain AB9 residue 27 CYS Chi-restraints excluded: chain AB9 residue 48 LYS Chi-restraints excluded: chain AB9 residue 52 GLN Chi-restraints excluded: chain AB10 residue 27 CYS Chi-restraints excluded: chain AB12 residue 27 CYS Chi-restraints excluded: chain AB15 residue 27 CYS Chi-restraints excluded: chain AB16 residue 27 CYS Chi-restraints excluded: chain EF1 residue 202 SER Chi-restraints excluded: chain EF1 residue 206 VAL Chi-restraints excluded: chain EF1 residue 209 ILE Chi-restraints excluded: chain EF1 residue 221 THR Chi-restraints excluded: chain EF1 residue 260 VAL Chi-restraints excluded: chain EF2 residue 202 SER Chi-restraints excluded: chain EF2 residue 206 VAL Chi-restraints excluded: chain EF2 residue 221 THR Chi-restraints excluded: chain EF2 residue 260 VAL Chi-restraints excluded: chain EF2 residue 261 SER Chi-restraints excluded: chain EF3 residue 209 ILE Chi-restraints excluded: chain EF3 residue 260 VAL Chi-restraints excluded: chain EF3 residue 261 SER Chi-restraints excluded: chain EF3 residue 395 LEU Chi-restraints excluded: chain EF4 residue 209 ILE Chi-restraints excluded: chain EF4 residue 221 THR Chi-restraints excluded: chain EF4 residue 259 ASP Chi-restraints excluded: chain EF4 residue 260 VAL Chi-restraints excluded: chain EF4 residue 355 VAL Chi-restraints excluded: chain EF5 residue 196 ARG Chi-restraints excluded: chain EF5 residue 260 VAL Chi-restraints excluded: chain EF6 residue 196 ARG Chi-restraints excluded: chain EF6 residue 209 ILE Chi-restraints excluded: chain EF6 residue 221 THR Chi-restraints excluded: chain EF6 residue 259 ASP Chi-restraints excluded: chain EF6 residue 260 VAL Chi-restraints excluded: chain EF6 residue 261 SER Chi-restraints excluded: chain EF6 residue 267 VAL Chi-restraints excluded: chain EF6 residue 355 VAL Chi-restraints excluded: chain EF7 residue 202 SER Chi-restraints excluded: chain EF7 residue 221 THR Chi-restraints excluded: chain EF7 residue 237 VAL Chi-restraints excluded: chain EF7 residue 260 VAL Chi-restraints excluded: chain EF7 residue 261 SER Chi-restraints excluded: chain EF7 residue 267 VAL Chi-restraints excluded: chain EF7 residue 271 SER Chi-restraints excluded: chain EF8 residue 206 VAL Chi-restraints excluded: chain EF8 residue 221 THR Chi-restraints excluded: chain EF8 residue 237 VAL Chi-restraints excluded: chain EF8 residue 238 GLN Chi-restraints excluded: chain EF8 residue 244 GLU Chi-restraints excluded: chain EF8 residue 259 ASP Chi-restraints excluded: chain EF8 residue 260 VAL Chi-restraints excluded: chain EF8 residue 261 SER Chi-restraints excluded: chain EF9 residue 206 VAL Chi-restraints excluded: chain EF9 residue 221 THR Chi-restraints excluded: chain EF9 residue 237 VAL Chi-restraints excluded: chain EF9 residue 261 SER Chi-restraints excluded: chain EF9 residue 267 VAL Chi-restraints excluded: chain EF10 residue 209 ILE Chi-restraints excluded: chain EF10 residue 221 THR Chi-restraints excluded: chain EF10 residue 237 VAL Chi-restraints excluded: chain EF10 residue 261 SER Chi-restraints excluded: chain EF10 residue 267 VAL Chi-restraints excluded: chain EF10 residue 268 ARG Chi-restraints excluded: chain EF10 residue 271 SER Chi-restraints excluded: chain EF10 residue 273 SER Chi-restraints excluded: chain EF10 residue 292 MET Chi-restraints excluded: chain EF10 residue 384 GLU Chi-restraints excluded: chain EF11 residue 206 VAL Chi-restraints excluded: chain EF11 residue 221 THR Chi-restraints excluded: chain EF11 residue 237 VAL Chi-restraints excluded: chain EF11 residue 261 SER Chi-restraints excluded: chain EF11 residue 267 VAL Chi-restraints excluded: chain EF11 residue 268 ARG Chi-restraints excluded: chain EF11 residue 292 MET Chi-restraints excluded: chain EF11 residue 384 GLU Chi-restraints excluded: chain EF12 residue 206 VAL Chi-restraints excluded: chain EF12 residue 209 ILE Chi-restraints excluded: chain EF12 residue 221 THR Chi-restraints excluded: chain EF12 residue 261 SER Chi-restraints excluded: chain EF12 residue 267 VAL Chi-restraints excluded: chain EF13 residue 200 ILE Chi-restraints excluded: chain EF13 residue 206 VAL Chi-restraints excluded: chain EF13 residue 221 THR Chi-restraints excluded: chain EF13 residue 253 THR Chi-restraints excluded: chain EF13 residue 267 VAL Chi-restraints excluded: chain EF13 residue 303 MET Chi-restraints excluded: chain EF13 residue 384 GLU Chi-restraints excluded: chain EF14 residue 206 VAL Chi-restraints excluded: chain EF14 residue 221 THR Chi-restraints excluded: chain EF14 residue 237 VAL Chi-restraints excluded: chain EF14 residue 238 GLN Chi-restraints excluded: chain EF14 residue 261 SER Chi-restraints excluded: chain EF15 residue 206 VAL Chi-restraints excluded: chain EF15 residue 209 ILE Chi-restraints excluded: chain EF15 residue 221 THR Chi-restraints excluded: chain EF15 residue 261 SER Chi-restraints excluded: chain EF15 residue 355 VAL Chi-restraints excluded: chain EF16 residue 206 VAL Chi-restraints excluded: chain EF16 residue 253 THR Chi-restraints excluded: chain EF17 residue 209 ILE Chi-restraints excluded: chain EF17 residue 221 THR Chi-restraints excluded: chain EF17 residue 260 VAL Chi-restraints excluded: chain EF17 residue 261 SER Chi-restraints excluded: chain EF17 residue 267 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [209, 263, 72, 264, 75, 235, 84, 37, 336, 271, 60] chunk 209 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 264 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 235 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 336 optimal weight: 0.4980 chunk 271 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.099859 restraints weight = 38922.016| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.49 r_work: 0.3006 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30124 Z= 0.138 Angle : 0.488 7.591 40511 Z= 0.259 Chirality : 0.039 0.150 4539 Planarity : 0.004 0.037 5304 Dihedral : 4.338 57.501 4179 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.68 % Allowed : 30.18 % Favored : 66.14 % 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: 0.63 (0.14), residues: 3876 helix: 2.81 (0.15), residues: 1190 sheet: -0.17 (0.17), residues: 935 loop : -0.96 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAB2 46 TYR 0.013 0.001 TYREF17 373 PHE 0.008 0.001 PHEEF12 317 TRP 0.007 0.001 TRPEF11 199 HIS 0.003 0.001 HISEF12 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (30090) covalent geometry : angle 0.48809 / 0.26 (40443) SS BOND : bond 0.00136 / 0.09 ( 34) SS BOND : angle 0.25598 / 0.16 ( 68) hydrogen bonds : bond 0.02877 / 1.90 ( 1156) hydrogen bonds : angle 4.43214 / 2.96 ( 3213) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 10981.14 seconds wall clock time: 186 minutes 29.46 seconds (11189.46 seconds total)