Starting phenix.real_space_refine on Sun Jul 5 21:20:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7spc_24770/07_2026/7spc_24770.cif Found real_map, /net/cci-nas-00/data/ceres_data/7spc_24770/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7spc_24770/07_2026/7spc_24770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7spc_24770/07_2026/7spc_24770.map" model { file = "/net/cci-nas-00/data/ceres_data/7spc_24770/07_2026/7spc_24770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7spc_24770/07_2026/7spc_24770.cif" } 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-dev-6108/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: 3.17, 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=17, 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 CYSAB3 27 " - pdb=" SG CYSAB2 35 " distance=2.35 Simple disulfide: pdb=" SG CYSAB4 27 " - pdb=" SG CYSAB3 35 " distance=2.35 Simple disulfide: pdb=" SG CYSAB5 27 " - pdb=" SG CYSAB4 35 " distance=2.35 Simple disulfide: pdb=" SG CYSAB6 27 " - pdb=" SG CYSAB5 35 " distance=2.35 Simple disulfide: pdb=" SG CYSAB7 27 " - pdb=" SG CYSAB6 35 " distance=2.35 Simple disulfide: pdb=" SG CYSAB8 27 " - pdb=" SG CYSAB7 35 " distance=2.35 Simple disulfide: pdb=" SG CYSAB9 27 " - pdb=" SG CYSAB8 35 " distance=2.35 Simple disulfide: pdb=" SG CYSAB10 27 " - pdb=" SG CYSAB9 35 " distance=2.35 Simple disulfide: pdb=" SG CYSAB11 27 " - pdb=" SG CYSAB10 35 " distance=2.35 Simple disulfide: pdb=" SG CYSAB12 27 " - pdb=" SG CYSAB11 35 " distance=2.35 Simple disulfide: pdb=" SG CYSAB13 27 " - pdb=" SG CYSAB12 35 " distance=2.35 Simple disulfide: pdb=" SG CYSAB14 27 " - pdb=" SG CYSAB13 35 " distance=2.35 Simple disulfide: pdb=" SG CYSAB15 27 " - pdb=" SG CYSAB14 35 " distance=2.35 Simple disulfide: pdb=" SG CYSAB16 27 " - pdb=" SG CYSAB15 35 " distance=2.35 Simple disulfide: pdb=" SG CYSAB17 27 " - pdb=" SG CYSAB16 35 " distance=2.35 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: 2.58 Conformation dependent library (CDL) restraints added in 1.6 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: 0.88 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: 6.46 Time building geometry restraints manager: 3.44 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: 1866 31.74 - 47.60: 527 47.60 - 63.47: 288 63.47 - 79.34: 35 Dihedral angle restraints: 18309 sinusoidal: 7140 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 18306 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: 2.03 - 2.60: 357 2.60 - 3.18: 25337 3.18 - 3.75: 46019 3.75 - 4.33: 65155 4.33 - 4.90: 107937 Nonbonded interactions: 244805 Sorted by model distance: nonbonded pdb=" SG CYSEF17 250 " pdb=" SG CYSEF17 274 " model vdw 2.028 3.760 nonbonded pdb=" SG CYSEF14 250 " pdb=" SG CYSEF14 274 " model vdw 2.029 3.760 nonbonded pdb=" SG CYSEF8 250 " pdb=" SG CYSEF8 274 " model vdw 2.029 3.760 nonbonded pdb=" SG CYSEF7 250 " pdb=" SG CYSEF7 274 " model vdw 2.029 3.760 nonbonded pdb=" SG CYSEF2 250 " pdb=" SG CYSEF2 274 " model vdw 2.029 3.760 ... (remaining 244800 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: 4.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.180 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.130 ------------------------------------------------------------------------------- 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 30107 Z= 0.782 Angle : 1.130 9.629 40477 Z= 0.821 Chirality : 0.073 0.350 4539 Planarity : 0.006 0.053 5304 Dihedral : 16.548 79.340 11084 Min Nonbonded Distance : 2.028 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 0.31780 / 20.84 ( 17) SS BOND : angle 0.19767 / 0.13 ( 34) 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 : 1.246 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: 0.7125 time to fit residues: 792.5947 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 : 1.159 ------------------------------------------------------------------------------- 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: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 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: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.139004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.109374 restraints weight = 37907.209| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.57 r_work: 0.3168 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30107 Z= 0.139 Angle : 0.489 7.904 40477 Z= 0.270 Chirality : 0.040 0.131 4539 Planarity : 0.004 0.047 5304 Dihedral : 5.275 57.374 4217 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 6.30 % Allowed : 28.80 % Favored : 64.90 % 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: 0.02 (0.13), residues: 3876 helix: 1.87 (0.14), residues: 1292 sheet: -0.06 (0.17), residues: 986 loop : -1.52 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGEF13 304 TYR 0.009 0.001 TYREF9 366 PHE 0.015 0.001 PHEEF10 197 TRP 0.013 0.002 TRPEF13 199 HIS 0.003 0.001 HISEF10 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (30090) covalent geometry : angle 0.48856 / 0.27 (40443) SS BOND : bond 0.00219 / 0.15 ( 17) SS BOND : angle 0.72635 / 0.47 ( 34) hydrogen bonds : bond 0.03337 / 2.21 ( 1156) hydrogen bonds : angle 5.14798 / 3.45 ( 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 726 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 529 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AB2 51 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7909 (tppt) REVERT: AB2 52 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.6362 (mp-120) REVERT: AB3 51 LYS cc_start: 0.7676 (tptt) cc_final: 0.7416 (tppt) REVERT: AB6 48 LYS cc_start: 0.7160 (tttp) cc_final: 0.6423 (tttt) REVERT: AB6 51 LYS cc_start: 0.7463 (tppp) cc_final: 0.7163 (tppt) REVERT: AB6 52 GLN cc_start: 0.6747 (OUTLIER) cc_final: 0.5535 (mp-120) REVERT: AB7 48 LYS cc_start: 0.7197 (tttp) cc_final: 0.6914 (tttt) REVERT: AB7 52 GLN cc_start: 0.6650 (OUTLIER) cc_final: 0.5823 (mp-120) REVERT: AB8 36 MET cc_start: 0.8409 (ttm) cc_final: 0.8087 (ttm) REVERT: AB9 43 GLN cc_start: 0.7426 (tp-100) cc_final: 0.7217 (tp40) REVERT: AB11 51 LYS cc_start: 0.8194 (tppp) cc_final: 0.7977 (tppt) REVERT: AB12 47 ASP cc_start: 0.7817 (m-30) cc_final: 0.7613 (m-30) REVERT: AB12 51 LYS cc_start: 0.8017 (tptt) cc_final: 0.7748 (tppt) REVERT: AB13 51 LYS cc_start: 0.8049 (tptt) cc_final: 0.7786 (tppt) REVERT: AB14 51 LYS cc_start: 0.8059 (tptt) cc_final: 0.7835 (tppt) REVERT: AB15 51 LYS cc_start: 0.8185 (tppp) cc_final: 0.7775 (tppt) REVERT: AB16 51 LYS cc_start: 0.8074 (tppp) cc_final: 0.7735 (tppt) REVERT: EF1 223 ASP cc_start: 0.8182 (t0) cc_final: 0.7673 (m-30) REVERT: EF2 207 GLU cc_start: 0.7811 (mp0) cc_final: 0.7491 (mt-10) REVERT: EF2 223 ASP cc_start: 0.8332 (t0) cc_final: 0.7790 (m-30) REVERT: EF2 284 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8649 (mmmt) REVERT: EF3 384 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8088 (mt-10) REVERT: EF4 221 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8589 (p) REVERT: EF4 244 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8307 (mt-10) REVERT: EF5 243 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7638 (mm-30) REVERT: EF5 284 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8588 (mmmt) REVERT: EF6 221 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8321 (t) REVERT: EF6 259 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7854 (t0) REVERT: EF6 284 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8661 (mmmt) REVERT: EF6 364 ASP cc_start: 0.7874 (t70) cc_final: 0.7543 (t0) REVERT: EF8 221 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.7947 (p) REVERT: EF8 225 ASN cc_start: 0.8758 (m-40) cc_final: 0.8556 (m110) REVERT: EF8 239 MET cc_start: 0.8353 (mtm) cc_final: 0.8095 (mtm) REVERT: EF9 364 ASP cc_start: 0.7913 (t70) cc_final: 0.7471 (t0) REVERT: EF10 364 ASP cc_start: 0.7941 (t70) cc_final: 0.7616 (t0) REVERT: EF11 239 MET cc_start: 0.8493 (mtm) cc_final: 0.8275 (mtm) REVERT: EF11 259 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7738 (t0) REVERT: EF12 243 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7487 (mm-30) REVERT: EF13 197 PHE cc_start: 0.9227 (m-80) cc_final: 0.8819 (m-80) REVERT: EF13 239 MET cc_start: 0.8843 (mtm) cc_final: 0.8529 (mtp) REVERT: EF13 259 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7950 (t0) REVERT: EF14 238 GLN cc_start: 0.8397 (mt0) cc_final: 0.8041 (mm-40) REVERT: EF14 244 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8398 (mt-10) REVERT: EF15 239 MET cc_start: 0.8920 (mtm) cc_final: 0.8707 (mtp) REVERT: EF15 259 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8094 (t0) REVERT: EF16 223 ASP cc_start: 0.8337 (t0) cc_final: 0.7903 (m-30) REVERT: EF16 244 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8333 (mt-10) REVERT: EF16 391 ASP cc_start: 0.8901 (m-30) cc_final: 0.8689 (m-30) REVERT: EF17 244 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8431 (mt-10) outliers start: 197 outliers final: 72 residues processed: 697 average time/residue: 0.6193 time to fit residues: 511.9594 Evaluate side-chains 560 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 470 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB2 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 27 CYS Chi-restraints excluded: chain AB7 residue 52 GLN Chi-restraints excluded: chain AB8 residue 27 CYS Chi-restraints excluded: chain AB8 residue 37 THR Chi-restraints excluded: chain AB9 residue 27 CYS Chi-restraints excluded: chain AB9 residue 52 GLN Chi-restraints excluded: chain EF1 residue 202 SER 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 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 284 LYS Chi-restraints excluded: chain EF3 residue 260 VAL 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 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 237 VAL Chi-restraints excluded: chain EF9 residue 244 GLU Chi-restraints excluded: chain EF9 residue 260 VAL 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 259 ASP 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 355 VAL 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 278 ASP 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 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: chunk 335 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 272 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 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: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.128044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.098082 restraints weight = 38762.679| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.56 r_work: 0.2989 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 30107 Z= 0.306 Angle : 0.601 7.796 40477 Z= 0.323 Chirality : 0.043 0.149 4539 Planarity : 0.004 0.042 5304 Dihedral : 5.678 57.837 4198 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.71 % Allowed : 27.11 % Favored : 66.18 % 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: 0.03 (0.13), residues: 3876 helix: 1.88 (0.14), residues: 1292 sheet: -0.41 (0.19), residues: 765 loop : -1.18 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAB15 46 TYR 0.013 0.002 TYREF12 373 PHE 0.013 0.002 PHEEF2 197 TRP 0.006 0.002 TRPEF16 199 HIS 0.004 0.001 HISEF17 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.31 (30090) covalent geometry : angle 0.60117 / 0.32 (40443) SS BOND : bond 0.00096 / 0.06 ( 17) SS BOND : angle 0.64672 / 0.44 ( 34) hydrogen bonds : bond 0.04300 / 2.84 ( 1156) hydrogen bonds : angle 5.25151 / 3.51 ( 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 697 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 487 time to evaluate : 1.137 Fit side-chains REVERT: AB2 52 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7261 (mm-40) REVERT: AB4 52 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6348 (mp-120) REVERT: AB6 51 LYS cc_start: 0.7797 (tppp) cc_final: 0.7541 (tppt) REVERT: AB6 52 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.7011 (mm-40) REVERT: AB7 48 LYS cc_start: 0.7403 (tttp) cc_final: 0.6674 (tttt) REVERT: AB7 52 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6069 (mp-120) REVERT: AB8 36 MET cc_start: 0.8459 (ttm) cc_final: 0.8062 (ttm) REVERT: AB9 52 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.6071 (mp-120) REVERT: AB11 51 LYS cc_start: 0.8083 (tppp) cc_final: 0.7767 (tppt) REVERT: AB12 51 LYS cc_start: 0.8158 (tptt) cc_final: 0.7735 (tppt) REVERT: AB13 51 LYS cc_start: 0.8134 (tptt) cc_final: 0.7842 (tppt) REVERT: AB14 51 LYS cc_start: 0.8111 (tptt) cc_final: 0.7736 (tppt) REVERT: AB15 51 LYS cc_start: 0.8188 (tppp) cc_final: 0.7757 (tppt) REVERT: AB16 51 LYS cc_start: 0.8281 (tppp) cc_final: 0.8056 (tppt) REVERT: EF1 196 ARG cc_start: 0.8078 (mtt90) cc_final: 0.7770 (mpp80) REVERT: EF1 364 ASP cc_start: 0.8125 (t70) cc_final: 0.7685 (t0) REVERT: EF2 268 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7877 (ttp-110) REVERT: EF3 229 MET cc_start: 0.7818 (ttm) cc_final: 0.7554 (ttp) REVERT: EF4 221 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8451 (p) REVERT: EF4 244 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8357 (mt-10) REVERT: EF4 305 ASN cc_start: 0.8416 (m-40) cc_final: 0.8037 (m-40) REVERT: EF4 399 GLU cc_start: 0.7414 (mp0) cc_final: 0.7135 (pm20) REVERT: EF5 305 ASN cc_start: 0.8397 (m-40) cc_final: 0.8101 (m-40) REVERT: EF6 284 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8758 (mmmt) REVERT: EF7 196 ARG cc_start: 0.7994 (mtt90) cc_final: 0.7601 (mpp80) REVERT: EF8 221 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8355 (p) REVERT: EF8 239 MET cc_start: 0.8752 (mtm) cc_final: 0.8458 (mtm) REVERT: EF8 391 ASP cc_start: 0.8922 (m-30) cc_final: 0.8706 (m-30) REVERT: EF9 221 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8247 (p) REVERT: EF9 223 ASP cc_start: 0.8381 (t0) cc_final: 0.7735 (m-30) REVERT: EF9 364 ASP cc_start: 0.7978 (t70) cc_final: 0.7537 (t0) REVERT: EF10 223 ASP cc_start: 0.8289 (t0) cc_final: 0.7797 (m-30) REVERT: EF10 239 MET cc_start: 0.8831 (mtm) cc_final: 0.8517 (mtp) REVERT: EF10 241 ASN cc_start: 0.9017 (m-40) cc_final: 0.8324 (m-40) REVERT: EF10 268 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7552 (ttm170) REVERT: EF10 364 ASP cc_start: 0.8129 (t70) cc_final: 0.7782 (t0) REVERT: EF11 253 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8559 (m) REVERT: EF11 259 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8212 (t70) REVERT: EF12 305 ASN cc_start: 0.8663 (m-40) cc_final: 0.8444 (m-40) REVERT: EF14 223 ASP cc_start: 0.8527 (t0) cc_final: 0.8069 (m-30) REVERT: EF14 238 GLN cc_start: 0.8439 (mt0) cc_final: 0.8172 (mt0) REVERT: EF14 268 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7773 (ttp-110) REVERT: EF14 305 ASN cc_start: 0.8565 (m-40) cc_final: 0.8313 (m-40) REVERT: EF14 364 ASP cc_start: 0.7828 (t70) cc_final: 0.7493 (t0) REVERT: EF14 384 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7974 (mt-10) REVERT: EF15 239 MET cc_start: 0.8979 (mtm) cc_final: 0.8745 (mtp) REVERT: EF16 223 ASP cc_start: 0.8311 (t0) cc_final: 0.8051 (m-30) REVERT: EF16 305 ASN cc_start: 0.8578 (m-40) cc_final: 0.8241 (m-40) REVERT: EF16 391 ASP cc_start: 0.8983 (m-30) cc_final: 0.8772 (m-30) REVERT: EF17 244 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8305 (mt-10) outliers start: 210 outliers final: 100 residues processed: 660 average time/residue: 0.5891 time to fit residues: 463.0563 Evaluate side-chains 529 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 412 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 AB2 residue 52 GLN Chi-restraints excluded: chain AB3 residue 23 SER Chi-restraints excluded: chain AB4 residue 23 SER 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 52 GLN Chi-restraints excluded: chain AB8 residue 23 SER Chi-restraints excluded: chain AB8 residue 37 THR 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 23 SER Chi-restraints excluded: chain AB12 residue 27 CYS Chi-restraints excluded: chain AB13 residue 23 SER Chi-restraints excluded: chain AB14 residue 34 THR Chi-restraints excluded: chain AB15 residue 23 SER 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 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 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 EF2 residue 268 ARG 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 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 244 GLU Chi-restraints excluded: chain EF4 residue 260 VAL Chi-restraints excluded: chain EF4 residue 261 SER Chi-restraints excluded: chain EF5 residue 202 SER Chi-restraints excluded: chain EF5 residue 221 THR Chi-restraints excluded: chain EF5 residue 260 VAL Chi-restraints excluded: chain EF5 residue 261 SER Chi-restraints excluded: chain EF6 residue 202 SER Chi-restraints excluded: chain EF6 residue 221 THR 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 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 209 ILE 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 261 SER Chi-restraints excluded: chain EF9 residue 267 VAL Chi-restraints excluded: chain EF10 residue 202 SER 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 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 EF11 residue 253 THR Chi-restraints excluded: chain EF11 residue 259 ASP Chi-restraints excluded: chain EF11 residue 267 VAL 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 237 VAL 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 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 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 253 THR 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 234 THR Chi-restraints excluded: chain EF15 residue 273 SER Chi-restraints excluded: chain EF15 residue 395 LEU Chi-restraints excluded: chain EF16 residue 206 VAL Chi-restraints excluded: chain EF16 residue 261 SER Chi-restraints excluded: chain EF17 residue 202 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 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: chunk 263 optimal weight: 0.7980 chunk 228 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 365 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 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 = 0.3576 r_free = 0.3576 target = 0.131316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.101669 restraints weight = 37880.851| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.55 r_work: 0.3063 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30107 Z= 0.123 Angle : 0.464 5.841 40477 Z= 0.251 Chirality : 0.039 0.149 4539 Planarity : 0.004 0.037 5304 Dihedral : 4.886 59.249 4192 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.21 % Allowed : 28.93 % Favored : 65.86 % 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: 0.35 (0.14), residues: 3876 helix: 2.21 (0.15), residues: 1292 sheet: -0.45 (0.19), residues: 765 loop : -0.92 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGEF11 304 TYR 0.012 0.001 TYREF15 373 PHE 0.010 0.001 PHEEF12 317 TRP 0.007 0.001 TRPEF11 257 HIS 0.005 0.001 HISEF11 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (30090) covalent geometry : angle 0.46427 / 0.25 (40443) SS BOND : bond 0.00086 / 0.06 ( 17) SS BOND : angle 0.49978 / 0.34 ( 34) hydrogen bonds : bond 0.02904 / 1.93 ( 1156) hydrogen bonds : angle 4.79091 / 3.19 ( 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 579 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 416 time to evaluate : 1.088 Fit side-chains REVERT: AB2 52 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.6975 (mm-40) REVERT: AB4 52 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6082 (mp-120) REVERT: AB5 51 LYS cc_start: 0.7725 (tppt) cc_final: 0.7268 (tppt) REVERT: AB6 51 LYS cc_start: 0.7786 (tppp) cc_final: 0.7503 (tppt) REVERT: AB6 52 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.5939 (mp-120) REVERT: AB7 48 LYS cc_start: 0.7224 (tttp) cc_final: 0.6513 (tttt) REVERT: AB7 52 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.5917 (mp-120) REVERT: AB9 52 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6023 (mp-120) REVERT: AB11 51 LYS cc_start: 0.8079 (tppp) cc_final: 0.7805 (tppt) REVERT: AB12 23 SER cc_start: 0.8624 (t) cc_final: 0.8375 (m) REVERT: AB12 51 LYS cc_start: 0.8128 (tptt) cc_final: 0.7748 (tppt) REVERT: AB13 51 LYS cc_start: 0.8106 (tptt) cc_final: 0.7838 (tppt) REVERT: AB14 51 LYS cc_start: 0.8080 (tptt) cc_final: 0.7788 (tppt) REVERT: AB15 51 LYS cc_start: 0.8185 (tppp) cc_final: 0.7794 (tppt) REVERT: EF1 244 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8410 (mt-10) REVERT: EF1 364 ASP cc_start: 0.7956 (t70) cc_final: 0.7532 (t0) REVERT: EF1 384 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7740 (mt-10) REVERT: EF3 244 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8366 (mt-10) REVERT: EF4 221 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8489 (p) REVERT: EF4 243 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7591 (mm-30) REVERT: EF4 244 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8464 (mt-10) REVERT: EF4 305 ASN cc_start: 0.8376 (m-40) cc_final: 0.8089 (m-40) REVERT: EF4 399 GLU cc_start: 0.7391 (mp0) cc_final: 0.7151 (pm20) REVERT: EF5 239 MET cc_start: 0.8952 (mtm) cc_final: 0.8750 (mtp) REVERT: EF8 196 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7525 (mtm180) REVERT: EF8 221 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8428 (p) REVERT: EF8 239 MET cc_start: 0.8688 (mtm) cc_final: 0.8375 (mtp) REVERT: EF9 221 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8189 (p) REVERT: EF9 241 ASN cc_start: 0.8831 (m-40) cc_final: 0.8044 (m-40) REVERT: EF10 241 ASN cc_start: 0.8883 (m-40) cc_final: 0.8224 (m-40) REVERT: EF10 259 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.7802 (t0) REVERT: EF10 384 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8120 (mt-10) REVERT: EF11 229 MET cc_start: 0.7829 (ttm) cc_final: 0.7406 (ttp) REVERT: EF12 244 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8457 (mt-10) REVERT: EF13 223 ASP cc_start: 0.8186 (t0) cc_final: 0.7905 (m-30) REVERT: EF13 242 ASP cc_start: 0.8804 (m-30) cc_final: 0.8529 (m-30) REVERT: EF13 384 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7927 (mt-10) REVERT: EF14 244 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8524 (mt-10) REVERT: EF14 384 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: EF16 221 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8430 (p) REVERT: EF16 223 ASP cc_start: 0.8292 (t0) cc_final: 0.8070 (m-30) REVERT: EF16 244 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8333 (mt-10) REVERT: EF16 391 ASP cc_start: 0.8916 (m-30) cc_final: 0.8709 (m-30) REVERT: EF17 244 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8427 (mt-10) REVERT: EF17 305 ASN cc_start: 0.8371 (m-40) cc_final: 0.8167 (m-40) outliers start: 163 outliers final: 77 residues processed: 553 average time/residue: 0.6367 time to fit residues: 414.6155 Evaluate side-chains 497 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 401 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 52 GLN 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 AB9 residue 27 CYS 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 EF1 residue 206 VAL Chi-restraints excluded: chain EF1 residue 221 THR Chi-restraints excluded: chain EF1 residue 244 GLU Chi-restraints excluded: chain EF1 residue 260 VAL Chi-restraints excluded: chain EF1 residue 261 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 209 ILE Chi-restraints excluded: chain EF3 residue 244 GLU 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 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 209 ILE Chi-restraints excluded: chain EF6 residue 221 THR Chi-restraints excluded: chain EF6 residue 253 THR 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 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 223 ASP 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 206 VAL Chi-restraints excluded: chain EF9 residue 221 THR 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 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 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 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 237 VAL Chi-restraints excluded: chain EF12 residue 244 GLU 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 267 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 56 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 257 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 273 optimal weight: 9.9990 chunk 348 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.130493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.100817 restraints weight = 38173.136| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.55 r_work: 0.3052 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30107 Z= 0.162 Angle : 0.485 6.185 40477 Z= 0.260 Chirality : 0.040 0.142 4539 Planarity : 0.004 0.038 5304 Dihedral : 4.830 59.748 4190 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.53 % Allowed : 29.09 % Favored : 65.38 % 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: 0.36 (0.14), residues: 3876 helix: 2.22 (0.15), residues: 1292 sheet: -0.51 (0.19), residues: 765 loop : -0.88 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAB14 46 TYR 0.015 0.001 TYREF15 373 PHE 0.009 0.001 PHEEF12 317 TRP 0.006 0.001 TRPEF7 257 HIS 0.003 0.001 HISEF4 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (30090) covalent geometry : angle 0.48466 / 0.26 (40443) SS BOND : bond 0.00080 / 0.05 ( 17) SS BOND : angle 0.42449 / 0.29 ( 34) hydrogen bonds : bond 0.03137 / 2.08 ( 1156) hydrogen bonds : angle 4.67369 / 3.11 ( 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 576 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 403 time to evaluate : 1.200 Fit side-chains REVERT: AB2 52 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.7118 (mm-40) REVERT: AB4 52 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6080 (mp-120) REVERT: AB6 51 LYS cc_start: 0.7802 (tppp) cc_final: 0.7543 (tppt) REVERT: AB6 52 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6968 (mm110) REVERT: AB7 48 LYS cc_start: 0.7342 (tttp) cc_final: 0.6589 (tttt) REVERT: AB7 52 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.5960 (mp-120) REVERT: AB9 52 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6054 (mp-120) REVERT: AB11 51 LYS cc_start: 0.8041 (tppp) cc_final: 0.7748 (tppt) REVERT: AB12 51 LYS cc_start: 0.8106 (tptt) cc_final: 0.7760 (tppt) REVERT: AB13 51 LYS cc_start: 0.8111 (tptt) cc_final: 0.7824 (tppt) REVERT: AB14 51 LYS cc_start: 0.8073 (tptt) cc_final: 0.7778 (tppt) REVERT: AB15 51 LYS cc_start: 0.8170 (tppp) cc_final: 0.7768 (tppt) REVERT: AB16 51 LYS cc_start: 0.8363 (tppt) cc_final: 0.8077 (tppt) REVERT: EF1 196 ARG cc_start: 0.7689 (ttm-80) cc_final: 0.7194 (mpp80) REVERT: EF1 364 ASP cc_start: 0.7955 (t70) cc_final: 0.7518 (t0) REVERT: EF2 207 GLU cc_start: 0.8107 (mp0) cc_final: 0.7780 (mt-10) REVERT: EF2 259 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8105 (t0) REVERT: EF3 244 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8221 (mt-10) REVERT: EF4 221 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8488 (p) REVERT: EF4 243 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7509 (mm-30) REVERT: EF4 244 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8438 (mt-10) REVERT: EF4 305 ASN cc_start: 0.8370 (m-40) cc_final: 0.8086 (m-40) REVERT: EF6 259 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.7846 (t0) REVERT: EF8 196 ARG cc_start: 0.7809 (mtm-85) cc_final: 0.7528 (mtm180) REVERT: EF8 221 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8385 (p) REVERT: EF8 239 MET cc_start: 0.8677 (mtm) cc_final: 0.8344 (mtp) REVERT: EF8 391 ASP cc_start: 0.8825 (m-30) cc_final: 0.8615 (m-30) REVERT: EF9 207 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7240 (mp0) REVERT: EF9 221 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8171 (p) REVERT: EF9 241 ASN cc_start: 0.8862 (m-40) cc_final: 0.8184 (m-40) REVERT: EF9 384 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: EF10 200 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8009 (mm) REVERT: EF10 241 ASN cc_start: 0.8984 (m-40) cc_final: 0.8272 (m-40) REVERT: EF10 259 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.7781 (t0) REVERT: EF10 268 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7502 (ttm170) REVERT: EF11 259 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.7705 (t0) REVERT: EF13 384 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: EF14 241 ASN cc_start: 0.8986 (m110) cc_final: 0.8610 (m-40) REVERT: EF14 244 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8510 (mt-10) REVERT: EF14 355 VAL cc_start: 0.6025 (OUTLIER) cc_final: 0.5753 (p) REVERT: EF15 259 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.7762 (t0) REVERT: EF16 221 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8448 (p) REVERT: EF16 223 ASP cc_start: 0.8277 (t0) cc_final: 0.8046 (m-30) REVERT: EF16 244 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8393 (mt-10) REVERT: EF16 391 ASP cc_start: 0.8927 (m-30) cc_final: 0.8726 (m-30) REVERT: EF17 244 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8420 (mt-10) outliers start: 173 outliers final: 105 residues processed: 555 average time/residue: 0.6073 time to fit residues: 398.5296 Evaluate side-chains 517 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 388 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 34 THR Chi-restraints excluded: chain AB2 residue 52 GLN 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 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 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 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 355 VAL 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 259 ASP Chi-restraints excluded: chain EF2 residue 260 VAL Chi-restraints excluded: chain EF2 residue 261 SER Chi-restraints excluded: chain EF2 residue 271 SER Chi-restraints excluded: chain EF3 residue 206 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 260 VAL Chi-restraints excluded: chain EF5 residue 261 SER Chi-restraints excluded: chain EF6 residue 209 ILE Chi-restraints excluded: chain EF6 residue 221 THR Chi-restraints excluded: chain EF6 residue 253 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 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 271 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 223 ASP 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 206 VAL Chi-restraints excluded: chain EF9 residue 209 ILE 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 EF9 residue 384 GLU Chi-restraints excluded: chain EF10 residue 200 ILE 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 EF11 residue 206 VAL Chi-restraints excluded: chain EF11 residue 221 THR Chi-restraints excluded: chain EF11 residue 259 ASP Chi-restraints excluded: chain EF11 residue 261 SER Chi-restraints excluded: chain EF11 residue 267 VAL 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 237 VAL 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 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 244 GLU Chi-restraints excluded: chain EF14 residue 355 VAL 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 209 ILE Chi-restraints excluded: chain EF16 residue 221 THR Chi-restraints excluded: chain EF16 residue 244 GLU Chi-restraints excluded: chain EF16 residue 253 THR Chi-restraints excluded: chain EF16 residue 261 SER 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 244 GLU 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: chunk 296 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 354 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 332 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.131499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102019 restraints weight = 37983.358| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.54 r_work: 0.3064 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30107 Z= 0.142 Angle : 0.468 6.133 40477 Z= 0.250 Chirality : 0.039 0.143 4539 Planarity : 0.004 0.037 5304 Dihedral : 4.674 59.771 4189 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.99 % Allowed : 29.57 % Favored : 65.44 % 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: 0.39 (0.14), residues: 3876 helix: 2.25 (0.15), residues: 1292 sheet: -0.52 (0.19), residues: 765 loop : -0.85 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAB2 46 TYR 0.014 0.001 TYREF17 373 PHE 0.008 0.001 PHEEF12 317 TRP 0.007 0.001 TRPEF11 199 HIS 0.003 0.001 HISEF4 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (30090) covalent geometry : angle 0.46775 / 0.25 (40443) SS BOND : bond 0.00080 / 0.05 ( 17) SS BOND : angle 0.34481 / 0.24 ( 34) hydrogen bonds : bond 0.02932 / 1.94 ( 1156) hydrogen bonds : angle 4.56298 / 3.04 ( 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 566 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 410 time to evaluate : 1.194 Fit side-chains REVERT: AB2 52 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.7104 (mm-40) REVERT: AB4 51 LYS cc_start: 0.8028 (tppt) cc_final: 0.7568 (tppt) REVERT: AB5 51 LYS cc_start: 0.7746 (tppt) cc_final: 0.7208 (tppt) REVERT: AB6 51 LYS cc_start: 0.7761 (tppp) cc_final: 0.7501 (tppt) REVERT: AB7 48 LYS cc_start: 0.7270 (tttp) cc_final: 0.6531 (tttt) REVERT: AB7 52 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6053 (mp-120) REVERT: AB9 52 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6065 (mp-120) REVERT: AB11 51 LYS cc_start: 0.8030 (tppp) cc_final: 0.7739 (tppt) REVERT: AB12 51 LYS cc_start: 0.8122 (tptt) cc_final: 0.7757 (tppt) REVERT: AB13 51 LYS cc_start: 0.8122 (tptt) cc_final: 0.7845 (tppt) REVERT: AB14 51 LYS cc_start: 0.8082 (tptt) cc_final: 0.7799 (tppt) REVERT: AB15 51 LYS cc_start: 0.8209 (tppp) cc_final: 0.7779 (tppt) REVERT: AB16 51 LYS cc_start: 0.8179 (tppt) cc_final: 0.7885 (tppt) REVERT: EF1 196 ARG cc_start: 0.7685 (ttm-80) cc_final: 0.7182 (mpp80) REVERT: EF1 364 ASP cc_start: 0.7952 (t70) cc_final: 0.7528 (t0) REVERT: EF1 384 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7753 (mt-10) REVERT: EF2 207 GLU cc_start: 0.8124 (mp0) cc_final: 0.7845 (mt-10) REVERT: EF2 268 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7695 (ttm170) REVERT: EF3 244 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8300 (mt-10) REVERT: EF4 221 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8500 (p) REVERT: EF4 243 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7530 (mm-30) REVERT: EF4 244 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8456 (mt-10) REVERT: EF4 305 ASN cc_start: 0.8370 (m-40) cc_final: 0.8102 (m-40) REVERT: EF6 207 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7301 (mp0) REVERT: EF6 259 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.7863 (t0) REVERT: EF7 303 MET cc_start: 0.8928 (tpt) cc_final: 0.8640 (tpt) REVERT: EF8 196 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7611 (mtm180) REVERT: EF8 221 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8465 (p) REVERT: EF8 239 MET cc_start: 0.8710 (mtm) cc_final: 0.8410 (mtp) REVERT: EF8 274 CYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7506 (m) REVERT: EF9 207 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7233 (mp0) REVERT: EF9 221 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8191 (p) REVERT: EF9 241 ASN cc_start: 0.8859 (m-40) cc_final: 0.8238 (m-40) REVERT: EF9 384 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8114 (mt-10) REVERT: EF10 241 ASN cc_start: 0.8852 (m-40) cc_final: 0.8224 (m110) REVERT: EF10 259 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.7789 (t0) REVERT: EF10 268 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7498 (ttm170) REVERT: EF10 384 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: EF11 244 GLU cc_start: 0.8600 (pt0) cc_final: 0.8307 (mt-10) REVERT: EF11 259 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.7757 (t0) REVERT: EF12 238 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8008 (mm-40) REVERT: EF12 279 ASP cc_start: 0.7928 (m-30) cc_final: 0.7673 (m-30) REVERT: EF13 223 ASP cc_start: 0.8158 (t0) cc_final: 0.7908 (m-30) REVERT: EF13 242 ASP cc_start: 0.8637 (m-30) cc_final: 0.8385 (m-30) REVERT: EF13 384 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: EF14 241 ASN cc_start: 0.8996 (m110) cc_final: 0.8613 (m-40) REVERT: EF14 384 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: EF16 221 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8453 (p) REVERT: EF16 223 ASP cc_start: 0.8296 (t0) cc_final: 0.8084 (m-30) REVERT: EF17 238 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8050 (mt0) outliers start: 156 outliers final: 98 residues processed: 546 average time/residue: 0.6406 time to fit residues: 411.7179 Evaluate side-chains 534 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 415 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 AB2 residue 34 THR Chi-restraints excluded: chain AB2 residue 52 GLN 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 52 GLN Chi-restraints excluded: chain AB9 residue 27 CYS 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 AB15 residue 27 CYS Chi-restraints excluded: chain AB16 residue 27 CYS Chi-restraints excluded: chain AB16 residue 34 THR 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 355 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 EF2 residue 268 ARG Chi-restraints excluded: chain EF3 residue 206 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 EF3 residue 261 SER Chi-restraints excluded: chain EF3 residue 390 GLN 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 EF5 residue 260 VAL Chi-restraints excluded: chain EF6 residue 209 ILE Chi-restraints excluded: chain EF6 residue 221 THR Chi-restraints excluded: chain EF6 residue 253 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 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 271 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 223 ASP 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 274 CYS Chi-restraints excluded: chain EF9 residue 206 VAL Chi-restraints excluded: chain EF9 residue 209 ILE 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 259 ASP Chi-restraints excluded: chain EF11 residue 261 SER Chi-restraints excluded: chain EF11 residue 267 VAL 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 237 VAL Chi-restraints excluded: chain EF12 residue 238 GLN 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 253 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 237 VAL Chi-restraints excluded: chain EF14 residue 355 VAL 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 209 ILE Chi-restraints excluded: chain EF16 residue 221 THR Chi-restraints excluded: chain EF16 residue 253 THR Chi-restraints excluded: chain EF16 residue 261 SER Chi-restraints excluded: chain EF16 residue 278 ASP Chi-restraints excluded: chain EF17 residue 221 THR Chi-restraints excluded: chain EF17 residue 238 GLN Chi-restraints excluded: chain EF17 residue 260 VAL 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: chunk 271 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 305 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 333 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 193 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 251 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.131913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102576 restraints weight = 38009.006| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.54 r_work: 0.3075 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30107 Z= 0.128 Angle : 0.460 6.299 40477 Z= 0.246 Chirality : 0.039 0.147 4539 Planarity : 0.003 0.036 5304 Dihedral : 4.557 59.259 4185 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.08 % Allowed : 29.67 % Favored : 65.25 % 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: 0.43 (0.14), residues: 3876 helix: 2.29 (0.15), residues: 1292 sheet: -0.53 (0.19), residues: 765 loop : -0.82 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAB14 46 TYR 0.012 0.001 TYREF17 373 PHE 0.008 0.001 PHEEF12 317 TRP 0.006 0.001 TRPEF17 199 HIS 0.004 0.001 HISEF11 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (30090) covalent geometry : angle 0.46039 / 0.25 (40443) SS BOND : bond 0.00074 / 0.05 ( 17) SS BOND : angle 0.30845 / 0.21 ( 34) hydrogen bonds : bond 0.02796 / 1.85 ( 1156) hydrogen bonds : angle 4.47385 / 2.98 ( 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 563 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 404 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: AB2 52 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.7134 (mm-40) REVERT: AB4 51 LYS cc_start: 0.8017 (tppt) cc_final: 0.7554 (tppt) REVERT: AB5 51 LYS cc_start: 0.7751 (tppt) cc_final: 0.7251 (tppt) REVERT: AB6 51 LYS cc_start: 0.7777 (tppp) cc_final: 0.7500 (tppt) REVERT: AB7 48 LYS cc_start: 0.7265 (tttp) cc_final: 0.6536 (tttt) REVERT: AB7 52 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6071 (mp-120) REVERT: AB9 52 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6016 (mp-120) REVERT: AB10 51 LYS cc_start: 0.8280 (tppt) cc_final: 0.7985 (tppt) REVERT: AB11 51 LYS cc_start: 0.8030 (tppp) cc_final: 0.7740 (tppt) REVERT: AB12 51 LYS cc_start: 0.8090 (tptt) cc_final: 0.7732 (tppt) REVERT: AB13 51 LYS cc_start: 0.8163 (tptt) cc_final: 0.7891 (tppt) REVERT: AB14 51 LYS cc_start: 0.8073 (tptt) cc_final: 0.7785 (tppt) REVERT: AB15 51 LYS cc_start: 0.8203 (tppp) cc_final: 0.7798 (tppt) REVERT: AB16 51 LYS cc_start: 0.8264 (tppt) cc_final: 0.7977 (tppt) REVERT: EF1 196 ARG cc_start: 0.7727 (ttm-80) cc_final: 0.7189 (mpp80) REVERT: EF1 364 ASP cc_start: 0.7887 (t70) cc_final: 0.7477 (t0) REVERT: EF1 384 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7789 (mt-10) REVERT: EF2 207 GLU cc_start: 0.8107 (mp0) cc_final: 0.7828 (mt-10) REVERT: EF2 268 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7680 (ttm170) REVERT: EF3 244 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8242 (mt-10) REVERT: EF4 221 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8496 (p) REVERT: EF4 243 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7480 (mm-30) REVERT: EF4 244 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8494 (mt-10) REVERT: EF5 244 GLU cc_start: 0.8554 (pt0) cc_final: 0.8314 (mt-10) REVERT: EF6 207 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7286 (mp0) REVERT: EF6 259 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7853 (t0) REVERT: EF8 196 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.7757 (mtm180) REVERT: EF8 221 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8472 (p) REVERT: EF8 239 MET cc_start: 0.8669 (mtm) cc_final: 0.8384 (mtp) REVERT: EF8 274 CYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7545 (m) REVERT: EF9 207 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7207 (mp0) REVERT: EF9 221 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8193 (p) REVERT: EF9 241 ASN cc_start: 0.8847 (m-40) cc_final: 0.8226 (m-40) REVERT: EF9 384 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: EF10 200 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7927 (mm) REVERT: EF10 238 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7634 (mt0) REVERT: EF10 241 ASN cc_start: 0.8807 (m-40) cc_final: 0.8153 (m110) REVERT: EF10 259 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.7780 (t0) REVERT: EF10 268 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7501 (ttm170) REVERT: EF10 384 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: EF11 244 GLU cc_start: 0.8566 (pt0) cc_final: 0.8307 (mt-10) REVERT: EF11 259 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.7709 (t0) REVERT: EF12 238 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7997 (mm-40) REVERT: EF12 279 ASP cc_start: 0.7889 (m-30) cc_final: 0.7640 (m-30) REVERT: EF13 223 ASP cc_start: 0.8135 (t0) cc_final: 0.7908 (m-30) REVERT: EF13 242 ASP cc_start: 0.8615 (m-30) cc_final: 0.8368 (m-30) REVERT: EF13 384 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7931 (mt-10) REVERT: EF14 241 ASN cc_start: 0.9039 (m110) cc_final: 0.8659 (m-40) REVERT: EF14 384 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: EF15 259 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.7779 (t0) REVERT: EF16 221 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8445 (p) REVERT: EF16 238 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: EF17 238 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7984 (mt0) outliers start: 159 outliers final: 104 residues processed: 540 average time/residue: 0.6336 time to fit residues: 402.7919 Evaluate side-chains 527 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 398 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB1 residue 23 SER Chi-restraints excluded: chain AB1 residue 34 THR Chi-restraints excluded: chain AB2 residue 27 CYS Chi-restraints excluded: chain AB2 residue 34 THR Chi-restraints excluded: chain AB2 residue 52 GLN 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 AB9 residue 52 GLN 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 AB15 residue 37 THR Chi-restraints excluded: chain AB16 residue 27 CYS Chi-restraints excluded: chain AB16 residue 34 THR 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 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 EF2 residue 268 ARG Chi-restraints excluded: chain EF3 residue 206 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 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 244 GLU Chi-restraints excluded: chain EF4 residue 260 VAL Chi-restraints excluded: chain EF5 residue 260 VAL Chi-restraints excluded: chain EF6 residue 209 ILE Chi-restraints excluded: chain EF6 residue 221 THR Chi-restraints excluded: chain EF6 residue 237 VAL Chi-restraints excluded: chain EF6 residue 253 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 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 271 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 223 ASP 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 274 CYS Chi-restraints excluded: chain EF9 residue 206 VAL Chi-restraints excluded: chain EF9 residue 209 ILE 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 384 GLU Chi-restraints excluded: chain EF10 residue 200 ILE 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 238 GLN 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 259 ASP Chi-restraints excluded: chain EF11 residue 261 SER Chi-restraints excluded: chain EF11 residue 267 VAL 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 237 VAL Chi-restraints excluded: chain EF12 residue 238 GLN Chi-restraints excluded: chain EF12 residue 267 VAL Chi-restraints excluded: chain EF12 residue 271 SER Chi-restraints excluded: chain EF12 residue 280 ASP Chi-restraints excluded: chain EF13 residue 206 VAL Chi-restraints excluded: chain EF13 residue 221 THR Chi-restraints excluded: chain EF13 residue 234 THR Chi-restraints excluded: chain EF13 residue 253 THR Chi-restraints excluded: chain EF13 residue 267 VAL Chi-restraints excluded: chain EF13 residue 292 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 261 SER Chi-restraints excluded: chain EF14 residue 355 VAL 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 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 238 GLN 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 238 GLN 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: chunk 40 optimal weight: 0.3980 chunk 130 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 321 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.132104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102804 restraints weight = 38048.843| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.54 r_work: 0.3077 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30107 Z= 0.128 Angle : 0.463 6.742 40477 Z= 0.247 Chirality : 0.039 0.142 4539 Planarity : 0.003 0.036 5304 Dihedral : 4.509 59.878 4185 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.89 % Allowed : 29.99 % Favored : 65.12 % 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: 0.46 (0.14), residues: 3876 helix: 2.33 (0.15), residues: 1292 sheet: -0.54 (0.19), residues: 765 loop : -0.79 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAB1 46 TYR 0.013 0.001 TYREF17 373 PHE 0.007 0.001 PHEEF12 317 TRP 0.007 0.001 TRPEF17 199 HIS 0.004 0.001 HISEF12 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (30090) covalent geometry : angle 0.46283 / 0.25 (40443) SS BOND : bond 0.00072 / 0.05 ( 17) SS BOND : angle 0.27461 / 0.19 ( 34) hydrogen bonds : bond 0.02765 / 1.83 ( 1156) hydrogen bonds : angle 4.40928 / 2.95 ( 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 551 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 398 time to evaluate : 1.423 Fit side-chains revert: symmetry clash REVERT: AB2 52 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.7132 (mm-40) REVERT: AB4 51 LYS cc_start: 0.8018 (tppt) cc_final: 0.7577 (tppt) REVERT: AB5 51 LYS cc_start: 0.7823 (tppt) cc_final: 0.7339 (tppt) REVERT: AB6 51 LYS cc_start: 0.7788 (tppp) cc_final: 0.7397 (tppt) REVERT: AB7 48 LYS cc_start: 0.7294 (tttp) cc_final: 0.6554 (tttt) REVERT: AB7 52 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6113 (mp-120) REVERT: AB8 51 LYS cc_start: 0.8072 (tppt) cc_final: 0.7853 (tppt) REVERT: AB9 52 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6030 (mp-120) REVERT: AB10 51 LYS cc_start: 0.8269 (tppt) cc_final: 0.7967 (tppt) REVERT: AB11 51 LYS cc_start: 0.8063 (tppp) cc_final: 0.7765 (tppt) REVERT: AB12 51 LYS cc_start: 0.8102 (tptt) cc_final: 0.7752 (tppt) REVERT: AB13 51 LYS cc_start: 0.8187 (tptt) cc_final: 0.7931 (tppt) REVERT: AB14 51 LYS cc_start: 0.8093 (tptt) cc_final: 0.7806 (tppt) REVERT: AB15 51 LYS cc_start: 0.8222 (tppp) cc_final: 0.7821 (tppt) REVERT: AB16 51 LYS cc_start: 0.8268 (tppt) cc_final: 0.7988 (tppt) REVERT: EF1 384 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7789 (mt-10) REVERT: EF2 196 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.7385 (mtm180) REVERT: EF2 207 GLU cc_start: 0.8113 (mp0) cc_final: 0.7842 (mt-10) REVERT: EF2 268 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7694 (ttm170) REVERT: EF3 244 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8216 (mt-10) REVERT: EF4 221 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8500 (p) REVERT: EF4 229 MET cc_start: 0.7176 (ttm) cc_final: 0.6954 (ttm) REVERT: EF4 243 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7534 (mm-30) REVERT: EF5 244 GLU cc_start: 0.8558 (pt0) cc_final: 0.8341 (mt-10) REVERT: EF6 207 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7313 (mp0) REVERT: EF6 259 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.7895 (t0) REVERT: EF8 196 ARG cc_start: 0.8013 (mtm-85) cc_final: 0.7794 (mtm180) REVERT: EF8 221 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8493 (p) REVERT: EF8 239 MET cc_start: 0.8690 (mtm) cc_final: 0.8419 (mtp) REVERT: EF8 244 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8314 (mt-10) REVERT: EF8 274 CYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7605 (m) REVERT: EF9 207 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7234 (mp0) REVERT: EF9 221 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8215 (p) REVERT: EF9 241 ASN cc_start: 0.8860 (m-40) cc_final: 0.8273 (m-40) REVERT: EF9 384 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8123 (mt-10) REVERT: EF10 241 ASN cc_start: 0.8850 (m-40) cc_final: 0.8170 (m110) REVERT: EF10 259 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.7760 (t0) REVERT: EF10 268 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7548 (ttm170) REVERT: EF10 384 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: EF11 259 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7738 (t0) REVERT: EF12 238 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8036 (mm-40) REVERT: EF12 279 ASP cc_start: 0.7877 (m-30) cc_final: 0.7625 (m-30) REVERT: EF13 207 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7427 (mp0) REVERT: EF13 242 ASP cc_start: 0.8645 (m-30) cc_final: 0.8407 (m-30) REVERT: EF13 384 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: EF14 241 ASN cc_start: 0.9083 (m110) cc_final: 0.8722 (m-40) REVERT: EF14 268 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7682 (ptp90) REVERT: EF15 259 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.7812 (t0) REVERT: EF16 221 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8467 (p) REVERT: EF16 238 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7550 (mt0) REVERT: EF16 292 MET cc_start: 0.8584 (tpp) cc_final: 0.8258 (tpp) REVERT: EF17 238 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7972 (mt0) outliers start: 153 outliers final: 108 residues processed: 531 average time/residue: 0.6573 time to fit residues: 409.5755 Evaluate side-chains 519 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 388 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB1 residue 23 SER Chi-restraints excluded: chain AB1 residue 34 THR Chi-restraints excluded: chain AB2 residue 27 CYS Chi-restraints excluded: chain AB2 residue 34 THR Chi-restraints excluded: chain AB2 residue 52 GLN 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 27 CYS Chi-restraints excluded: chain AB7 residue 52 GLN Chi-restraints excluded: chain AB9 residue 27 CYS Chi-restraints excluded: chain AB9 residue 52 GLN Chi-restraints excluded: chain AB12 residue 27 CYS Chi-restraints excluded: chain AB15 residue 27 CYS Chi-restraints excluded: chain AB15 residue 37 THR Chi-restraints excluded: chain AB16 residue 27 CYS Chi-restraints excluded: chain AB16 residue 34 THR 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 273 SER Chi-restraints excluded: chain EF1 residue 355 VAL 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 EF2 residue 268 ARG Chi-restraints excluded: chain EF2 residue 271 SER Chi-restraints excluded: chain EF3 residue 206 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 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 260 VAL Chi-restraints excluded: chain EF5 residue 206 VAL Chi-restraints excluded: chain EF5 residue 260 VAL Chi-restraints excluded: chain EF6 residue 209 ILE Chi-restraints excluded: chain EF6 residue 221 THR Chi-restraints excluded: chain EF6 residue 237 VAL Chi-restraints excluded: chain EF6 residue 253 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 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 271 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 223 ASP Chi-restraints excluded: chain EF8 residue 237 VAL Chi-restraints excluded: chain EF8 residue 244 GLU Chi-restraints excluded: chain EF8 residue 260 VAL Chi-restraints excluded: chain EF8 residue 261 SER Chi-restraints excluded: chain EF8 residue 274 CYS Chi-restraints excluded: chain EF9 residue 206 VAL Chi-restraints excluded: chain EF9 residue 209 ILE 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 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 384 GLU Chi-restraints excluded: chain EF11 residue 206 VAL Chi-restraints excluded: chain EF11 residue 221 THR Chi-restraints excluded: chain EF11 residue 259 ASP Chi-restraints excluded: chain EF11 residue 261 SER Chi-restraints excluded: chain EF11 residue 267 VAL 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 237 VAL Chi-restraints excluded: chain EF12 residue 238 GLN Chi-restraints excluded: chain EF12 residue 267 VAL Chi-restraints excluded: chain EF12 residue 271 SER Chi-restraints excluded: chain EF12 residue 280 ASP 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 292 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 261 SER Chi-restraints excluded: chain EF14 residue 268 ARG Chi-restraints excluded: chain EF14 residue 355 VAL 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 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 238 GLN Chi-restraints excluded: chain EF16 residue 253 THR 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 238 GLN Chi-restraints excluded: chain EF17 residue 260 VAL Chi-restraints excluded: chain EF17 residue 261 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 67 optimal weight: 0.8980 chunk 302 optimal weight: 1.9990 chunk 303 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 238 optimal weight: 0.7980 chunk 150 optimal weight: 0.3980 chunk 220 optimal weight: 0.7980 chunk 252 optimal weight: 0.7980 chunk 331 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.132578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.103487 restraints weight = 38026.311| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.53 r_work: 0.3090 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30107 Z= 0.120 Angle : 0.454 7.256 40477 Z= 0.242 Chirality : 0.039 0.143 4539 Planarity : 0.003 0.036 5304 Dihedral : 4.455 59.486 4185 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.48 % Allowed : 30.21 % Favored : 65.31 % 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: 2.38 (0.15), residues: 1292 sheet: -0.55 (0.19), residues: 765 loop : -0.78 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAB1 46 TYR 0.011 0.001 TYREF17 373 PHE 0.007 0.001 PHEEF12 317 TRP 0.007 0.001 TRPEF17 199 HIS 0.004 0.001 HISEF11 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (30090) covalent geometry : angle 0.45459 / 0.24 (40443) SS BOND : bond 0.00079 / 0.05 ( 17) SS BOND : angle 0.23524 / 0.16 ( 34) hydrogen bonds : bond 0.02681 / 1.77 ( 1156) hydrogen bonds : angle 4.34691 / 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 540 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 400 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: AB2 52 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.7145 (mm-40) REVERT: AB4 51 LYS cc_start: 0.8005 (tppt) cc_final: 0.7575 (tppt) REVERT: AB5 51 LYS cc_start: 0.7851 (tppt) cc_final: 0.7387 (tppt) REVERT: AB6 51 LYS cc_start: 0.7773 (tppp) cc_final: 0.7371 (tppt) REVERT: AB7 48 LYS cc_start: 0.7271 (tttp) cc_final: 0.6658 (tttt) REVERT: AB7 52 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6165 (mp-120) REVERT: AB8 51 LYS cc_start: 0.8089 (tppt) cc_final: 0.7883 (tppt) REVERT: AB9 52 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6048 (mp-120) REVERT: AB10 51 LYS cc_start: 0.8288 (tppt) cc_final: 0.7975 (tppt) REVERT: AB11 51 LYS cc_start: 0.8059 (tppp) cc_final: 0.7756 (tppt) REVERT: AB12 51 LYS cc_start: 0.8084 (tptt) cc_final: 0.7760 (tppt) REVERT: AB13 51 LYS cc_start: 0.8161 (tptt) cc_final: 0.7906 (tppt) REVERT: AB14 51 LYS cc_start: 0.8057 (tptt) cc_final: 0.7776 (tppt) REVERT: AB15 51 LYS cc_start: 0.8208 (tppp) cc_final: 0.7812 (tppt) REVERT: AB16 51 LYS cc_start: 0.8332 (tppt) cc_final: 0.8015 (tppt) REVERT: EF1 384 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7769 (mt-10) REVERT: EF2 196 ARG cc_start: 0.7683 (ttm-80) cc_final: 0.7345 (mtm180) REVERT: EF2 207 GLU cc_start: 0.8120 (mp0) cc_final: 0.7854 (mt-10) REVERT: EF2 268 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7692 (ttm170) REVERT: EF3 244 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8206 (mt-10) REVERT: EF4 221 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8515 (p) REVERT: EF5 244 GLU cc_start: 0.8517 (pt0) cc_final: 0.8296 (mt-10) REVERT: EF8 196 ARG cc_start: 0.8001 (mtm-85) cc_final: 0.7661 (mtm180) REVERT: EF8 221 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8494 (p) REVERT: EF8 239 MET cc_start: 0.8661 (mtm) cc_final: 0.8407 (mtp) REVERT: EF8 244 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8317 (mt-10) REVERT: EF8 274 CYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7598 (m) REVERT: EF9 207 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7277 (mp0) REVERT: EF9 221 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8179 (p) REVERT: EF9 241 ASN cc_start: 0.8846 (m-40) cc_final: 0.8259 (m-40) REVERT: EF9 384 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: EF10 241 ASN cc_start: 0.8800 (m-40) cc_final: 0.8118 (m110) REVERT: EF10 259 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7732 (t0) REVERT: EF10 268 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7450 (ttm170) REVERT: EF10 384 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: EF11 259 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7716 (t0) REVERT: EF12 238 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8030 (mm-40) REVERT: EF12 279 ASP cc_start: 0.7860 (m-30) cc_final: 0.7621 (m-30) REVERT: EF13 207 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7397 (mp0) REVERT: EF13 242 ASP cc_start: 0.8632 (m-30) cc_final: 0.8404 (m-30) REVERT: EF13 384 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: EF14 241 ASN cc_start: 0.9047 (m110) cc_final: 0.8653 (m-40) REVERT: EF14 384 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7585 (mm-30) REVERT: EF15 241 ASN cc_start: 0.8936 (m110) cc_final: 0.8488 (m-40) REVERT: EF15 259 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.7789 (t0) REVERT: EF16 221 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8392 (p) REVERT: EF16 292 MET cc_start: 0.8680 (tpp) cc_final: 0.8339 (tpp) outliers start: 140 outliers final: 107 residues processed: 528 average time/residue: 0.6874 time to fit residues: 427.6569 Evaluate side-chains 512 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 386 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB1 residue 34 THR Chi-restraints excluded: chain AB2 residue 27 CYS Chi-restraints excluded: chain AB2 residue 34 THR Chi-restraints excluded: chain AB2 residue 52 GLN 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 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 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 AB15 residue 37 THR Chi-restraints excluded: chain AB16 residue 27 CYS Chi-restraints excluded: chain AB16 residue 34 THR 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 273 SER Chi-restraints excluded: chain EF1 residue 355 VAL 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 EF2 residue 268 ARG Chi-restraints excluded: chain EF3 residue 206 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 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 260 VAL Chi-restraints excluded: chain EF5 residue 260 VAL Chi-restraints excluded: chain EF6 residue 209 ILE Chi-restraints excluded: chain EF6 residue 221 THR Chi-restraints excluded: chain EF6 residue 237 VAL Chi-restraints excluded: chain EF6 residue 253 THR 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 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 271 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 223 ASP Chi-restraints excluded: chain EF8 residue 237 VAL Chi-restraints excluded: chain EF8 residue 244 GLU Chi-restraints excluded: chain EF8 residue 260 VAL Chi-restraints excluded: chain EF8 residue 261 SER Chi-restraints excluded: chain EF8 residue 274 CYS Chi-restraints excluded: chain EF9 residue 206 VAL Chi-restraints excluded: chain EF9 residue 209 ILE 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 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 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 259 ASP Chi-restraints excluded: chain EF11 residue 261 SER Chi-restraints excluded: chain EF11 residue 267 VAL 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 237 VAL Chi-restraints excluded: chain EF12 residue 238 GLN Chi-restraints excluded: chain EF12 residue 267 VAL Chi-restraints excluded: chain EF12 residue 271 SER Chi-restraints excluded: chain EF12 residue 280 ASP 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 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 355 VAL Chi-restraints excluded: chain EF15 residue 206 VAL Chi-restraints excluded: chain EF15 residue 221 THR Chi-restraints excluded: chain EF15 residue 229 MET Chi-restraints excluded: chain EF15 residue 259 ASP 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 261 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 77 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 354 optimal weight: 2.9990 chunk 306 optimal weight: 0.9980 chunk 249 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 338 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.124894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.096303 restraints weight = 39300.998| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.42 r_work: 0.2949 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 30107 Z= 0.246 Angle : 0.554 8.125 40477 Z= 0.295 Chirality : 0.042 0.143 4539 Planarity : 0.004 0.041 5304 Dihedral : 4.904 59.851 4185 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.48 % Allowed : 30.50 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3876 helix: 2.63 (0.15), residues: 1190 sheet: -0.53 (0.19), residues: 765 loop : -0.79 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAB1 46 TYR 0.016 0.001 TYREF10 373 PHE 0.008 0.001 PHEEF11 205 TRP 0.011 0.001 TRPEF1 199 HIS 0.003 0.001 HISEF17 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.25 (30090) covalent geometry : angle 0.55459 / 0.29 (40443) SS BOND : bond 0.00134 / 0.09 ( 17) SS BOND : angle 0.34621 / 0.23 ( 34) hydrogen bonds : bond 0.03625 / 2.39 ( 1156) hydrogen bonds : angle 4.62372 / 3.10 ( 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 540 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 400 time to evaluate : 1.204 Fit side-chains revert: symmetry clash REVERT: AB4 51 LYS cc_start: 0.7894 (tppt) cc_final: 0.7446 (tppt) REVERT: AB5 51 LYS cc_start: 0.7681 (tppt) cc_final: 0.7203 (tppt) REVERT: AB6 51 LYS cc_start: 0.7847 (tppp) cc_final: 0.7446 (tppt) REVERT: AB6 52 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7078 (mm-40) REVERT: AB8 51 LYS cc_start: 0.8032 (tppt) cc_final: 0.7758 (tppt) REVERT: AB10 51 LYS cc_start: 0.8200 (tppt) cc_final: 0.7850 (tppt) REVERT: AB11 51 LYS cc_start: 0.7956 (tppp) cc_final: 0.7687 (tppt) REVERT: AB12 51 LYS cc_start: 0.8007 (tptt) cc_final: 0.7637 (tppt) REVERT: AB13 51 LYS cc_start: 0.8070 (tptt) cc_final: 0.7790 (tppt) REVERT: AB14 51 LYS cc_start: 0.8082 (tptt) cc_final: 0.7762 (tppt) REVERT: AB15 51 LYS cc_start: 0.8159 (tppp) cc_final: 0.7735 (tppt) REVERT: EF1 364 ASP cc_start: 0.7918 (t70) cc_final: 0.7497 (t0) REVERT: EF2 305 ASN cc_start: 0.8403 (m-40) cc_final: 0.7961 (m-40) REVERT: EF4 259 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7823 (t0) REVERT: EF4 305 ASN cc_start: 0.8419 (m-40) cc_final: 0.8097 (m-40) REVERT: EF8 221 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8345 (p) REVERT: EF8 239 MET cc_start: 0.8548 (mtm) cc_final: 0.8191 (mtp) REVERT: EF8 274 CYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7576 (m) REVERT: EF9 207 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7110 (mp0) REVERT: EF9 221 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8160 (p) REVERT: EF9 384 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8070 (mt-10) REVERT: EF10 241 ASN cc_start: 0.8916 (m-40) cc_final: 0.8168 (m110) REVERT: EF10 268 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7361 (ttm170) REVERT: EF10 384 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: EF11 196 ARG cc_start: 0.8162 (mpp80) cc_final: 0.7804 (mpp80) REVERT: EF11 259 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7647 (t0) REVERT: EF12 279 ASP cc_start: 0.7777 (m-30) cc_final: 0.7530 (m-30) REVERT: EF13 242 ASP cc_start: 0.8617 (m-30) cc_final: 0.8364 (m-30) REVERT: EF13 384 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7924 (mt-10) REVERT: EF14 241 ASN cc_start: 0.8960 (m110) cc_final: 0.8547 (m-40) REVERT: EF14 384 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7662 (tt0) REVERT: EF16 221 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8341 (p) REVERT: EF16 223 ASP cc_start: 0.8182 (t0) cc_final: 0.7960 (m-30) REVERT: EF16 279 ASP cc_start: 0.7905 (m-30) cc_final: 0.7561 (m-30) outliers start: 140 outliers final: 111 residues processed: 529 average time/residue: 0.6567 time to fit residues: 410.7797 Evaluate side-chains 507 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 385 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB1 residue 23 SER Chi-restraints excluded: chain AB1 residue 34 THR Chi-restraints excluded: chain AB2 residue 27 CYS Chi-restraints excluded: chain AB2 residue 34 THR 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 AB8 residue 37 THR Chi-restraints excluded: chain AB9 residue 27 CYS 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 AB12 residue 34 THR Chi-restraints excluded: chain AB15 residue 27 CYS Chi-restraints excluded: chain AB15 residue 34 THR Chi-restraints excluded: chain AB15 residue 37 THR Chi-restraints excluded: chain AB16 residue 27 CYS Chi-restraints excluded: chain AB16 residue 34 THR 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 273 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 244 GLU 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 260 VAL Chi-restraints excluded: chain EF6 residue 209 ILE Chi-restraints excluded: chain EF6 residue 221 THR Chi-restraints excluded: chain EF6 residue 237 VAL Chi-restraints excluded: chain EF6 residue 253 THR 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 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 223 ASP Chi-restraints excluded: chain EF8 residue 237 VAL Chi-restraints excluded: chain EF8 residue 244 GLU Chi-restraints excluded: chain EF8 residue 260 VAL Chi-restraints excluded: chain EF8 residue 261 SER Chi-restraints excluded: chain EF8 residue 273 SER Chi-restraints excluded: chain EF8 residue 274 CYS Chi-restraints excluded: chain EF9 residue 206 VAL Chi-restraints excluded: chain EF9 residue 209 ILE 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 261 SER Chi-restraints excluded: chain EF9 residue 267 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 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 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 259 ASP Chi-restraints excluded: chain EF11 residue 261 SER Chi-restraints excluded: chain EF11 residue 267 VAL 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 237 VAL Chi-restraints excluded: chain EF12 residue 267 VAL Chi-restraints excluded: chain EF12 residue 271 SER Chi-restraints excluded: chain EF12 residue 280 ASP Chi-restraints excluded: chain EF13 residue 206 VAL Chi-restraints excluded: chain EF13 residue 221 THR Chi-restraints excluded: chain EF13 residue 234 THR Chi-restraints excluded: chain EF13 residue 253 THR Chi-restraints excluded: chain EF13 residue 267 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 237 VAL Chi-restraints excluded: chain EF14 residue 261 SER Chi-restraints excluded: chain EF14 residue 355 VAL 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 261 SER 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: chunk 209 optimal weight: 0.6980 chunk 263 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 264 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 235 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 336 optimal weight: 4.9990 chunk 271 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.127141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.098870 restraints weight = 39062.149| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.49 r_work: 0.2993 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30107 Z= 0.176 Angle : 0.509 7.355 40477 Z= 0.271 Chirality : 0.040 0.150 4539 Planarity : 0.004 0.037 5304 Dihedral : 4.511 58.861 4179 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.00 % Allowed : 30.95 % Favored : 65.06 % 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: 2.68 (0.15), residues: 1190 sheet: -0.21 (0.17), residues: 935 loop : -1.00 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAB1 46 TYR 0.015 0.001 TYREF17 373 PHE 0.008 0.001 PHEEF12 317 TRP 0.007 0.001 TRPEF11 199 HIS 0.003 0.001 HISEF14 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (30090) covalent geometry : angle 0.50952 / 0.27 (40443) SS BOND : bond 0.00085 / 0.06 ( 17) SS BOND : angle 0.32137 / 0.22 ( 34) hydrogen bonds : bond 0.03151 / 2.08 ( 1156) hydrogen bonds : angle 4.51624 / 3.03 ( 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: 11462.18 seconds wall clock time: 195 minutes 6.99 seconds (11706.99 seconds total)