Starting phenix.real_space_refine on Thu Mar 5 19:12:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qx7_4662/03_2026/6qx7_4662.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qx7_4662/03_2026/6qx7_4662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qx7_4662/03_2026/6qx7_4662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qx7_4662/03_2026/6qx7_4662.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qx7_4662/03_2026/6qx7_4662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qx7_4662/03_2026/6qx7_4662.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.083 sd= 1.000 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 84 5.16 5 C 16164 2.51 5 N 4152 2.21 5 O 4764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25164 Number of models: 1 Model: "" Number of chains: 1 Chain: "0a" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Restraints were copied for chains: 0b, 0c, 0d, 0e, 0f, 0g, 0h, 0i, 0j, 0k, 0l Time building chain proxies: 2.26, per 1000 atoms: 0.09 Number of scatterers: 25164 At special positions: 0 Unit cell: (159.728, 159.728, 91.12, 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 84 16.00 O 4764 8.00 N 4152 7.00 C 16164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.92 Conformation dependent library (CDL) restraints added in 784.8 milliseconds 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5928 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 48 sheets defined 41.4% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain '0a' and resid 22 through 33 removed outlier: 3.854A pdb=" N LEU0a 28 " --> pdb=" O PHE0a 24 " (cutoff:3.500A) Processing helix chain '0a' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0a 54 " --> pdb=" O PRO0a 50 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N SER0a 56 " --> pdb=" O PHE0a 52 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE0a 57 " --> pdb=" O LEU0a 53 " (cutoff:3.500A) Processing helix chain '0a' and resid 130 through 154 Processing helix chain '0a' and resid 155 through 157 No H-bonds generated for 'chain '0a' and resid 155 through 157' Processing helix chain '0a' and resid 167 through 178 removed outlier: 4.148A pdb=" N GLN0a 173 " --> pdb=" O LEU0a 169 " (cutoff:3.500A) Processing helix chain '0a' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0a 212 " --> pdb=" O ASP0a 208 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU0a 220 " --> pdb=" O ALA0a 216 " (cutoff:3.500A) Processing helix chain '0a' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0a 256 " --> pdb=" O SER0a 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0a 257 " --> pdb=" O SER0a 253 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER0a 260 " --> pdb=" O VAL0a 256 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG0a 261 " --> pdb=" O PHE0a 257 " (cutoff:3.500A) Processing helix chain '0a' and resid 264 through 272 removed outlier: 4.957A pdb=" N GLU0a 270 " --> pdb=" O GLU0a 266 " (cutoff:3.500A) Processing helix chain '0b' and resid 22 through 33 removed outlier: 3.854A pdb=" N LEU0b 28 " --> pdb=" O PHE0b 24 " (cutoff:3.500A) Processing helix chain '0b' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0b 54 " --> pdb=" O PRO0b 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER0b 56 " --> pdb=" O PHE0b 52 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE0b 57 " --> pdb=" O LEU0b 53 " (cutoff:3.500A) Processing helix chain '0b' and resid 130 through 154 Processing helix chain '0b' and resid 155 through 157 No H-bonds generated for 'chain '0b' and resid 155 through 157' Processing helix chain '0b' and resid 167 through 178 removed outlier: 4.148A pdb=" N GLN0b 173 " --> pdb=" O LEU0b 169 " (cutoff:3.500A) Processing helix chain '0b' and resid 206 through 225 removed outlier: 3.709A pdb=" N ALA0b 212 " --> pdb=" O ASP0b 208 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU0b 220 " --> pdb=" O ALA0b 216 " (cutoff:3.500A) Processing helix chain '0b' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0b 256 " --> pdb=" O SER0b 252 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE0b 257 " --> pdb=" O SER0b 253 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER0b 260 " --> pdb=" O VAL0b 256 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG0b 261 " --> pdb=" O PHE0b 257 " (cutoff:3.500A) Processing helix chain '0b' and resid 264 through 272 removed outlier: 4.957A pdb=" N GLU0b 270 " --> pdb=" O GLU0b 266 " (cutoff:3.500A) Processing helix chain '0c' and resid 22 through 33 removed outlier: 3.853A pdb=" N LEU0c 28 " --> pdb=" O PHE0c 24 " (cutoff:3.500A) Processing helix chain '0c' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0c 54 " --> pdb=" O PRO0c 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER0c 56 " --> pdb=" O PHE0c 52 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE0c 57 " --> pdb=" O LEU0c 53 " (cutoff:3.500A) Processing helix chain '0c' and resid 130 through 154 Processing helix chain '0c' and resid 155 through 157 No H-bonds generated for 'chain '0c' and resid 155 through 157' Processing helix chain '0c' and resid 167 through 178 removed outlier: 4.148A pdb=" N GLN0c 173 " --> pdb=" O LEU0c 169 " (cutoff:3.500A) Processing helix chain '0c' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0c 212 " --> pdb=" O ASP0c 208 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU0c 220 " --> pdb=" O ALA0c 216 " (cutoff:3.500A) Processing helix chain '0c' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0c 256 " --> pdb=" O SER0c 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0c 257 " --> pdb=" O SER0c 253 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER0c 260 " --> pdb=" O VAL0c 256 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG0c 261 " --> pdb=" O PHE0c 257 " (cutoff:3.500A) Processing helix chain '0c' and resid 264 through 272 removed outlier: 4.957A pdb=" N GLU0c 270 " --> pdb=" O GLU0c 266 " (cutoff:3.500A) Processing helix chain '0d' and resid 22 through 33 removed outlier: 3.853A pdb=" N LEU0d 28 " --> pdb=" O PHE0d 24 " (cutoff:3.500A) Processing helix chain '0d' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0d 54 " --> pdb=" O PRO0d 50 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N SER0d 56 " --> pdb=" O PHE0d 52 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE0d 57 " --> pdb=" O LEU0d 53 " (cutoff:3.500A) Processing helix chain '0d' and resid 130 through 154 Processing helix chain '0d' and resid 155 through 157 No H-bonds generated for 'chain '0d' and resid 155 through 157' Processing helix chain '0d' and resid 167 through 178 removed outlier: 4.149A pdb=" N GLN0d 173 " --> pdb=" O LEU0d 169 " (cutoff:3.500A) Processing helix chain '0d' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0d 212 " --> pdb=" O ASP0d 208 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU0d 220 " --> pdb=" O ALA0d 216 " (cutoff:3.500A) Processing helix chain '0d' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0d 256 " --> pdb=" O SER0d 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0d 257 " --> pdb=" O SER0d 253 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER0d 260 " --> pdb=" O VAL0d 256 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG0d 261 " --> pdb=" O PHE0d 257 " (cutoff:3.500A) Processing helix chain '0d' and resid 264 through 272 removed outlier: 4.957A pdb=" N GLU0d 270 " --> pdb=" O GLU0d 266 " (cutoff:3.500A) Processing helix chain '0e' and resid 22 through 33 removed outlier: 3.853A pdb=" N LEU0e 28 " --> pdb=" O PHE0e 24 " (cutoff:3.500A) Processing helix chain '0e' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0e 54 " --> pdb=" O PRO0e 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER0e 56 " --> pdb=" O PHE0e 52 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE0e 57 " --> pdb=" O LEU0e 53 " (cutoff:3.500A) Processing helix chain '0e' and resid 130 through 154 Processing helix chain '0e' and resid 155 through 157 No H-bonds generated for 'chain '0e' and resid 155 through 157' Processing helix chain '0e' and resid 167 through 178 removed outlier: 4.149A pdb=" N GLN0e 173 " --> pdb=" O LEU0e 169 " (cutoff:3.500A) Processing helix chain '0e' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0e 212 " --> pdb=" O ASP0e 208 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU0e 220 " --> pdb=" O ALA0e 216 " (cutoff:3.500A) Processing helix chain '0e' and resid 250 through 263 removed outlier: 3.839A pdb=" N VAL0e 256 " --> pdb=" O SER0e 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0e 257 " --> pdb=" O SER0e 253 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER0e 260 " --> pdb=" O VAL0e 256 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG0e 261 " --> pdb=" O PHE0e 257 " (cutoff:3.500A) Processing helix chain '0e' and resid 264 through 272 removed outlier: 4.957A pdb=" N GLU0e 270 " --> pdb=" O GLU0e 266 " (cutoff:3.500A) Processing helix chain '0f' and resid 22 through 33 removed outlier: 3.854A pdb=" N LEU0f 28 " --> pdb=" O PHE0f 24 " (cutoff:3.500A) Processing helix chain '0f' and resid 49 through 59 removed outlier: 3.598A pdb=" N GLU0f 54 " --> pdb=" O PRO0f 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER0f 56 " --> pdb=" O PHE0f 52 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE0f 57 " --> pdb=" O LEU0f 53 " (cutoff:3.500A) Processing helix chain '0f' and resid 130 through 154 Processing helix chain '0f' and resid 155 through 157 No H-bonds generated for 'chain '0f' and resid 155 through 157' Processing helix chain '0f' and resid 167 through 178 removed outlier: 4.148A pdb=" N GLN0f 173 " --> pdb=" O LEU0f 169 " (cutoff:3.500A) Processing helix chain '0f' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0f 212 " --> pdb=" O ASP0f 208 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU0f 220 " --> pdb=" O ALA0f 216 " (cutoff:3.500A) Processing helix chain '0f' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0f 256 " --> pdb=" O SER0f 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0f 257 " --> pdb=" O SER0f 253 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER0f 260 " --> pdb=" O VAL0f 256 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG0f 261 " --> pdb=" O PHE0f 257 " (cutoff:3.500A) Processing helix chain '0f' and resid 264 through 272 removed outlier: 4.958A pdb=" N GLU0f 270 " --> pdb=" O GLU0f 266 " (cutoff:3.500A) Processing helix chain '0g' and resid 22 through 33 removed outlier: 3.854A pdb=" N LEU0g 28 " --> pdb=" O PHE0g 24 " (cutoff:3.500A) Processing helix chain '0g' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0g 54 " --> pdb=" O PRO0g 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER0g 56 " --> pdb=" O PHE0g 52 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE0g 57 " --> pdb=" O LEU0g 53 " (cutoff:3.500A) Processing helix chain '0g' and resid 130 through 154 Processing helix chain '0g' and resid 155 through 157 No H-bonds generated for 'chain '0g' and resid 155 through 157' Processing helix chain '0g' and resid 167 through 178 removed outlier: 4.149A pdb=" N GLN0g 173 " --> pdb=" O LEU0g 169 " (cutoff:3.500A) Processing helix chain '0g' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0g 212 " --> pdb=" O ASP0g 208 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU0g 220 " --> pdb=" O ALA0g 216 " (cutoff:3.500A) Processing helix chain '0g' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0g 256 " --> pdb=" O SER0g 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0g 257 " --> pdb=" O SER0g 253 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER0g 260 " --> pdb=" O VAL0g 256 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG0g 261 " --> pdb=" O PHE0g 257 " (cutoff:3.500A) Processing helix chain '0g' and resid 264 through 272 removed outlier: 4.958A pdb=" N GLU0g 270 " --> pdb=" O GLU0g 266 " (cutoff:3.500A) Processing helix chain '0h' and resid 22 through 33 removed outlier: 3.854A pdb=" N LEU0h 28 " --> pdb=" O PHE0h 24 " (cutoff:3.500A) Processing helix chain '0h' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0h 54 " --> pdb=" O PRO0h 50 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N SER0h 56 " --> pdb=" O PHE0h 52 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE0h 57 " --> pdb=" O LEU0h 53 " (cutoff:3.500A) Processing helix chain '0h' and resid 130 through 154 Processing helix chain '0h' and resid 155 through 157 No H-bonds generated for 'chain '0h' and resid 155 through 157' Processing helix chain '0h' and resid 167 through 178 removed outlier: 4.149A pdb=" N GLN0h 173 " --> pdb=" O LEU0h 169 " (cutoff:3.500A) Processing helix chain '0h' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0h 212 " --> pdb=" O ASP0h 208 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU0h 220 " --> pdb=" O ALA0h 216 " (cutoff:3.500A) Processing helix chain '0h' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0h 256 " --> pdb=" O SER0h 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0h 257 " --> pdb=" O SER0h 253 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER0h 260 " --> pdb=" O VAL0h 256 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG0h 261 " --> pdb=" O PHE0h 257 " (cutoff:3.500A) Processing helix chain '0h' and resid 264 through 272 removed outlier: 4.956A pdb=" N GLU0h 270 " --> pdb=" O GLU0h 266 " (cutoff:3.500A) Processing helix chain '0i' and resid 22 through 33 removed outlier: 3.854A pdb=" N LEU0i 28 " --> pdb=" O PHE0i 24 " (cutoff:3.500A) Processing helix chain '0i' and resid 49 through 59 removed outlier: 3.596A pdb=" N GLU0i 54 " --> pdb=" O PRO0i 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER0i 56 " --> pdb=" O PHE0i 52 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE0i 57 " --> pdb=" O LEU0i 53 " (cutoff:3.500A) Processing helix chain '0i' and resid 130 through 154 Processing helix chain '0i' and resid 155 through 157 No H-bonds generated for 'chain '0i' and resid 155 through 157' Processing helix chain '0i' and resid 167 through 178 removed outlier: 4.148A pdb=" N GLN0i 173 " --> pdb=" O LEU0i 169 " (cutoff:3.500A) Processing helix chain '0i' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0i 212 " --> pdb=" O ASP0i 208 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU0i 220 " --> pdb=" O ALA0i 216 " (cutoff:3.500A) Processing helix chain '0i' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0i 256 " --> pdb=" O SER0i 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0i 257 " --> pdb=" O SER0i 253 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER0i 260 " --> pdb=" O VAL0i 256 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG0i 261 " --> pdb=" O PHE0i 257 " (cutoff:3.500A) Processing helix chain '0i' and resid 264 through 272 removed outlier: 4.957A pdb=" N GLU0i 270 " --> pdb=" O GLU0i 266 " (cutoff:3.500A) Processing helix chain '0j' and resid 22 through 33 removed outlier: 3.854A pdb=" N LEU0j 28 " --> pdb=" O PHE0j 24 " (cutoff:3.500A) Processing helix chain '0j' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0j 54 " --> pdb=" O PRO0j 50 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N SER0j 56 " --> pdb=" O PHE0j 52 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE0j 57 " --> pdb=" O LEU0j 53 " (cutoff:3.500A) Processing helix chain '0j' and resid 130 through 154 Processing helix chain '0j' and resid 155 through 157 No H-bonds generated for 'chain '0j' and resid 155 through 157' Processing helix chain '0j' and resid 167 through 178 removed outlier: 4.147A pdb=" N GLN0j 173 " --> pdb=" O LEU0j 169 " (cutoff:3.500A) Processing helix chain '0j' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0j 212 " --> pdb=" O ASP0j 208 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU0j 220 " --> pdb=" O ALA0j 216 " (cutoff:3.500A) Processing helix chain '0j' and resid 250 through 263 removed outlier: 3.837A pdb=" N VAL0j 256 " --> pdb=" O SER0j 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0j 257 " --> pdb=" O SER0j 253 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER0j 260 " --> pdb=" O VAL0j 256 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG0j 261 " --> pdb=" O PHE0j 257 " (cutoff:3.500A) Processing helix chain '0j' and resid 264 through 272 removed outlier: 4.958A pdb=" N GLU0j 270 " --> pdb=" O GLU0j 266 " (cutoff:3.500A) Processing helix chain '0k' and resid 22 through 33 removed outlier: 3.853A pdb=" N LEU0k 28 " --> pdb=" O PHE0k 24 " (cutoff:3.500A) Processing helix chain '0k' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0k 54 " --> pdb=" O PRO0k 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER0k 56 " --> pdb=" O PHE0k 52 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE0k 57 " --> pdb=" O LEU0k 53 " (cutoff:3.500A) Processing helix chain '0k' and resid 130 through 154 Processing helix chain '0k' and resid 155 through 157 No H-bonds generated for 'chain '0k' and resid 155 through 157' Processing helix chain '0k' and resid 167 through 178 removed outlier: 4.149A pdb=" N GLN0k 173 " --> pdb=" O LEU0k 169 " (cutoff:3.500A) Processing helix chain '0k' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0k 212 " --> pdb=" O ASP0k 208 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU0k 220 " --> pdb=" O ALA0k 216 " (cutoff:3.500A) Processing helix chain '0k' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0k 256 " --> pdb=" O SER0k 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0k 257 " --> pdb=" O SER0k 253 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER0k 260 " --> pdb=" O VAL0k 256 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG0k 261 " --> pdb=" O PHE0k 257 " (cutoff:3.500A) Processing helix chain '0k' and resid 264 through 272 removed outlier: 4.957A pdb=" N GLU0k 270 " --> pdb=" O GLU0k 266 " (cutoff:3.500A) Processing helix chain '0l' and resid 22 through 33 removed outlier: 3.854A pdb=" N LEU0l 28 " --> pdb=" O PHE0l 24 " (cutoff:3.500A) Processing helix chain '0l' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0l 54 " --> pdb=" O PRO0l 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER0l 56 " --> pdb=" O PHE0l 52 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE0l 57 " --> pdb=" O LEU0l 53 " (cutoff:3.500A) Processing helix chain '0l' and resid 130 through 154 Processing helix chain '0l' and resid 155 through 157 No H-bonds generated for 'chain '0l' and resid 155 through 157' Processing helix chain '0l' and resid 167 through 178 removed outlier: 4.148A pdb=" N GLN0l 173 " --> pdb=" O LEU0l 169 " (cutoff:3.500A) Processing helix chain '0l' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0l 212 " --> pdb=" O ASP0l 208 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU0l 220 " --> pdb=" O ALA0l 216 " (cutoff:3.500A) Processing helix chain '0l' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0l 256 " --> pdb=" O SER0l 252 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE0l 257 " --> pdb=" O SER0l 253 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER0l 260 " --> pdb=" O VAL0l 256 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG0l 261 " --> pdb=" O PHE0l 257 " (cutoff:3.500A) Processing helix chain '0l' and resid 264 through 272 removed outlier: 4.958A pdb=" N GLU0l 270 " --> pdb=" O GLU0l 266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '0a' and resid 40 through 42 Processing sheet with id=AA2, first strand: chain '0a' and resid 62 through 63 Processing sheet with id=AA3, first strand: chain '0a' and resid 78 through 80 Processing sheet with id=AA4, first strand: chain '0a' and resid 160 through 161 Processing sheet with id=AA5, first strand: chain '0a' and resid 184 through 185 removed outlier: 7.111A pdb=" N VAL0a 184 " --> pdb=" O ILE0l 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain '0b' and resid 40 through 42 Processing sheet with id=AA7, first strand: chain '0b' and resid 62 through 63 Processing sheet with id=AA8, first strand: chain '0b' and resid 78 through 80 Processing sheet with id=AA9, first strand: chain '0b' and resid 160 through 161 Processing sheet with id=AB1, first strand: chain '0c' and resid 40 through 42 Processing sheet with id=AB2, first strand: chain '0c' and resid 62 through 63 Processing sheet with id=AB3, first strand: chain '0c' and resid 78 through 80 Processing sheet with id=AB4, first strand: chain '0c' and resid 160 through 161 Processing sheet with id=AB5, first strand: chain '0d' and resid 40 through 42 Processing sheet with id=AB6, first strand: chain '0d' and resid 62 through 63 Processing sheet with id=AB7, first strand: chain '0d' and resid 78 through 80 Processing sheet with id=AB8, first strand: chain '0d' and resid 160 through 161 Processing sheet with id=AB9, first strand: chain '0e' and resid 40 through 42 Processing sheet with id=AC1, first strand: chain '0e' and resid 62 through 63 Processing sheet with id=AC2, first strand: chain '0e' and resid 78 through 80 Processing sheet with id=AC3, first strand: chain '0e' and resid 160 through 161 Processing sheet with id=AC4, first strand: chain '0f' and resid 40 through 42 Processing sheet with id=AC5, first strand: chain '0f' and resid 62 through 63 Processing sheet with id=AC6, first strand: chain '0f' and resid 78 through 80 Processing sheet with id=AC7, first strand: chain '0f' and resid 160 through 161 Processing sheet with id=AC8, first strand: chain '0g' and resid 40 through 42 Processing sheet with id=AC9, first strand: chain '0g' and resid 62 through 63 Processing sheet with id=AD1, first strand: chain '0g' and resid 78 through 80 Processing sheet with id=AD2, first strand: chain '0g' and resid 160 through 161 Processing sheet with id=AD3, first strand: chain '0h' and resid 40 through 42 Processing sheet with id=AD4, first strand: chain '0h' and resid 62 through 63 Processing sheet with id=AD5, first strand: chain '0h' and resid 78 through 80 Processing sheet with id=AD6, first strand: chain '0h' and resid 160 through 161 Processing sheet with id=AD7, first strand: chain '0i' and resid 40 through 42 Processing sheet with id=AD8, first strand: chain '0i' and resid 62 through 63 Processing sheet with id=AD9, first strand: chain '0i' and resid 78 through 80 Processing sheet with id=AE1, first strand: chain '0i' and resid 160 through 161 Processing sheet with id=AE2, first strand: chain '0j' and resid 40 through 42 Processing sheet with id=AE3, first strand: chain '0j' and resid 62 through 63 Processing sheet with id=AE4, first strand: chain '0j' and resid 78 through 80 Processing sheet with id=AE5, first strand: chain '0j' and resid 160 through 161 Processing sheet with id=AE6, first strand: chain '0k' and resid 40 through 42 Processing sheet with id=AE7, first strand: chain '0k' and resid 62 through 63 Processing sheet with id=AE8, first strand: chain '0k' and resid 78 through 80 Processing sheet with id=AE9, first strand: chain '0k' and resid 160 through 161 Processing sheet with id=AF1, first strand: chain '0l' and resid 40 through 42 Processing sheet with id=AF2, first strand: chain '0l' and resid 62 through 63 Processing sheet with id=AF3, first strand: chain '0l' and resid 78 through 80 863 hydrogen bonds defined for protein. 2481 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: 3.83 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6951 1.33 - 1.45: 4657 1.45 - 1.57: 13976 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 25728 Sorted by residual: bond pdb=" N ILE0c 227 " pdb=" CA ILE0c 227 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.11e-02 8.12e+03 1.50e+01 bond pdb=" N ILE0k 227 " pdb=" CA ILE0k 227 " ideal model delta sigma weight residual 1.456 1.498 -0.043 1.11e-02 8.12e+03 1.48e+01 bond pdb=" N ILE0f 227 " pdb=" CA ILE0f 227 " ideal model delta sigma weight residual 1.456 1.498 -0.043 1.11e-02 8.12e+03 1.47e+01 bond pdb=" N ILE0b 227 " pdb=" CA ILE0b 227 " ideal model delta sigma weight residual 1.456 1.498 -0.043 1.11e-02 8.12e+03 1.47e+01 bond pdb=" N ILE0i 227 " pdb=" CA ILE0i 227 " ideal model delta sigma weight residual 1.456 1.498 -0.043 1.11e-02 8.12e+03 1.47e+01 ... (remaining 25723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 32337 2.05 - 4.10: 2151 4.10 - 6.14: 264 6.14 - 8.19: 60 8.19 - 10.24: 48 Bond angle restraints: 34860 Sorted by residual: angle pdb=" N ALA0j 187 " pdb=" CA ALA0j 187 " pdb=" C ALA0j 187 " ideal model delta sigma weight residual 108.07 116.19 -8.12 1.38e+00 5.25e-01 3.46e+01 angle pdb=" N ALA0f 187 " pdb=" CA ALA0f 187 " pdb=" C ALA0f 187 " ideal model delta sigma weight residual 108.07 116.19 -8.12 1.38e+00 5.25e-01 3.46e+01 angle pdb=" N ALA0h 187 " pdb=" CA ALA0h 187 " pdb=" C ALA0h 187 " ideal model delta sigma weight residual 108.07 116.18 -8.11 1.38e+00 5.25e-01 3.46e+01 angle pdb=" N ALA0i 187 " pdb=" CA ALA0i 187 " pdb=" C ALA0i 187 " ideal model delta sigma weight residual 108.07 116.18 -8.11 1.38e+00 5.25e-01 3.45e+01 angle pdb=" N ALA0a 187 " pdb=" CA ALA0a 187 " pdb=" C ALA0a 187 " ideal model delta sigma weight residual 108.07 116.15 -8.08 1.38e+00 5.25e-01 3.43e+01 ... (remaining 34855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.44: 12962 10.44 - 20.88: 1811 20.88 - 31.33: 407 31.33 - 41.77: 204 41.77 - 52.21: 84 Dihedral angle restraints: 15468 sinusoidal: 6300 harmonic: 9168 Sorted by residual: dihedral pdb=" CA THR0b 91 " pdb=" C THR0b 91 " pdb=" N VAL0b 92 " pdb=" CA VAL0b 92 " ideal model delta harmonic sigma weight residual 180.00 -137.44 -42.56 0 5.00e+00 4.00e-02 7.24e+01 dihedral pdb=" CA THR0k 91 " pdb=" C THR0k 91 " pdb=" N VAL0k 92 " pdb=" CA VAL0k 92 " ideal model delta harmonic sigma weight residual 180.00 -137.51 -42.49 0 5.00e+00 4.00e-02 7.22e+01 dihedral pdb=" CA THR0j 91 " pdb=" C THR0j 91 " pdb=" N VAL0j 92 " pdb=" CA VAL0j 92 " ideal model delta harmonic sigma weight residual 180.00 -137.51 -42.49 0 5.00e+00 4.00e-02 7.22e+01 ... (remaining 15465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2347 0.048 - 0.096: 918 0.096 - 0.144: 313 0.144 - 0.192: 154 0.192 - 0.240: 24 Chirality restraints: 3756 Sorted by residual: chirality pdb=" CB VAL0d 70 " pdb=" CA VAL0d 70 " pdb=" CG1 VAL0d 70 " pdb=" CG2 VAL0d 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB VAL0c 70 " pdb=" CA VAL0c 70 " pdb=" CG1 VAL0c 70 " pdb=" CG2 VAL0c 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB VAL0g 70 " pdb=" CA VAL0g 70 " pdb=" CG1 VAL0g 70 " pdb=" CG2 VAL0g 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 3753 not shown) Planarity restraints: 4548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN0e 59 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.24e+00 pdb=" C GLN0e 59 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN0e 59 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE0e 60 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN0b 59 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.21e+00 pdb=" C GLN0b 59 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN0b 59 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE0b 60 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN0l 59 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C GLN0l 59 " 0.050 2.00e-02 2.50e+03 pdb=" O GLN0l 59 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE0l 60 " -0.017 2.00e-02 2.50e+03 ... (remaining 4545 not shown) Histogram of nonbonded interaction distances: 0.73 - 1.56: 36 1.56 - 2.40: 172 2.40 - 3.23: 25127 3.23 - 4.07: 62972 4.07 - 4.90: 114396 Warning: very small nonbonded interaction distances. Nonbonded interactions: 202703 Sorted by model distance: nonbonded pdb=" CD GLU0f 248 " pdb=" O LYS0g 228 " model vdw 0.726 3.270 nonbonded pdb=" CD GLU0j 248 " pdb=" O LYS0k 228 " model vdw 0.734 3.270 nonbonded pdb=" CD GLU0i 248 " pdb=" O LYS0j 228 " model vdw 0.739 3.270 nonbonded pdb=" CD GLU0e 248 " pdb=" O LYS0f 228 " model vdw 0.740 3.270 nonbonded pdb=" CD GLU0k 248 " pdb=" O LYS0l 228 " model vdw 0.742 3.270 ... (remaining 202698 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: 0.05 Found NCS groups: ncs_group { reference = chain '0a' selection = chain '0b' selection = chain '0c' selection = chain '0d' selection = chain '0e' selection = chain '0f' selection = chain '0g' selection = chain '0h' selection = chain '0i' selection = chain '0j' selection = chain '0k' selection = chain '0l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 17.410 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5858 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 : 0.006 0.047 25728 Z= 0.325 Angle : 1.156 10.241 34860 Z= 0.697 Chirality : 0.064 0.240 3756 Planarity : 0.006 0.047 4548 Dihedral : 11.549 52.212 9540 Min Nonbonded Distance : 0.726 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 1.59 % Allowed : 14.29 % Favored : 84.13 % Rotamer: Outliers : 1.75 % Allowed : 0.88 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.94 (0.12), residues: 3024 helix: -3.25 (0.10), residues: 1056 sheet: -3.14 (0.26), residues: 372 loop : -3.39 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG0d 110 TYR 0.023 0.004 TYR0h 175 PHE 0.027 0.004 PHE0k 24 TRP 0.014 0.004 TRP0e 41 HIS 0.006 0.003 HIS0g 188 Details of bonding type rmsd covalent geometry : bond 0.00627 (25728) covalent geometry : angle 1.15643 (34860) hydrogen bonds : bond 0.26299 ( 863) hydrogen bonds : angle 9.12997 ( 2481) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 1108 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 40 GLU cc_start: 0.6422 (mm-30) cc_final: 0.5850 (mt-10) REVERT: 0a 68 ASP cc_start: 0.5120 (m-30) cc_final: 0.4772 (m-30) REVERT: 0a 141 LEU cc_start: 0.8707 (tp) cc_final: 0.8373 (mt) REVERT: 0a 152 GLN cc_start: 0.8414 (mt0) cc_final: 0.8071 (mt0) REVERT: 0a 213 GLN cc_start: 0.8022 (tp40) cc_final: 0.7812 (tp40) REVERT: 0a 217 VAL cc_start: 0.8103 (t) cc_final: 0.7618 (t) REVERT: 0a 281 ARG cc_start: 0.8059 (mmm160) cc_final: 0.7654 (mmm-85) REVERT: 0b 30 TYR cc_start: 0.6539 (t80) cc_final: 0.6276 (t80) REVERT: 0b 40 GLU cc_start: 0.6436 (mm-30) cc_final: 0.6114 (mt-10) REVERT: 0b 44 LEU cc_start: 0.7667 (mt) cc_final: 0.7411 (mt) REVERT: 0b 68 ASP cc_start: 0.4736 (m-30) cc_final: 0.4254 (m-30) REVERT: 0b 141 LEU cc_start: 0.8723 (tp) cc_final: 0.8492 (mt) REVERT: 0b 213 GLN cc_start: 0.7909 (tp40) cc_final: 0.7683 (tp40) REVERT: 0b 217 VAL cc_start: 0.8196 (t) cc_final: 0.7705 (t) REVERT: 0b 249 GLN cc_start: 0.5696 (tt0) cc_final: 0.5094 (tt0) REVERT: 0b 281 ARG cc_start: 0.8143 (mmm160) cc_final: 0.7826 (mmm160) REVERT: 0c 40 GLU cc_start: 0.6603 (mm-30) cc_final: 0.6296 (mt-10) REVERT: 0c 44 LEU cc_start: 0.7948 (mt) cc_final: 0.7691 (mt) REVERT: 0c 68 ASP cc_start: 0.4894 (m-30) cc_final: 0.4671 (m-30) REVERT: 0c 141 LEU cc_start: 0.8851 (tp) cc_final: 0.8582 (mt) REVERT: 0c 145 LYS cc_start: 0.7365 (tttp) cc_final: 0.7151 (tptp) REVERT: 0c 262 GLU cc_start: 0.7416 (tp30) cc_final: 0.7162 (tp30) REVERT: 0c 270 GLU cc_start: 0.5124 (mt-10) cc_final: 0.4790 (mt-10) REVERT: 0d 40 GLU cc_start: 0.6456 (mm-30) cc_final: 0.6058 (mt-10) REVERT: 0d 50 PRO cc_start: 0.5941 (Cg_endo) cc_final: 0.5649 (Cg_exo) REVERT: 0d 68 ASP cc_start: 0.5136 (m-30) cc_final: 0.4681 (m-30) REVERT: 0d 141 LEU cc_start: 0.8783 (tp) cc_final: 0.8469 (mt) REVERT: 0d 152 GLN cc_start: 0.8343 (mt0) cc_final: 0.8083 (mt0) REVERT: 0d 213 GLN cc_start: 0.8033 (tp40) cc_final: 0.7696 (tp40) REVERT: 0d 217 VAL cc_start: 0.8156 (t) cc_final: 0.7837 (t) REVERT: 0d 281 ARG cc_start: 0.8003 (mmm160) cc_final: 0.7748 (mmm-85) REVERT: 0e 30 TYR cc_start: 0.6692 (t80) cc_final: 0.6422 (t80) REVERT: 0e 68 ASP cc_start: 0.4659 (m-30) cc_final: 0.4138 (m-30) REVERT: 0e 108 ASN cc_start: 0.3251 (t0) cc_final: 0.2904 (p0) REVERT: 0e 141 LEU cc_start: 0.8827 (tp) cc_final: 0.8547 (mt) REVERT: 0e 152 GLN cc_start: 0.8393 (mt0) cc_final: 0.8140 (mt0) REVERT: 0e 213 GLN cc_start: 0.7807 (tp40) cc_final: 0.7493 (tp40) REVERT: 0e 217 VAL cc_start: 0.8180 (t) cc_final: 0.7779 (t) REVERT: 0e 249 GLN cc_start: 0.6037 (tt0) cc_final: 0.5435 (tt0) REVERT: 0e 281 ARG cc_start: 0.7982 (mmm160) cc_final: 0.7359 (mmm160) REVERT: 0f 40 GLU cc_start: 0.6686 (mm-30) cc_final: 0.6152 (mt-10) REVERT: 0f 44 LEU cc_start: 0.7853 (mt) cc_final: 0.7599 (mt) REVERT: 0f 50 PRO cc_start: 0.5907 (Cg_endo) cc_final: 0.5615 (Cg_exo) REVERT: 0f 141 LEU cc_start: 0.8894 (tp) cc_final: 0.8643 (mt) REVERT: 0f 249 GLN cc_start: 0.5547 (tt0) cc_final: 0.5237 (tt0) REVERT: 0f 270 GLU cc_start: 0.5172 (mt-10) cc_final: 0.4819 (mt-10) REVERT: 0g 32 GLN cc_start: 0.7676 (mt0) cc_final: 0.7249 (mt0) REVERT: 0g 36 TYR cc_start: 0.7103 (p90) cc_final: 0.6729 (p90) REVERT: 0g 40 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6093 (mt-10) REVERT: 0g 50 PRO cc_start: 0.5893 (Cg_endo) cc_final: 0.5598 (Cg_exo) REVERT: 0g 68 ASP cc_start: 0.5328 (m-30) cc_final: 0.4856 (m-30) REVERT: 0g 141 LEU cc_start: 0.8747 (tp) cc_final: 0.8424 (mt) REVERT: 0g 152 GLN cc_start: 0.8442 (mt0) cc_final: 0.8202 (mt0) REVERT: 0g 213 GLN cc_start: 0.8059 (tp40) cc_final: 0.7789 (tp40) REVERT: 0g 217 VAL cc_start: 0.8156 (t) cc_final: 0.7870 (t) REVERT: 0g 281 ARG cc_start: 0.8085 (mmm160) cc_final: 0.7775 (mmm-85) REVERT: 0h 30 TYR cc_start: 0.6542 (t80) cc_final: 0.6249 (t80) REVERT: 0h 40 GLU cc_start: 0.6493 (mm-30) cc_final: 0.6167 (mt-10) REVERT: 0h 44 LEU cc_start: 0.7614 (mt) cc_final: 0.7373 (mt) REVERT: 0h 68 ASP cc_start: 0.4539 (m-30) cc_final: 0.4205 (m-30) REVERT: 0h 106 LEU cc_start: 0.4200 (tp) cc_final: 0.3920 (tp) REVERT: 0h 141 LEU cc_start: 0.8766 (tp) cc_final: 0.8498 (mt) REVERT: 0h 213 GLN cc_start: 0.7922 (tp40) cc_final: 0.7648 (tp40) REVERT: 0h 217 VAL cc_start: 0.8193 (t) cc_final: 0.7689 (t) REVERT: 0h 249 GLN cc_start: 0.5725 (tt0) cc_final: 0.5162 (tt0) REVERT: 0h 281 ARG cc_start: 0.8133 (mmm160) cc_final: 0.7859 (mmm160) REVERT: 0i 40 GLU cc_start: 0.6763 (mm-30) cc_final: 0.6174 (mt-10) REVERT: 0i 68 ASP cc_start: 0.5032 (m-30) cc_final: 0.4738 (m-30) REVERT: 0i 141 LEU cc_start: 0.8874 (tp) cc_final: 0.8441 (mt) REVERT: 0i 249 GLN cc_start: 0.5506 (tt0) cc_final: 0.5281 (tt0) REVERT: 0i 270 GLU cc_start: 0.5103 (mt-10) cc_final: 0.4839 (mt-10) REVERT: 0j 40 GLU cc_start: 0.6431 (mm-30) cc_final: 0.5876 (mt-10) REVERT: 0j 68 ASP cc_start: 0.5173 (m-30) cc_final: 0.4849 (m-30) REVERT: 0j 141 LEU cc_start: 0.8783 (tp) cc_final: 0.8437 (mt) REVERT: 0j 213 GLN cc_start: 0.8014 (tp40) cc_final: 0.7790 (tp40) REVERT: 0j 217 VAL cc_start: 0.8166 (t) cc_final: 0.7932 (t) REVERT: 0j 281 ARG cc_start: 0.8044 (mmm160) cc_final: 0.7762 (mmm-85) REVERT: 0k 30 TYR cc_start: 0.6668 (t80) cc_final: 0.6366 (t80) REVERT: 0k 40 GLU cc_start: 0.6427 (mm-30) cc_final: 0.6199 (mt-10) REVERT: 0k 44 LEU cc_start: 0.7692 (mt) cc_final: 0.7326 (mt) REVERT: 0k 68 ASP cc_start: 0.4747 (m-30) cc_final: 0.4257 (m-30) REVERT: 0k 141 LEU cc_start: 0.8792 (tp) cc_final: 0.8556 (mt) REVERT: 0k 213 GLN cc_start: 0.7935 (tp40) cc_final: 0.7676 (tp40) REVERT: 0k 217 VAL cc_start: 0.8195 (t) cc_final: 0.7722 (t) REVERT: 0k 228 LYS cc_start: 0.6013 (OUTLIER) cc_final: 0.5652 (mmtm) REVERT: 0k 281 ARG cc_start: 0.8060 (mmm160) cc_final: 0.7722 (mmm160) REVERT: 0l 40 GLU cc_start: 0.6677 (mm-30) cc_final: 0.6365 (mt-10) REVERT: 0l 44 LEU cc_start: 0.7871 (mt) cc_final: 0.7580 (mt) REVERT: 0l 68 ASP cc_start: 0.4925 (m-30) cc_final: 0.4694 (m-30) REVERT: 0l 106 LEU cc_start: 0.4175 (tp) cc_final: 0.3842 (tt) REVERT: 0l 141 LEU cc_start: 0.8820 (tp) cc_final: 0.8300 (mt) REVERT: 0l 205 TYR cc_start: 0.8462 (t80) cc_final: 0.8169 (t80) REVERT: 0l 217 VAL cc_start: 0.7937 (t) cc_final: 0.7423 (t) REVERT: 0l 250 ILE cc_start: 0.6933 (pt) cc_final: 0.6631 (pt) REVERT: 0l 262 GLU cc_start: 0.7436 (tp30) cc_final: 0.7119 (tp30) outliers start: 48 outliers final: 20 residues processed: 1144 average time/residue: 0.1762 time to fit residues: 308.6167 Evaluate side-chains 746 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 725 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 12 ILE Chi-restraints excluded: chain 0a residue 225 LEU Chi-restraints excluded: chain 0b residue 12 ILE Chi-restraints excluded: chain 0b residue 225 LEU Chi-restraints excluded: chain 0c residue 12 ILE Chi-restraints excluded: chain 0d residue 12 ILE Chi-restraints excluded: chain 0d residue 225 LEU Chi-restraints excluded: chain 0e residue 12 ILE Chi-restraints excluded: chain 0e residue 225 LEU Chi-restraints excluded: chain 0f residue 12 ILE Chi-restraints excluded: chain 0g residue 12 ILE Chi-restraints excluded: chain 0g residue 225 LEU Chi-restraints excluded: chain 0h residue 12 ILE Chi-restraints excluded: chain 0h residue 225 LEU Chi-restraints excluded: chain 0i residue 12 ILE Chi-restraints excluded: chain 0j residue 12 ILE Chi-restraints excluded: chain 0j residue 225 LEU Chi-restraints excluded: chain 0k residue 12 ILE Chi-restraints excluded: chain 0k residue 225 LEU Chi-restraints excluded: chain 0k residue 228 LYS Chi-restraints excluded: chain 0l residue 12 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 168 GLN 0a 173 GLN 0a 188 HIS 0b 89 GLN 0b 123 ASN 0b 153 ASN ** 0b 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 173 GLN 0b 188 HIS ** 0c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 89 GLN 0c 123 ASN ** 0c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 168 GLN 0c 173 GLN 0c 188 HIS 0d 26 HIS 0d 89 GLN 0d 123 ASN 0d 153 ASN ** 0d 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 168 GLN 0d 173 GLN 0d 188 HIS 0e 26 HIS 0e 89 GLN 0e 123 ASN ** 0e 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 168 GLN 0e 188 HIS ** 0f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 89 GLN 0f 123 ASN 0f 167 ASN 0f 168 GLN 0f 173 GLN 0f 188 HIS 0g 26 HIS 0g 89 GLN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 153 ASN 0g 167 ASN 0g 168 GLN 0g 173 GLN 0g 188 HIS 0h 26 HIS 0h 89 GLN 0h 123 ASN 0h 153 ASN ** 0h 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 173 GLN 0h 188 HIS 0i 32 GLN 0i 89 GLN 0i 123 ASN ** 0i 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 168 GLN 0i 188 HIS 0j 26 HIS 0j 123 ASN 0j 153 ASN 0j 167 ASN 0j 168 GLN 0j 173 GLN 0j 188 HIS ** 0k 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 26 HIS 0k 123 ASN 0k 153 ASN 0k 167 ASN 0k 168 GLN 0k 188 HIS ** 0l 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 123 ASN ** 0l 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 168 GLN 0l 173 GLN 0l 188 HIS Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.212984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.199828 restraints weight = 46435.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.202970 restraints weight = 29672.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.205350 restraints weight = 20261.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.206788 restraints weight = 14586.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.207850 restraints weight = 11212.017| |-----------------------------------------------------------------------------| r_work (final): 0.4523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5937 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25728 Z= 0.178 Angle : 0.836 7.280 34860 Z= 0.458 Chirality : 0.050 0.191 3756 Planarity : 0.005 0.047 4548 Dihedral : 8.933 56.470 3392 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 1.59 % Allowed : 14.68 % Favored : 83.73 % Rotamer: Outliers : 4.20 % Allowed : 13.34 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.68 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.14), residues: 3024 helix: -1.62 (0.14), residues: 1140 sheet: -3.30 (0.25), residues: 372 loop : -2.75 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG0j 162 TYR 0.030 0.002 TYR0g 36 PHE 0.032 0.002 PHE0g 24 TRP 0.018 0.002 TRP0g 41 HIS 0.009 0.002 HIS0k 26 Details of bonding type rmsd covalent geometry : bond 0.00388 (25728) covalent geometry : angle 0.83603 (34860) hydrogen bonds : bond 0.04976 ( 863) hydrogen bonds : angle 5.87231 ( 2481) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 799 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 18 GLN cc_start: 0.7751 (mm110) cc_final: 0.7520 (tp40) REVERT: 0a 36 TYR cc_start: 0.5882 (p90) cc_final: 0.5659 (p90) REVERT: 0a 40 GLU cc_start: 0.6078 (mm-30) cc_final: 0.5745 (mt-10) REVERT: 0a 100 TYR cc_start: 0.5331 (OUTLIER) cc_final: 0.4435 (t80) REVERT: 0a 140 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8276 (tm-30) REVERT: 0a 141 LEU cc_start: 0.8647 (tp) cc_final: 0.8301 (mt) REVERT: 0a 153 ASN cc_start: 0.7098 (t0) cc_final: 0.6765 (t0) REVERT: 0b 18 GLN cc_start: 0.7670 (mm110) cc_final: 0.7343 (tp-100) REVERT: 0b 123 ASN cc_start: 0.7718 (t0) cc_final: 0.7355 (t0) REVERT: 0b 186 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.6848 (m-80) REVERT: 0b 222 MET cc_start: 0.8206 (mmm) cc_final: 0.7886 (mmm) REVERT: 0b 225 LEU cc_start: 0.8613 (mt) cc_final: 0.8136 (mt) REVERT: 0c 18 GLN cc_start: 0.6543 (mt0) cc_final: 0.6328 (mt0) REVERT: 0c 22 ARG cc_start: 0.7567 (mtp85) cc_final: 0.7283 (mtt-85) REVERT: 0c 100 TYR cc_start: 0.5398 (OUTLIER) cc_final: 0.4688 (t80) REVERT: 0c 141 LEU cc_start: 0.8763 (tp) cc_final: 0.8537 (mt) REVERT: 0c 220 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7161 (tp30) REVERT: 0c 222 MET cc_start: 0.8339 (mmm) cc_final: 0.8108 (mmm) REVERT: 0d 18 GLN cc_start: 0.7708 (mm110) cc_final: 0.7480 (tp40) REVERT: 0d 100 TYR cc_start: 0.4893 (OUTLIER) cc_final: 0.3928 (t80) REVERT: 0d 126 MET cc_start: 0.8282 (mtt) cc_final: 0.7895 (mtt) REVERT: 0d 140 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8281 (tm-30) REVERT: 0d 141 LEU cc_start: 0.8772 (tp) cc_final: 0.8453 (mt) REVERT: 0d 217 VAL cc_start: 0.7587 (t) cc_final: 0.7115 (t) REVERT: 0e 18 GLN cc_start: 0.7810 (mm110) cc_final: 0.7282 (tp-100) REVERT: 0e 30 TYR cc_start: 0.6887 (t80) cc_final: 0.6438 (t80) REVERT: 0e 123 ASN cc_start: 0.7700 (t0) cc_final: 0.7363 (t0) REVERT: 0e 126 MET cc_start: 0.8429 (mtt) cc_final: 0.8024 (mtt) REVERT: 0e 213 GLN cc_start: 0.7598 (tp40) cc_final: 0.7356 (tm-30) REVERT: 0f 22 ARG cc_start: 0.7451 (mtp85) cc_final: 0.7213 (mtt-85) REVERT: 0f 30 TYR cc_start: 0.6791 (t80) cc_final: 0.5776 (t80) REVERT: 0f 205 TYR cc_start: 0.8430 (t80) cc_final: 0.8085 (t80) REVERT: 0f 220 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6964 (tp30) REVERT: 0f 225 LEU cc_start: 0.8600 (mt) cc_final: 0.8386 (mp) REVERT: 0g 18 GLN cc_start: 0.7777 (mm110) cc_final: 0.6926 (tp-100) REVERT: 0g 100 TYR cc_start: 0.5296 (OUTLIER) cc_final: 0.4161 (t80) REVERT: 0g 124 ASN cc_start: 0.7951 (p0) cc_final: 0.7622 (p0) REVERT: 0g 140 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8259 (tm-30) REVERT: 0g 141 LEU cc_start: 0.8631 (tp) cc_final: 0.8293 (mt) REVERT: 0g 217 VAL cc_start: 0.7548 (t) cc_final: 0.7167 (t) REVERT: 0h 44 LEU cc_start: 0.7267 (mt) cc_final: 0.6988 (mt) REVERT: 0h 141 LEU cc_start: 0.8595 (tp) cc_final: 0.8390 (mt) REVERT: 0h 145 LYS cc_start: 0.7883 (tmtt) cc_final: 0.7644 (tptp) REVERT: 0h 194 ASP cc_start: 0.6898 (t0) cc_final: 0.6583 (t0) REVERT: 0h 225 LEU cc_start: 0.8609 (mt) cc_final: 0.8122 (mt) REVERT: 0i 26 HIS cc_start: 0.8180 (t-90) cc_final: 0.7877 (t-90) REVERT: 0i 141 LEU cc_start: 0.8819 (tp) cc_final: 0.8539 (mt) REVERT: 0i 194 ASP cc_start: 0.6728 (t0) cc_final: 0.6093 (t0) REVERT: 0i 222 MET cc_start: 0.8290 (mmm) cc_final: 0.7971 (mmm) REVERT: 0j 100 TYR cc_start: 0.5420 (OUTLIER) cc_final: 0.4414 (t80) REVERT: 0k 18 GLN cc_start: 0.7509 (mm110) cc_final: 0.6431 (tt0) REVERT: 0k 30 TYR cc_start: 0.6900 (t80) cc_final: 0.6522 (t80) REVERT: 0k 123 ASN cc_start: 0.7606 (t0) cc_final: 0.7253 (t0) REVERT: 0k 126 MET cc_start: 0.8341 (mtt) cc_final: 0.7888 (mtt) REVERT: 0k 152 GLN cc_start: 0.7805 (mt0) cc_final: 0.7523 (mt0) REVERT: 0k 186 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.6868 (m-80) REVERT: 0k 222 MET cc_start: 0.8229 (mmm) cc_final: 0.7985 (mmm) REVERT: 0k 225 LEU cc_start: 0.8593 (mt) cc_final: 0.8088 (mt) outliers start: 115 outliers final: 56 residues processed: 881 average time/residue: 0.1897 time to fit residues: 249.8188 Evaluate side-chains 733 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 670 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 25 ILE Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 170 SER Chi-restraints excluded: chain 0b residue 25 ILE Chi-restraints excluded: chain 0b residue 33 SER Chi-restraints excluded: chain 0b residue 100 TYR Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0b residue 278 VAL Chi-restraints excluded: chain 0c residue 12 ILE Chi-restraints excluded: chain 0c residue 25 ILE Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 170 SER Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0c residue 207 VAL Chi-restraints excluded: chain 0c residue 278 VAL Chi-restraints excluded: chain 0d residue 25 ILE Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0d residue 278 VAL Chi-restraints excluded: chain 0e residue 25 ILE Chi-restraints excluded: chain 0e residue 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL Chi-restraints excluded: chain 0f residue 12 ILE Chi-restraints excluded: chain 0f residue 100 TYR Chi-restraints excluded: chain 0f residue 170 SER Chi-restraints excluded: chain 0f residue 186 PHE Chi-restraints excluded: chain 0f residue 198 VAL Chi-restraints excluded: chain 0f residue 207 VAL Chi-restraints excluded: chain 0f residue 278 VAL Chi-restraints excluded: chain 0g residue 12 ILE Chi-restraints excluded: chain 0g residue 25 ILE Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 170 SER Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 278 VAL Chi-restraints excluded: chain 0h residue 12 ILE Chi-restraints excluded: chain 0h residue 25 ILE Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0h residue 278 VAL Chi-restraints excluded: chain 0i residue 25 ILE Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 133 THR Chi-restraints excluded: chain 0i residue 170 SER Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0i residue 278 VAL Chi-restraints excluded: chain 0j residue 25 ILE Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 170 SER Chi-restraints excluded: chain 0j residue 278 VAL Chi-restraints excluded: chain 0k residue 25 ILE Chi-restraints excluded: chain 0k residue 100 TYR Chi-restraints excluded: chain 0k residue 186 PHE Chi-restraints excluded: chain 0k residue 198 VAL Chi-restraints excluded: chain 0k residue 207 VAL Chi-restraints excluded: chain 0k residue 278 VAL Chi-restraints excluded: chain 0l residue 12 ILE Chi-restraints excluded: chain 0l residue 54 GLU Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 170 SER Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 223 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 121 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 170 optimal weight: 0.7980 chunk 206 optimal weight: 10.0000 chunk 293 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 144 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 167 ASN ** 0b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 151 ASN ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 167 ASN 0b 168 GLN ** 0b 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 32 GLN 0c 58 HIS ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 167 ASN 0c 211 ASN 0d 59 GLN ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 167 ASN 0e 167 ASN 0e 173 GLN 0f 32 GLN ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 59 GLN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 151 ASN ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 167 ASN 0h 168 GLN ** 0h 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 173 GLN ** 0j 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 59 GLN ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 151 ASN ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 151 ASN ** 0k 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 32 GLN ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 167 ASN 0l 211 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.207583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.194932 restraints weight = 46864.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.197958 restraints weight = 30161.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.200115 restraints weight = 20762.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.201566 restraints weight = 15071.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.202607 restraints weight = 11401.550| |-----------------------------------------------------------------------------| r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25728 Z= 0.182 Angle : 0.798 10.544 34860 Z= 0.437 Chirality : 0.048 0.257 3756 Planarity : 0.005 0.063 4548 Dihedral : 8.396 59.652 3358 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.79 % Allowed : 16.20 % Favored : 83.00 % Rotamer: Outliers : 3.98 % Allowed : 13.27 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.15), residues: 3024 helix: -0.93 (0.14), residues: 1140 sheet: -3.31 (0.24), residues: 372 loop : -2.52 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG0c 281 TYR 0.025 0.002 TYR0f 205 PHE 0.028 0.002 PHE0g 24 TRP 0.014 0.002 TRP0e 23 HIS 0.003 0.001 HIS0d 58 Details of bonding type rmsd covalent geometry : bond 0.00398 (25728) covalent geometry : angle 0.79797 (34860) hydrogen bonds : bond 0.04755 ( 863) hydrogen bonds : angle 5.54563 ( 2481) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 724 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 18 GLN cc_start: 0.7533 (mm110) cc_final: 0.7050 (tp40) REVERT: 0a 100 TYR cc_start: 0.5485 (OUTLIER) cc_final: 0.4661 (t80) REVERT: 0a 151 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8030 (t0) REVERT: 0a 186 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7180 (m-80) REVERT: 0a 194 ASP cc_start: 0.6882 (t0) cc_final: 0.6669 (t0) REVERT: 0a 213 GLN cc_start: 0.7927 (tp40) cc_final: 0.7394 (tm-30) REVERT: 0a 220 GLU cc_start: 0.7483 (tp30) cc_final: 0.7223 (tp30) REVERT: 0a 249 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7421 (mm-40) REVERT: 0b 18 GLN cc_start: 0.7629 (mm110) cc_final: 0.7156 (tp-100) REVERT: 0b 44 LEU cc_start: 0.7301 (mt) cc_final: 0.7019 (mt) REVERT: 0b 153 ASN cc_start: 0.7218 (t0) cc_final: 0.7013 (t0) REVERT: 0b 186 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7082 (m-80) REVERT: 0b 194 ASP cc_start: 0.7681 (t0) cc_final: 0.7211 (t0) REVERT: 0b 221 MET cc_start: 0.6923 (tpp) cc_final: 0.6591 (tpp) REVERT: 0b 222 MET cc_start: 0.8384 (mmm) cc_final: 0.8116 (mmm) REVERT: 0c 32 GLN cc_start: 0.7842 (mt0) cc_final: 0.7325 (mt0) REVERT: 0c 100 TYR cc_start: 0.5689 (OUTLIER) cc_final: 0.4950 (t80) REVERT: 0d 18 GLN cc_start: 0.7527 (mm110) cc_final: 0.6803 (tp40) REVERT: 0d 40 GLU cc_start: 0.6337 (mm-30) cc_final: 0.6108 (mm-30) REVERT: 0d 100 TYR cc_start: 0.5211 (OUTLIER) cc_final: 0.4489 (t80) REVERT: 0d 141 LEU cc_start: 0.8811 (tp) cc_final: 0.8505 (mt) REVERT: 0d 151 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8153 (t0) REVERT: 0d 152 GLN cc_start: 0.7984 (mt0) cc_final: 0.7648 (mt0) REVERT: 0d 186 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7059 (m-80) REVERT: 0d 213 GLN cc_start: 0.8036 (tp40) cc_final: 0.7559 (tm-30) REVERT: 0d 249 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7062 (mm-40) REVERT: 0e 18 GLN cc_start: 0.7495 (mm110) cc_final: 0.7176 (tp-100) REVERT: 0e 30 TYR cc_start: 0.7068 (t80) cc_final: 0.6540 (t80) REVERT: 0e 186 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.6926 (m-80) REVERT: 0e 213 GLN cc_start: 0.7831 (tp40) cc_final: 0.7543 (tm-30) REVERT: 0e 214 LYS cc_start: 0.8157 (ttpp) cc_final: 0.7853 (ttpp) REVERT: 0e 221 MET cc_start: 0.6867 (tpp) cc_final: 0.6558 (tpp) REVERT: 0e 222 MET cc_start: 0.8295 (mmm) cc_final: 0.8030 (mmm) REVERT: 0f 128 PHE cc_start: 0.7313 (m-80) cc_final: 0.6906 (m-80) REVERT: 0f 186 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7060 (m-80) REVERT: 0f 194 ASP cc_start: 0.7131 (t0) cc_final: 0.6719 (t0) REVERT: 0f 205 TYR cc_start: 0.8687 (t80) cc_final: 0.8250 (t80) REVERT: 0f 220 GLU cc_start: 0.7288 (mm-30) cc_final: 0.7053 (tp30) REVERT: 0g 40 GLU cc_start: 0.6383 (mm-30) cc_final: 0.6074 (mm-30) REVERT: 0g 100 TYR cc_start: 0.5219 (OUTLIER) cc_final: 0.4439 (t80) REVERT: 0g 140 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8339 (tm-30) REVERT: 0g 141 LEU cc_start: 0.8751 (tp) cc_final: 0.8354 (mt) REVERT: 0g 151 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8080 (t0) REVERT: 0g 152 GLN cc_start: 0.7969 (mt0) cc_final: 0.7612 (mt0) REVERT: 0g 186 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7051 (m-80) REVERT: 0g 220 GLU cc_start: 0.7353 (tp30) cc_final: 0.7016 (tp30) REVERT: 0g 249 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7547 (mm-40) REVERT: 0h 30 TYR cc_start: 0.7288 (t80) cc_final: 0.6745 (t80) REVERT: 0h 44 LEU cc_start: 0.7342 (mt) cc_final: 0.7051 (mt) REVERT: 0h 116 ASP cc_start: 0.4778 (t0) cc_final: 0.4517 (t70) REVERT: 0h 126 MET cc_start: 0.8716 (mtp) cc_final: 0.8483 (mtp) REVERT: 0h 186 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7125 (m-80) REVERT: 0h 194 ASP cc_start: 0.7819 (t0) cc_final: 0.7482 (t0) REVERT: 0h 220 GLU cc_start: 0.7327 (tp30) cc_final: 0.7063 (tp30) REVERT: 0i 40 GLU cc_start: 0.6349 (mm-30) cc_final: 0.5944 (mt-10) REVERT: 0i 194 ASP cc_start: 0.7845 (t0) cc_final: 0.7410 (t0) REVERT: 0j 40 GLU cc_start: 0.6420 (mm-30) cc_final: 0.6182 (mm-30) REVERT: 0j 100 TYR cc_start: 0.5267 (OUTLIER) cc_final: 0.4454 (t80) REVERT: 0j 186 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7022 (m-80) REVERT: 0j 249 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7301 (mm-40) REVERT: 0j 281 ARG cc_start: 0.7583 (mmm-85) cc_final: 0.7074 (mmm160) REVERT: 0k 18 GLN cc_start: 0.7172 (mm110) cc_final: 0.6204 (tp-100) REVERT: 0k 30 TYR cc_start: 0.7147 (t80) cc_final: 0.6515 (t80) REVERT: 0k 44 LEU cc_start: 0.7417 (mt) cc_final: 0.7096 (mt) REVERT: 0k 186 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7081 (m-80) REVERT: 0k 194 ASP cc_start: 0.7667 (t0) cc_final: 0.7261 (t0) REVERT: 0k 213 GLN cc_start: 0.7665 (tm-30) cc_final: 0.7458 (tm-30) REVERT: 0l 32 GLN cc_start: 0.7271 (mt0) cc_final: 0.6941 (mt0) REVERT: 0l 213 GLN cc_start: 0.7920 (tp40) cc_final: 0.7329 (tm-30) REVERT: 0l 214 LYS cc_start: 0.7950 (ttpp) cc_final: 0.7639 (ttpp) outliers start: 109 outliers final: 44 residues processed: 802 average time/residue: 0.1819 time to fit residues: 220.9368 Evaluate side-chains 710 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 649 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 151 ASN Chi-restraints excluded: chain 0a residue 170 SER Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0b residue 33 SER Chi-restraints excluded: chain 0b residue 37 GLN Chi-restraints excluded: chain 0b residue 54 GLU Chi-restraints excluded: chain 0b residue 100 TYR Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0b residue 278 VAL Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 170 SER Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0c residue 217 VAL Chi-restraints excluded: chain 0c residue 278 VAL Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 136 LEU Chi-restraints excluded: chain 0d residue 151 ASN Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0e residue 54 GLU Chi-restraints excluded: chain 0e residue 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL Chi-restraints excluded: chain 0f residue 12 ILE Chi-restraints excluded: chain 0f residue 136 LEU Chi-restraints excluded: chain 0f residue 186 PHE Chi-restraints excluded: chain 0f residue 198 VAL Chi-restraints excluded: chain 0f residue 207 VAL Chi-restraints excluded: chain 0f residue 278 VAL Chi-restraints excluded: chain 0g residue 54 GLU Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 136 LEU Chi-restraints excluded: chain 0g residue 151 ASN Chi-restraints excluded: chain 0g residue 170 SER Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0h residue 37 GLN Chi-restraints excluded: chain 0h residue 100 TYR Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0h residue 278 VAL Chi-restraints excluded: chain 0i residue 170 SER Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0i residue 217 VAL Chi-restraints excluded: chain 0i residue 278 VAL Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 170 SER Chi-restraints excluded: chain 0j residue 186 PHE Chi-restraints excluded: chain 0j residue 277 LYS Chi-restraints excluded: chain 0k residue 54 GLU Chi-restraints excluded: chain 0k residue 186 PHE Chi-restraints excluded: chain 0k residue 198 VAL Chi-restraints excluded: chain 0k residue 278 VAL Chi-restraints excluded: chain 0l residue 33 SER Chi-restraints excluded: chain 0l residue 170 SER Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 207 VAL Chi-restraints excluded: chain 0l residue 217 VAL Chi-restraints excluded: chain 0l residue 221 MET Chi-restraints excluded: chain 0l residue 223 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 148 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 chunk 258 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 149 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 68 optimal weight: 0.4980 chunk 146 optimal weight: 0.0770 overall best weight: 2.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 21 ASN 0a 43 ASN 0a 59 GLN ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 173 GLN ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 151 ASN ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 153 ASN 0c 173 GLN ** 0d 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 173 GLN ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 151 ASN ** 0e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 173 GLN 0f 58 HIS ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 151 ASN ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 153 ASN ** 0g 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 211 ASN ** 0j 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 59 GLN ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 151 ASN ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 213 GLN ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 153 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.201256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.188503 restraints weight = 46452.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.191458 restraints weight = 30246.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.193572 restraints weight = 20916.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.194951 restraints weight = 15226.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.196046 restraints weight = 11726.421| |-----------------------------------------------------------------------------| r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 25728 Z= 0.224 Angle : 0.835 8.663 34860 Z= 0.455 Chirality : 0.050 0.177 3756 Planarity : 0.005 0.054 4548 Dihedral : 8.179 55.552 3350 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.40 % Allowed : 16.60 % Favored : 83.00 % Rotamer: Outliers : 4.24 % Allowed : 16.30 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.15), residues: 3024 helix: -0.62 (0.15), residues: 1116 sheet: -3.25 (0.24), residues: 372 loop : -2.47 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG0c 281 TYR 0.031 0.002 TYR0f 30 PHE 0.029 0.002 PHE0c 199 TRP 0.014 0.002 TRP0a 41 HIS 0.004 0.001 HIS0e 58 Details of bonding type rmsd covalent geometry : bond 0.00493 (25728) covalent geometry : angle 0.83498 (34860) hydrogen bonds : bond 0.04918 ( 863) hydrogen bonds : angle 5.57351 ( 2481) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 725 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 18 GLN cc_start: 0.7519 (mm110) cc_final: 0.6580 (tp-100) REVERT: 0a 19 LYS cc_start: 0.8785 (mmtm) cc_final: 0.8556 (mmmt) REVERT: 0a 40 GLU cc_start: 0.6598 (mm-30) cc_final: 0.6172 (mm-30) REVERT: 0a 100 TYR cc_start: 0.6522 (OUTLIER) cc_final: 0.5423 (t80) REVERT: 0a 186 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7224 (m-80) REVERT: 0a 213 GLN cc_start: 0.7970 (tp40) cc_final: 0.7650 (tm-30) REVERT: 0b 18 GLN cc_start: 0.7784 (mm110) cc_final: 0.7225 (tp-100) REVERT: 0b 22 ARG cc_start: 0.7465 (tpp-160) cc_final: 0.7230 (tpp-160) REVERT: 0b 44 LEU cc_start: 0.7664 (mt) cc_final: 0.7302 (mt) REVERT: 0b 186 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7032 (m-80) REVERT: 0b 194 ASP cc_start: 0.8101 (t0) cc_final: 0.7766 (t0) REVERT: 0b 214 LYS cc_start: 0.8225 (ttpp) cc_final: 0.7932 (ttpp) REVERT: 0b 218 TRP cc_start: 0.7121 (t-100) cc_final: 0.6885 (t-100) REVERT: 0b 249 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7598 (mm-40) REVERT: 0c 100 TYR cc_start: 0.6055 (OUTLIER) cc_final: 0.5265 (t80) REVERT: 0c 153 ASN cc_start: 0.7210 (t0) cc_final: 0.6960 (t0) REVERT: 0c 220 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7418 (tp30) REVERT: 0c 222 MET cc_start: 0.8308 (mmm) cc_final: 0.8100 (mmm) REVERT: 0c 249 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7467 (mm-40) REVERT: 0d 18 GLN cc_start: 0.7612 (mm110) cc_final: 0.7252 (tp-100) REVERT: 0d 100 TYR cc_start: 0.6190 (OUTLIER) cc_final: 0.5179 (t80) REVERT: 0d 152 GLN cc_start: 0.8172 (mt0) cc_final: 0.7852 (mt0) REVERT: 0d 153 ASN cc_start: 0.7167 (t0) cc_final: 0.6853 (t0) REVERT: 0d 186 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7103 (m-80) REVERT: 0d 213 GLN cc_start: 0.7992 (tp40) cc_final: 0.7663 (tm-30) REVERT: 0e 18 GLN cc_start: 0.7823 (mm110) cc_final: 0.7098 (tp-100) REVERT: 0e 30 TYR cc_start: 0.7068 (t80) cc_final: 0.6417 (t80) REVERT: 0e 186 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7096 (m-10) REVERT: 0e 213 GLN cc_start: 0.7943 (tp40) cc_final: 0.7696 (tm-30) REVERT: 0e 214 LYS cc_start: 0.8329 (ttpp) cc_final: 0.7998 (ttpp) REVERT: 0e 218 TRP cc_start: 0.7297 (t-100) cc_final: 0.7041 (t60) REVERT: 0f 30 TYR cc_start: 0.6712 (t80) cc_final: 0.5968 (t80) REVERT: 0f 194 ASP cc_start: 0.7794 (t0) cc_final: 0.7501 (t0) REVERT: 0g 18 GLN cc_start: 0.7769 (tp-100) cc_final: 0.7291 (tp40) REVERT: 0g 100 TYR cc_start: 0.6222 (OUTLIER) cc_final: 0.5190 (t80) REVERT: 0g 141 LEU cc_start: 0.9019 (tp) cc_final: 0.8680 (mt) REVERT: 0g 152 GLN cc_start: 0.8222 (mt0) cc_final: 0.7928 (mt0) REVERT: 0g 153 ASN cc_start: 0.7267 (t0) cc_final: 0.6889 (t0) REVERT: 0g 197 GLU cc_start: 0.7584 (pt0) cc_final: 0.7377 (pt0) REVERT: 0g 213 GLN cc_start: 0.8035 (tp40) cc_final: 0.7579 (tm-30) REVERT: 0h 30 TYR cc_start: 0.7001 (t80) cc_final: 0.6349 (t80) REVERT: 0h 44 LEU cc_start: 0.7469 (mt) cc_final: 0.7161 (mt) REVERT: 0h 186 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7009 (m-10) REVERT: 0h 197 GLU cc_start: 0.7626 (pt0) cc_final: 0.7388 (pt0) REVERT: 0h 218 TRP cc_start: 0.7136 (t-100) cc_final: 0.6876 (t-100) REVERT: 0i 194 ASP cc_start: 0.8244 (t0) cc_final: 0.7858 (t0) REVERT: 0i 220 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7294 (tp30) REVERT: 0i 250 ILE cc_start: 0.8333 (mm) cc_final: 0.8077 (mm) REVERT: 0j 18 GLN cc_start: 0.7717 (tp40) cc_final: 0.7162 (tp40) REVERT: 0j 100 TYR cc_start: 0.6225 (OUTLIER) cc_final: 0.5221 (t80) REVERT: 0j 186 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7009 (m-80) REVERT: 0j 197 GLU cc_start: 0.7690 (pt0) cc_final: 0.7388 (pt0) REVERT: 0j 213 GLN cc_start: 0.8096 (tp40) cc_final: 0.7468 (tm-30) REVERT: 0j 214 LYS cc_start: 0.8252 (ttpp) cc_final: 0.7913 (ttpp) REVERT: 0k 18 GLN cc_start: 0.7480 (mm110) cc_final: 0.7133 (tp-100) REVERT: 0k 22 ARG cc_start: 0.7494 (tpp-160) cc_final: 0.7268 (tpp-160) REVERT: 0k 30 TYR cc_start: 0.6914 (t80) cc_final: 0.6265 (t80) REVERT: 0k 44 LEU cc_start: 0.7653 (mt) cc_final: 0.7269 (mt) REVERT: 0k 153 ASN cc_start: 0.7371 (t0) cc_final: 0.7093 (t0) REVERT: 0k 186 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: 0k 197 GLU cc_start: 0.7591 (pt0) cc_final: 0.7372 (pt0) REVERT: 0k 213 GLN cc_start: 0.7951 (tm130) cc_final: 0.7633 (tm-30) REVERT: 0k 218 TRP cc_start: 0.7274 (t-100) cc_final: 0.7011 (t60) REVERT: 0k 222 MET cc_start: 0.8162 (mmm) cc_final: 0.7900 (mmm) REVERT: 0l 18 GLN cc_start: 0.7035 (mt0) cc_final: 0.6752 (mm-40) REVERT: 0l 22 ARG cc_start: 0.7441 (tpp-160) cc_final: 0.6443 (tpp-160) REVERT: 0l 146 GLU cc_start: 0.6645 (tt0) cc_final: 0.6374 (tt0) outliers start: 116 outliers final: 68 residues processed: 823 average time/residue: 0.1661 time to fit residues: 210.0343 Evaluate side-chains 725 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 645 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 136 LEU Chi-restraints excluded: chain 0a residue 170 SER Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0a residue 217 VAL Chi-restraints excluded: chain 0b residue 33 SER Chi-restraints excluded: chain 0b residue 37 GLN Chi-restraints excluded: chain 0b residue 54 GLU Chi-restraints excluded: chain 0b residue 100 TYR Chi-restraints excluded: chain 0b residue 150 VAL Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 136 LEU Chi-restraints excluded: chain 0c residue 170 SER Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0c residue 223 THR Chi-restraints excluded: chain 0c residue 278 VAL Chi-restraints excluded: chain 0d residue 37 GLN Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 136 LEU Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0d residue 198 VAL Chi-restraints excluded: chain 0d residue 217 VAL Chi-restraints excluded: chain 0e residue 54 GLU Chi-restraints excluded: chain 0e residue 101 GLN Chi-restraints excluded: chain 0e residue 170 SER Chi-restraints excluded: chain 0e residue 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL Chi-restraints excluded: chain 0f residue 52 PHE Chi-restraints excluded: chain 0f residue 100 TYR Chi-restraints excluded: chain 0f residue 133 THR Chi-restraints excluded: chain 0f residue 136 LEU Chi-restraints excluded: chain 0f residue 170 SER Chi-restraints excluded: chain 0f residue 186 PHE Chi-restraints excluded: chain 0f residue 193 SER Chi-restraints excluded: chain 0f residue 198 VAL Chi-restraints excluded: chain 0f residue 217 VAL Chi-restraints excluded: chain 0g residue 54 GLU Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 136 LEU Chi-restraints excluded: chain 0g residue 170 SER Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 198 VAL Chi-restraints excluded: chain 0g residue 217 VAL Chi-restraints excluded: chain 0h residue 24 PHE Chi-restraints excluded: chain 0h residue 33 SER Chi-restraints excluded: chain 0h residue 37 GLN Chi-restraints excluded: chain 0h residue 100 TYR Chi-restraints excluded: chain 0h residue 136 LEU Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0i residue 33 SER Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 133 THR Chi-restraints excluded: chain 0i residue 136 LEU Chi-restraints excluded: chain 0i residue 170 SER Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0i residue 278 VAL Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 136 LEU Chi-restraints excluded: chain 0j residue 150 VAL Chi-restraints excluded: chain 0j residue 170 SER Chi-restraints excluded: chain 0j residue 186 PHE Chi-restraints excluded: chain 0j residue 198 VAL Chi-restraints excluded: chain 0j residue 277 LYS Chi-restraints excluded: chain 0k residue 33 SER Chi-restraints excluded: chain 0k residue 54 GLU Chi-restraints excluded: chain 0k residue 100 TYR Chi-restraints excluded: chain 0k residue 136 LEU Chi-restraints excluded: chain 0k residue 186 PHE Chi-restraints excluded: chain 0k residue 198 VAL Chi-restraints excluded: chain 0l residue 33 SER Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 170 SER Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 217 VAL Chi-restraints excluded: chain 0l residue 278 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 100 optimal weight: 0.2980 chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 223 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 134 optimal weight: 0.1980 chunk 263 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 18 GLN 0a 43 ASN ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 21 ASN 0c 58 HIS ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 173 GLN ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 153 ASN 0g 59 GLN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 173 GLN ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 151 ASN ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 59 GLN ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 173 GLN ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.213249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.200933 restraints weight = 48949.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.204048 restraints weight = 30778.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.206346 restraints weight = 20777.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.207711 restraints weight = 14717.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.208873 restraints weight = 11159.229| |-----------------------------------------------------------------------------| r_work (final): 0.4548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.6637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25728 Z= 0.146 Angle : 0.755 8.840 34860 Z= 0.409 Chirality : 0.047 0.169 3756 Planarity : 0.005 0.057 4548 Dihedral : 7.525 37.104 3348 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.40 % Allowed : 15.31 % Favored : 84.29 % Rotamer: Outliers : 4.35 % Allowed : 19.41 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.16), residues: 3024 helix: 0.03 (0.16), residues: 1068 sheet: -3.42 (0.27), residues: 300 loop : -2.26 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG0c 281 TYR 0.022 0.002 TYR0h 36 PHE 0.025 0.002 PHE0a 24 TRP 0.011 0.001 TRP0e 41 HIS 0.005 0.000 HIS0c 58 Details of bonding type rmsd covalent geometry : bond 0.00316 (25728) covalent geometry : angle 0.75505 (34860) hydrogen bonds : bond 0.03839 ( 863) hydrogen bonds : angle 5.07795 ( 2481) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 705 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 24 PHE cc_start: 0.5109 (p90) cc_final: 0.4842 (p90) REVERT: 0a 100 TYR cc_start: 0.6507 (OUTLIER) cc_final: 0.5665 (t80) REVERT: 0a 153 ASN cc_start: 0.6939 (t0) cc_final: 0.6479 (t0) REVERT: 0a 186 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7123 (m-80) REVERT: 0a 213 GLN cc_start: 0.7855 (tp40) cc_final: 0.7623 (tm-30) REVERT: 0b 18 GLN cc_start: 0.7519 (mm110) cc_final: 0.6763 (tp-100) REVERT: 0b 30 TYR cc_start: 0.6893 (t80) cc_final: 0.5782 (t80) REVERT: 0b 44 LEU cc_start: 0.7601 (mt) cc_final: 0.7205 (mt) REVERT: 0b 186 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7016 (m-80) REVERT: 0b 194 ASP cc_start: 0.7941 (t0) cc_final: 0.7707 (t0) REVERT: 0b 214 LYS cc_start: 0.8083 (ttpp) cc_final: 0.7851 (ttpp) REVERT: 0b 218 TRP cc_start: 0.6968 (t-100) cc_final: 0.6684 (t60) REVERT: 0c 30 TYR cc_start: 0.6540 (t80) cc_final: 0.5577 (t80) REVERT: 0c 100 TYR cc_start: 0.6558 (OUTLIER) cc_final: 0.5775 (t80) REVERT: 0c 153 ASN cc_start: 0.7458 (t0) cc_final: 0.7250 (t0) REVERT: 0c 209 LYS cc_start: 0.8531 (mmtt) cc_final: 0.8315 (mmtp) REVERT: 0c 213 GLN cc_start: 0.7960 (tp40) cc_final: 0.7208 (tm-30) REVERT: 0c 220 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6965 (mt-10) REVERT: 0d 18 GLN cc_start: 0.7368 (mm110) cc_final: 0.6652 (tp-100) REVERT: 0d 22 ARG cc_start: 0.7182 (tpp-160) cc_final: 0.6695 (tpp-160) REVERT: 0d 100 TYR cc_start: 0.6459 (OUTLIER) cc_final: 0.5704 (t80) REVERT: 0d 153 ASN cc_start: 0.7005 (t0) cc_final: 0.6390 (t0) REVERT: 0d 186 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7044 (m-80) REVERT: 0d 213 GLN cc_start: 0.7929 (tp40) cc_final: 0.7582 (tm-30) REVERT: 0d 220 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6426 (mt-10) REVERT: 0d 221 MET cc_start: 0.6947 (tpp) cc_final: 0.6694 (tpp) REVERT: 0e 30 TYR cc_start: 0.6955 (t80) cc_final: 0.6359 (t80) REVERT: 0e 186 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7201 (m-80) REVERT: 0e 214 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7738 (ttpp) REVERT: 0e 218 TRP cc_start: 0.7047 (t-100) cc_final: 0.6786 (t60) REVERT: 0e 220 GLU cc_start: 0.7405 (tp30) cc_final: 0.7189 (mt-10) REVERT: 0f 18 GLN cc_start: 0.6693 (tt0) cc_final: 0.6382 (tt0) REVERT: 0f 30 TYR cc_start: 0.7203 (t80) cc_final: 0.6489 (t80) REVERT: 0f 100 TYR cc_start: 0.6408 (OUTLIER) cc_final: 0.5703 (t80) REVERT: 0f 151 ASN cc_start: 0.8251 (t0) cc_final: 0.8006 (t0) REVERT: 0f 194 ASP cc_start: 0.7694 (t0) cc_final: 0.7427 (t0) REVERT: 0f 213 GLN cc_start: 0.8137 (tp40) cc_final: 0.7721 (tp40) REVERT: 0f 220 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6868 (mt-10) REVERT: 0g 24 PHE cc_start: 0.5360 (p90) cc_final: 0.5098 (p90) REVERT: 0g 100 TYR cc_start: 0.6439 (OUTLIER) cc_final: 0.5678 (t80) REVERT: 0g 140 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8328 (tm-30) REVERT: 0g 141 LEU cc_start: 0.8881 (tp) cc_final: 0.8561 (mt) REVERT: 0g 213 GLN cc_start: 0.7939 (tp40) cc_final: 0.7648 (tm-30) REVERT: 0g 221 MET cc_start: 0.6908 (tpp) cc_final: 0.6639 (tpp) REVERT: 0h 18 GLN cc_start: 0.7606 (tp-100) cc_final: 0.7097 (tp-100) REVERT: 0h 30 TYR cc_start: 0.7011 (t80) cc_final: 0.6326 (t80) REVERT: 0h 44 LEU cc_start: 0.7556 (mt) cc_final: 0.7314 (mt) REVERT: 0h 186 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.6944 (m-10) REVERT: 0i 100 TYR cc_start: 0.6643 (OUTLIER) cc_final: 0.5920 (t80) REVERT: 0i 123 ASN cc_start: 0.7806 (t0) cc_final: 0.7433 (t0) REVERT: 0i 151 ASN cc_start: 0.8239 (t0) cc_final: 0.7985 (t0) REVERT: 0i 186 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7284 (m-80) REVERT: 0i 194 ASP cc_start: 0.8176 (t0) cc_final: 0.7777 (t0) REVERT: 0i 213 GLN cc_start: 0.8187 (tp40) cc_final: 0.7861 (tp40) REVERT: 0i 221 MET cc_start: 0.7125 (tpp) cc_final: 0.6899 (tpp) REVERT: 0i 250 ILE cc_start: 0.8253 (mm) cc_final: 0.8041 (mm) REVERT: 0j 37 GLN cc_start: 0.7470 (tt0) cc_final: 0.7250 (tt0) REVERT: 0j 100 TYR cc_start: 0.6471 (OUTLIER) cc_final: 0.5683 (t80) REVERT: 0j 124 ASN cc_start: 0.7631 (p0) cc_final: 0.7343 (p0) REVERT: 0j 213 GLN cc_start: 0.7885 (tp40) cc_final: 0.7619 (tm-30) REVERT: 0j 220 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6834 (mt-10) REVERT: 0k 30 TYR cc_start: 0.7095 (t80) cc_final: 0.6397 (t80) REVERT: 0k 44 LEU cc_start: 0.7629 (mt) cc_final: 0.7334 (mt) REVERT: 0k 153 ASN cc_start: 0.7303 (t0) cc_final: 0.7025 (t0) REVERT: 0l 100 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.5911 (t80) REVERT: 0l 140 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8376 (tm-30) REVERT: 0l 146 GLU cc_start: 0.6574 (tt0) cc_final: 0.6310 (tt0) REVERT: 0l 153 ASN cc_start: 0.7331 (t0) cc_final: 0.7102 (t0) REVERT: 0l 213 GLN cc_start: 0.7912 (tp40) cc_final: 0.7372 (tm-30) REVERT: 0l 221 MET cc_start: 0.7195 (tpp) cc_final: 0.6961 (tpp) outliers start: 119 outliers final: 69 residues processed: 793 average time/residue: 0.1732 time to fit residues: 212.3436 Evaluate side-chains 728 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 645 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 52 PHE Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0b residue 33 SER Chi-restraints excluded: chain 0b residue 52 PHE Chi-restraints excluded: chain 0b residue 54 GLU Chi-restraints excluded: chain 0b residue 100 TYR Chi-restraints excluded: chain 0b residue 150 VAL Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 124 ASN Chi-restraints excluded: chain 0c residue 185 ILE Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0c residue 207 VAL Chi-restraints excluded: chain 0c residue 223 THR Chi-restraints excluded: chain 0d residue 37 GLN Chi-restraints excluded: chain 0d residue 52 PHE Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 170 SER Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0d residue 217 VAL Chi-restraints excluded: chain 0e residue 24 PHE Chi-restraints excluded: chain 0e residue 52 PHE Chi-restraints excluded: chain 0e residue 54 GLU Chi-restraints excluded: chain 0e residue 141 LEU Chi-restraints excluded: chain 0e residue 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL Chi-restraints excluded: chain 0e residue 221 MET Chi-restraints excluded: chain 0f residue 100 TYR Chi-restraints excluded: chain 0f residue 170 SER Chi-restraints excluded: chain 0f residue 186 PHE Chi-restraints excluded: chain 0f residue 198 VAL Chi-restraints excluded: chain 0g residue 52 PHE Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 170 SER Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 198 VAL Chi-restraints excluded: chain 0g residue 217 VAL Chi-restraints excluded: chain 0h residue 24 PHE Chi-restraints excluded: chain 0h residue 33 SER Chi-restraints excluded: chain 0h residue 52 PHE Chi-restraints excluded: chain 0h residue 100 TYR Chi-restraints excluded: chain 0h residue 136 LEU Chi-restraints excluded: chain 0h residue 141 LEU Chi-restraints excluded: chain 0h residue 150 VAL Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0h residue 278 VAL Chi-restraints excluded: chain 0i residue 33 SER Chi-restraints excluded: chain 0i residue 37 GLN Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 185 ILE Chi-restraints excluded: chain 0i residue 186 PHE Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0j residue 52 PHE Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 136 LEU Chi-restraints excluded: chain 0j residue 170 SER Chi-restraints excluded: chain 0j residue 186 PHE Chi-restraints excluded: chain 0j residue 198 VAL Chi-restraints excluded: chain 0j residue 217 VAL Chi-restraints excluded: chain 0j residue 277 LYS Chi-restraints excluded: chain 0k residue 24 PHE Chi-restraints excluded: chain 0k residue 52 PHE Chi-restraints excluded: chain 0k residue 54 GLU Chi-restraints excluded: chain 0k residue 100 TYR Chi-restraints excluded: chain 0k residue 170 SER Chi-restraints excluded: chain 0k residue 185 ILE Chi-restraints excluded: chain 0k residue 186 PHE Chi-restraints excluded: chain 0k residue 198 VAL Chi-restraints excluded: chain 0k residue 217 VAL Chi-restraints excluded: chain 0k residue 278 VAL Chi-restraints excluded: chain 0l residue 33 SER Chi-restraints excluded: chain 0l residue 37 GLN Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 136 LEU Chi-restraints excluded: chain 0l residue 170 SER Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 207 VAL Chi-restraints excluded: chain 0l residue 217 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 215 optimal weight: 4.9990 chunk 209 optimal weight: 0.1980 chunk 255 optimal weight: 0.7980 chunk 291 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 283 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 151 ASN ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 153 ASN ** 0b 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 21 ASN ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 151 ASN ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 211 ASN ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 151 ASN ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 59 GLN ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 211 ASN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 151 ASN ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 153 ASN ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 173 GLN 0j 59 GLN ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 173 GLN ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 151 ASN ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 173 GLN ** 0l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 211 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.212313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.199581 restraints weight = 49338.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.203074 restraints weight = 29879.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.205493 restraints weight = 19406.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.206938 restraints weight = 13397.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.208210 restraints weight = 9859.024| |-----------------------------------------------------------------------------| r_work (final): 0.4535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.7012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25728 Z= 0.149 Angle : 0.758 9.466 34860 Z= 0.409 Chirality : 0.047 0.199 3756 Planarity : 0.005 0.059 4548 Dihedral : 7.352 36.898 3348 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.40 % Allowed : 14.55 % Favored : 85.05 % Rotamer: Outliers : 3.91 % Allowed : 21.38 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.16), residues: 3024 helix: 0.11 (0.16), residues: 1080 sheet: -3.41 (0.27), residues: 300 loop : -2.18 (0.17), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG0c 22 TYR 0.018 0.002 TYR0b 36 PHE 0.025 0.002 PHE0a 24 TRP 0.011 0.001 TRP0k 218 HIS 0.002 0.000 HIS0h 26 Details of bonding type rmsd covalent geometry : bond 0.00328 (25728) covalent geometry : angle 0.75754 (34860) hydrogen bonds : bond 0.03696 ( 863) hydrogen bonds : angle 4.93941 ( 2481) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 676 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 24 PHE cc_start: 0.5157 (p90) cc_final: 0.4811 (p90) REVERT: 0a 100 TYR cc_start: 0.6558 (OUTLIER) cc_final: 0.5780 (t80) REVERT: 0a 153 ASN cc_start: 0.6872 (t0) cc_final: 0.6536 (t0) REVERT: 0a 186 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.6983 (m-80) REVERT: 0a 213 GLN cc_start: 0.7901 (tp40) cc_final: 0.7543 (tm-30) REVERT: 0a 220 GLU cc_start: 0.7290 (tp30) cc_final: 0.6903 (mt-10) REVERT: 0b 30 TYR cc_start: 0.6904 (t80) cc_final: 0.5557 (t80) REVERT: 0b 44 LEU cc_start: 0.7446 (mt) cc_final: 0.7092 (mt) REVERT: 0b 112 MET cc_start: 0.5336 (ppp) cc_final: 0.4721 (ptt) REVERT: 0b 186 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7038 (m-80) REVERT: 0b 194 ASP cc_start: 0.8116 (t0) cc_final: 0.7837 (t0) REVERT: 0b 214 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7941 (ttpp) REVERT: 0b 218 TRP cc_start: 0.6904 (t-100) cc_final: 0.6614 (t60) REVERT: 0c 100 TYR cc_start: 0.6468 (OUTLIER) cc_final: 0.6015 (t80) REVERT: 0c 153 ASN cc_start: 0.7463 (t0) cc_final: 0.7013 (t0) REVERT: 0c 209 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8481 (mmtp) REVERT: 0c 213 GLN cc_start: 0.8105 (tp40) cc_final: 0.7393 (tm-30) REVERT: 0c 220 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6962 (mt-10) REVERT: 0c 221 MET cc_start: 0.7187 (tpp) cc_final: 0.6756 (tpp) REVERT: 0c 225 LEU cc_start: 0.8299 (mt) cc_final: 0.8018 (mp) REVERT: 0d 18 GLN cc_start: 0.7388 (mm110) cc_final: 0.6909 (tp-100) REVERT: 0d 100 TYR cc_start: 0.6486 (OUTLIER) cc_final: 0.5823 (t80) REVERT: 0d 140 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8346 (tm-30) REVERT: 0d 153 ASN cc_start: 0.7134 (t0) cc_final: 0.6777 (t0) REVERT: 0d 186 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7042 (m-80) REVERT: 0d 213 GLN cc_start: 0.7993 (tp40) cc_final: 0.7685 (tm-30) REVERT: 0d 220 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6634 (mt-10) REVERT: 0e 18 GLN cc_start: 0.7477 (tp-100) cc_final: 0.7214 (tp-100) REVERT: 0e 30 TYR cc_start: 0.6993 (t80) cc_final: 0.6386 (t80) REVERT: 0e 112 MET cc_start: 0.5348 (ppp) cc_final: 0.4571 (ptt) REVERT: 0e 137 PHE cc_start: 0.7348 (m-10) cc_final: 0.7038 (m-80) REVERT: 0e 186 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7184 (m-80) REVERT: 0e 218 TRP cc_start: 0.6987 (t-100) cc_final: 0.6702 (t60) REVERT: 0e 220 GLU cc_start: 0.7371 (tp30) cc_final: 0.7163 (mt-10) REVERT: 0f 30 TYR cc_start: 0.7255 (t80) cc_final: 0.6602 (t80) REVERT: 0f 112 MET cc_start: 0.5140 (ppp) cc_final: 0.4817 (ppp) REVERT: 0f 213 GLN cc_start: 0.8142 (tp40) cc_final: 0.7827 (tm-30) REVERT: 0f 220 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6831 (mt-10) REVERT: 0f 221 MET cc_start: 0.7012 (tpp) cc_final: 0.6603 (tpp) REVERT: 0f 225 LEU cc_start: 0.8348 (mt) cc_final: 0.8023 (mp) REVERT: 0f 269 ASN cc_start: 0.7701 (t0) cc_final: 0.7402 (t0) REVERT: 0g 24 PHE cc_start: 0.5163 (p90) cc_final: 0.4925 (p90) REVERT: 0g 100 TYR cc_start: 0.6484 (OUTLIER) cc_final: 0.5796 (t80) REVERT: 0g 140 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8412 (tm-30) REVERT: 0g 141 LEU cc_start: 0.8946 (tp) cc_final: 0.8609 (mt) REVERT: 0g 213 GLN cc_start: 0.8003 (tp40) cc_final: 0.7643 (tm-30) REVERT: 0g 221 MET cc_start: 0.7034 (tpp) cc_final: 0.6811 (tpp) REVERT: 0h 18 GLN cc_start: 0.7396 (tp-100) cc_final: 0.7135 (tp-100) REVERT: 0h 30 TYR cc_start: 0.6962 (t80) cc_final: 0.6312 (t80) REVERT: 0h 44 LEU cc_start: 0.7686 (mt) cc_final: 0.7350 (mt) REVERT: 0h 112 MET cc_start: 0.5239 (ppp) cc_final: 0.4507 (ptt) REVERT: 0h 124 ASN cc_start: 0.7683 (p0) cc_final: 0.7425 (p0) REVERT: 0h 137 PHE cc_start: 0.7509 (m-80) cc_final: 0.7250 (m-80) REVERT: 0h 185 ILE cc_start: 0.7340 (OUTLIER) cc_final: 0.6724 (pt) REVERT: 0i 151 ASN cc_start: 0.8225 (t0) cc_final: 0.8000 (t0) REVERT: 0i 186 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: 0i 194 ASP cc_start: 0.8241 (t0) cc_final: 0.7867 (t0) REVERT: 0i 213 GLN cc_start: 0.8184 (tp40) cc_final: 0.7864 (tp40) REVERT: 0i 221 MET cc_start: 0.7186 (tpp) cc_final: 0.6964 (tpp) REVERT: 0i 250 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.8038 (mm) REVERT: 0j 22 ARG cc_start: 0.7321 (tpp-160) cc_final: 0.6992 (tpp-160) REVERT: 0j 100 TYR cc_start: 0.6573 (OUTLIER) cc_final: 0.5848 (t80) REVERT: 0j 213 GLN cc_start: 0.7937 (tp40) cc_final: 0.7729 (tm-30) REVERT: 0j 220 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6729 (mt-10) REVERT: 0k 30 TYR cc_start: 0.7027 (t80) cc_final: 0.6423 (t80) REVERT: 0k 44 LEU cc_start: 0.7802 (mt) cc_final: 0.7473 (mt) REVERT: 0k 112 MET cc_start: 0.5464 (ppp) cc_final: 0.4805 (ptt) REVERT: 0k 124 ASN cc_start: 0.7922 (p0) cc_final: 0.7666 (p0) REVERT: 0k 153 ASN cc_start: 0.7401 (t0) cc_final: 0.7048 (t0) REVERT: 0k 185 ILE cc_start: 0.7371 (OUTLIER) cc_final: 0.6828 (pt) REVERT: 0k 267 LYS cc_start: 0.3559 (mmmt) cc_final: 0.3320 (mtpt) REVERT: 0l 112 MET cc_start: 0.6198 (ptm) cc_final: 0.5713 (ppp) REVERT: 0l 140 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8388 (tm-30) REVERT: 0l 209 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8376 (mmtp) REVERT: 0l 213 GLN cc_start: 0.8041 (tp40) cc_final: 0.7474 (tm-30) REVERT: 0l 220 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6903 (mt-10) REVERT: 0l 221 MET cc_start: 0.7225 (tpp) cc_final: 0.7014 (tpp) outliers start: 107 outliers final: 76 residues processed: 760 average time/residue: 0.1713 time to fit residues: 202.5428 Evaluate side-chains 704 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 615 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 52 PHE Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 141 LEU Chi-restraints excluded: chain 0a residue 170 SER Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0a residue 276 VAL Chi-restraints excluded: chain 0b residue 24 PHE Chi-restraints excluded: chain 0b residue 52 PHE Chi-restraints excluded: chain 0b residue 54 GLU Chi-restraints excluded: chain 0b residue 100 TYR Chi-restraints excluded: chain 0b residue 136 LEU Chi-restraints excluded: chain 0b residue 150 VAL Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 136 LEU Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0c residue 207 VAL Chi-restraints excluded: chain 0d residue 37 GLN Chi-restraints excluded: chain 0d residue 52 PHE Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 126 MET Chi-restraints excluded: chain 0d residue 170 SER Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0d residue 217 VAL Chi-restraints excluded: chain 0e residue 24 PHE Chi-restraints excluded: chain 0e residue 37 GLN Chi-restraints excluded: chain 0e residue 52 PHE Chi-restraints excluded: chain 0e residue 54 GLU Chi-restraints excluded: chain 0e residue 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL Chi-restraints excluded: chain 0e residue 217 VAL Chi-restraints excluded: chain 0e residue 221 MET Chi-restraints excluded: chain 0f residue 100 TYR Chi-restraints excluded: chain 0f residue 136 LEU Chi-restraints excluded: chain 0f residue 170 SER Chi-restraints excluded: chain 0f residue 186 PHE Chi-restraints excluded: chain 0f residue 198 VAL Chi-restraints excluded: chain 0f residue 207 VAL Chi-restraints excluded: chain 0g residue 52 PHE Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 170 SER Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 198 VAL Chi-restraints excluded: chain 0g residue 217 VAL Chi-restraints excluded: chain 0h residue 24 PHE Chi-restraints excluded: chain 0h residue 33 SER Chi-restraints excluded: chain 0h residue 52 PHE Chi-restraints excluded: chain 0h residue 100 TYR Chi-restraints excluded: chain 0h residue 136 LEU Chi-restraints excluded: chain 0h residue 170 SER Chi-restraints excluded: chain 0h residue 185 ILE Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0h residue 278 VAL Chi-restraints excluded: chain 0i residue 33 SER Chi-restraints excluded: chain 0i residue 37 GLN Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 136 LEU Chi-restraints excluded: chain 0i residue 170 SER Chi-restraints excluded: chain 0i residue 186 PHE Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0i residue 250 ILE Chi-restraints excluded: chain 0j residue 52 PHE Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 170 SER Chi-restraints excluded: chain 0j residue 186 PHE Chi-restraints excluded: chain 0j residue 198 VAL Chi-restraints excluded: chain 0j residue 277 LYS Chi-restraints excluded: chain 0k residue 24 PHE Chi-restraints excluded: chain 0k residue 33 SER Chi-restraints excluded: chain 0k residue 52 PHE Chi-restraints excluded: chain 0k residue 54 GLU Chi-restraints excluded: chain 0k residue 100 TYR Chi-restraints excluded: chain 0k residue 150 VAL Chi-restraints excluded: chain 0k residue 170 SER Chi-restraints excluded: chain 0k residue 185 ILE Chi-restraints excluded: chain 0k residue 186 PHE Chi-restraints excluded: chain 0k residue 198 VAL Chi-restraints excluded: chain 0k residue 278 VAL Chi-restraints excluded: chain 0l residue 33 SER Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 136 LEU Chi-restraints excluded: chain 0l residue 170 SER Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 217 VAL Chi-restraints excluded: chain 0l residue 223 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 7.9990 chunk 238 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 265 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 254 optimal weight: 2.9990 chunk 275 optimal weight: 0.0010 chunk 86 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 151 ASN ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 151 ASN ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 59 GLN ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 173 GLN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 37 GLN ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 58 HIS ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 167 ASN ** 0j 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 151 ASN ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 211 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.207952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.195023 restraints weight = 48774.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.198377 restraints weight = 30066.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.200806 restraints weight = 19852.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.202280 restraints weight = 13825.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.203480 restraints weight = 10286.495| |-----------------------------------------------------------------------------| r_work (final): 0.4478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.7304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25728 Z= 0.181 Angle : 0.795 9.027 34860 Z= 0.428 Chirality : 0.049 0.212 3756 Planarity : 0.005 0.082 4548 Dihedral : 7.467 37.203 3348 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.40 % Allowed : 16.01 % Favored : 83.60 % Rotamer: Outliers : 3.76 % Allowed : 23.17 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.16), residues: 3024 helix: 0.06 (0.16), residues: 1080 sheet: -3.28 (0.28), residues: 300 loop : -2.23 (0.17), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG0c 22 TYR 0.021 0.002 TYR0d 205 PHE 0.025 0.002 PHE0g 65 TRP 0.011 0.001 TRP0l 41 HIS 0.002 0.001 HIS0a 58 Details of bonding type rmsd covalent geometry : bond 0.00400 (25728) covalent geometry : angle 0.79459 (34860) hydrogen bonds : bond 0.04129 ( 863) hydrogen bonds : angle 5.09268 ( 2481) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 648 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 20 ARG cc_start: 0.6844 (mmm160) cc_final: 0.6613 (mmm160) REVERT: 0a 24 PHE cc_start: 0.5072 (p90) cc_final: 0.4761 (p90) REVERT: 0a 100 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.5714 (t80) REVERT: 0a 112 MET cc_start: 0.5381 (ppp) cc_final: 0.4113 (ptt) REVERT: 0a 213 GLN cc_start: 0.8047 (tp40) cc_final: 0.7658 (tm-30) REVERT: 0a 220 GLU cc_start: 0.7287 (tp30) cc_final: 0.6961 (mt-10) REVERT: 0b 18 GLN cc_start: 0.7627 (tp-100) cc_final: 0.7421 (tp-100) REVERT: 0b 44 LEU cc_start: 0.7567 (mt) cc_final: 0.7179 (mt) REVERT: 0b 194 ASP cc_start: 0.8268 (t0) cc_final: 0.7942 (t0) REVERT: 0b 214 LYS cc_start: 0.8337 (ttpp) cc_final: 0.8053 (ttpp) REVERT: 0c 100 TYR cc_start: 0.6770 (OUTLIER) cc_final: 0.5965 (t80) REVERT: 0c 112 MET cc_start: 0.5136 (ppp) cc_final: 0.3169 (mmp) REVERT: 0c 146 GLU cc_start: 0.6710 (tt0) cc_final: 0.6490 (tt0) REVERT: 0c 186 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7333 (m-80) REVERT: 0c 213 GLN cc_start: 0.8170 (tp40) cc_final: 0.7529 (tm-30) REVERT: 0c 220 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6876 (mt-10) REVERT: 0c 221 MET cc_start: 0.7274 (tpp) cc_final: 0.6785 (tpp) REVERT: 0c 225 LEU cc_start: 0.8344 (mt) cc_final: 0.7818 (mp) REVERT: 0d 18 GLN cc_start: 0.7464 (mm110) cc_final: 0.6901 (tp-100) REVERT: 0d 22 ARG cc_start: 0.7273 (tpp-160) cc_final: 0.6815 (tpp-160) REVERT: 0d 100 TYR cc_start: 0.6761 (OUTLIER) cc_final: 0.5785 (t80) REVERT: 0d 113 LYS cc_start: 0.4220 (mmtt) cc_final: 0.2428 (tttp) REVERT: 0d 126 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8305 (mtm) REVERT: 0d 153 ASN cc_start: 0.7275 (t0) cc_final: 0.6955 (t0) REVERT: 0d 213 GLN cc_start: 0.8021 (tp40) cc_final: 0.7701 (tm-30) REVERT: 0d 220 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6645 (mt-10) REVERT: 0e 18 GLN cc_start: 0.7609 (tp-100) cc_final: 0.7393 (tp-100) REVERT: 0e 30 TYR cc_start: 0.7244 (t80) cc_final: 0.6581 (t80) REVERT: 0e 137 PHE cc_start: 0.7304 (m-10) cc_final: 0.6941 (m-80) REVERT: 0e 140 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8464 (tm-30) REVERT: 0e 186 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7085 (m-80) REVERT: 0e 218 TRP cc_start: 0.7066 (t-100) cc_final: 0.6742 (t60) REVERT: 0e 220 GLU cc_start: 0.7493 (tp30) cc_final: 0.7262 (mt-10) REVERT: 0f 112 MET cc_start: 0.5176 (ppp) cc_final: 0.4974 (ppp) REVERT: 0f 146 GLU cc_start: 0.6752 (tt0) cc_final: 0.6384 (tt0) REVERT: 0f 193 SER cc_start: 0.6904 (p) cc_final: 0.6362 (t) REVERT: 0f 213 GLN cc_start: 0.8233 (tp40) cc_final: 0.7936 (tm-30) REVERT: 0f 220 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6859 (mt-10) REVERT: 0f 221 MET cc_start: 0.7148 (tpp) cc_final: 0.6817 (tpp) REVERT: 0f 225 LEU cc_start: 0.8327 (mt) cc_final: 0.8019 (mp) REVERT: 0f 269 ASN cc_start: 0.7813 (t0) cc_final: 0.7489 (t0) REVERT: 0g 24 PHE cc_start: 0.5312 (p90) cc_final: 0.5112 (p90) REVERT: 0g 100 TYR cc_start: 0.6717 (OUTLIER) cc_final: 0.5714 (t80) REVERT: 0g 140 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8413 (tm-30) REVERT: 0g 153 ASN cc_start: 0.7284 (t0) cc_final: 0.6956 (t0) REVERT: 0g 213 GLN cc_start: 0.8144 (tp40) cc_final: 0.7489 (tm-30) REVERT: 0h 30 TYR cc_start: 0.6825 (t80) cc_final: 0.6279 (t80) REVERT: 0h 44 LEU cc_start: 0.7861 (mt) cc_final: 0.7568 (mt) REVERT: 0h 112 MET cc_start: 0.5328 (ppp) cc_final: 0.4559 (ptt) REVERT: 0i 112 MET cc_start: 0.5211 (ppp) cc_final: 0.3364 (mmp) REVERT: 0i 151 ASN cc_start: 0.8315 (t0) cc_final: 0.8037 (t0) REVERT: 0i 186 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: 0i 194 ASP cc_start: 0.8399 (t0) cc_final: 0.8044 (t0) REVERT: 0i 213 GLN cc_start: 0.8202 (tp40) cc_final: 0.7898 (tp40) REVERT: 0i 221 MET cc_start: 0.7218 (tpp) cc_final: 0.7012 (tpp) REVERT: 0i 250 ILE cc_start: 0.8382 (mm) cc_final: 0.8139 (mm) REVERT: 0i 269 ASN cc_start: 0.7865 (t0) cc_final: 0.7567 (t0) REVERT: 0j 18 GLN cc_start: 0.7567 (tp-100) cc_final: 0.6718 (tp-100) REVERT: 0j 22 ARG cc_start: 0.7422 (tpp-160) cc_final: 0.6753 (tpp-160) REVERT: 0j 100 TYR cc_start: 0.6777 (OUTLIER) cc_final: 0.5771 (t80) REVERT: 0j 112 MET cc_start: 0.5249 (ppp) cc_final: 0.3963 (ptt) REVERT: 0j 153 ASN cc_start: 0.7367 (t0) cc_final: 0.6966 (t0) REVERT: 0j 213 GLN cc_start: 0.8028 (tp40) cc_final: 0.7668 (tm-30) REVERT: 0j 222 MET cc_start: 0.8015 (mmm) cc_final: 0.7778 (mmm) REVERT: 0j 225 LEU cc_start: 0.8412 (mt) cc_final: 0.8048 (mp) REVERT: 0k 18 GLN cc_start: 0.7541 (tp-100) cc_final: 0.7318 (tp-100) REVERT: 0k 30 TYR cc_start: 0.7168 (t80) cc_final: 0.6798 (t80) REVERT: 0k 44 LEU cc_start: 0.7790 (mt) cc_final: 0.7501 (mt) REVERT: 0k 112 MET cc_start: 0.5482 (ppp) cc_final: 0.4592 (ptt) REVERT: 0k 124 ASN cc_start: 0.8031 (p0) cc_final: 0.7722 (p0) REVERT: 0l 18 GLN cc_start: 0.7780 (tp-100) cc_final: 0.6947 (tp-100) REVERT: 0l 22 ARG cc_start: 0.7304 (tpp-160) cc_final: 0.6988 (tpp-160) REVERT: 0l 146 GLU cc_start: 0.6775 (tt0) cc_final: 0.6499 (tt0) REVERT: 0l 186 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.6999 (m-80) REVERT: 0l 209 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8626 (mmtp) REVERT: 0l 213 GLN cc_start: 0.8171 (tp40) cc_final: 0.7544 (tm-30) REVERT: 0l 220 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7024 (mt-10) outliers start: 103 outliers final: 72 residues processed: 728 average time/residue: 0.1643 time to fit residues: 185.7180 Evaluate side-chains 685 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 603 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 52 PHE Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 141 LEU Chi-restraints excluded: chain 0a residue 150 VAL Chi-restraints excluded: chain 0a residue 170 SER Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0a residue 276 VAL Chi-restraints excluded: chain 0b residue 24 PHE Chi-restraints excluded: chain 0b residue 52 PHE Chi-restraints excluded: chain 0b residue 54 GLU Chi-restraints excluded: chain 0b residue 100 TYR Chi-restraints excluded: chain 0b residue 136 LEU Chi-restraints excluded: chain 0b residue 150 VAL Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 136 LEU Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0d residue 37 GLN Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 126 MET Chi-restraints excluded: chain 0d residue 170 SER Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0d residue 217 VAL Chi-restraints excluded: chain 0e residue 24 PHE Chi-restraints excluded: chain 0e residue 37 GLN Chi-restraints excluded: chain 0e residue 52 PHE Chi-restraints excluded: chain 0e residue 54 GLU Chi-restraints excluded: chain 0e residue 150 VAL Chi-restraints excluded: chain 0e residue 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL Chi-restraints excluded: chain 0e residue 221 MET Chi-restraints excluded: chain 0f residue 100 TYR Chi-restraints excluded: chain 0f residue 136 LEU Chi-restraints excluded: chain 0f residue 170 SER Chi-restraints excluded: chain 0f residue 186 PHE Chi-restraints excluded: chain 0f residue 198 VAL Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 170 SER Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 198 VAL Chi-restraints excluded: chain 0g residue 217 VAL Chi-restraints excluded: chain 0g residue 276 VAL Chi-restraints excluded: chain 0h residue 24 PHE Chi-restraints excluded: chain 0h residue 33 SER Chi-restraints excluded: chain 0h residue 52 PHE Chi-restraints excluded: chain 0h residue 100 TYR Chi-restraints excluded: chain 0h residue 136 LEU Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0i residue 37 GLN Chi-restraints excluded: chain 0i residue 54 GLU Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 136 LEU Chi-restraints excluded: chain 0i residue 170 SER Chi-restraints excluded: chain 0i residue 186 PHE Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0j residue 52 PHE Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 170 SER Chi-restraints excluded: chain 0j residue 186 PHE Chi-restraints excluded: chain 0j residue 198 VAL Chi-restraints excluded: chain 0j residue 277 LYS Chi-restraints excluded: chain 0k residue 24 PHE Chi-restraints excluded: chain 0k residue 33 SER Chi-restraints excluded: chain 0k residue 52 PHE Chi-restraints excluded: chain 0k residue 54 GLU Chi-restraints excluded: chain 0k residue 100 TYR Chi-restraints excluded: chain 0k residue 136 LEU Chi-restraints excluded: chain 0k residue 150 VAL Chi-restraints excluded: chain 0k residue 186 PHE Chi-restraints excluded: chain 0k residue 198 VAL Chi-restraints excluded: chain 0l residue 33 SER Chi-restraints excluded: chain 0l residue 37 GLN Chi-restraints excluded: chain 0l residue 54 GLU Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 170 SER Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 217 VAL Chi-restraints excluded: chain 0l residue 223 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 251 optimal weight: 0.9990 chunk 266 optimal weight: 0.0020 chunk 282 optimal weight: 0.5980 chunk 208 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 211 optimal weight: 0.2980 chunk 272 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 32 GLN ** 0b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 59 GLN ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 59 GLN ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 173 GLN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 173 GLN ** 0j 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 168 GLN ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 59 GLN ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 153 ASN ** 0l 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 173 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.239939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.234174 restraints weight = 57308.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.235203 restraints weight = 37744.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.236043 restraints weight = 25531.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.236496 restraints weight = 16957.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.236631 restraints weight = 13141.381| |-----------------------------------------------------------------------------| r_work (final): 0.4632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5815 moved from start: 0.7628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25728 Z= 0.144 Angle : 0.770 10.588 34860 Z= 0.411 Chirality : 0.047 0.195 3756 Planarity : 0.005 0.059 4548 Dihedral : 7.083 37.109 3348 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.40 % Allowed : 13.79 % Favored : 85.81 % Rotamer: Outliers : 3.22 % Allowed : 24.78 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.17), residues: 3024 helix: 0.32 (0.16), residues: 1080 sheet: -2.34 (0.27), residues: 420 loop : -2.06 (0.18), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG0c 281 TYR 0.018 0.001 TYR0h 36 PHE 0.026 0.002 PHE0e 65 TRP 0.015 0.001 TRP0b 218 HIS 0.003 0.000 HIS0c 26 Details of bonding type rmsd covalent geometry : bond 0.00316 (25728) covalent geometry : angle 0.77011 (34860) hydrogen bonds : bond 0.03551 ( 863) hydrogen bonds : angle 4.90759 ( 2481) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 651 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 24 PHE cc_start: 0.4486 (p90) cc_final: 0.4220 (p90) REVERT: 0a 112 MET cc_start: 0.5211 (ppp) cc_final: 0.3943 (ptt) REVERT: 0b 30 TYR cc_start: 0.6711 (t80) cc_final: 0.5840 (t80) REVERT: 0b 44 LEU cc_start: 0.7351 (mt) cc_final: 0.7090 (mt) REVERT: 0b 112 MET cc_start: 0.5512 (ppp) cc_final: 0.4472 (ptt) REVERT: 0c 100 TYR cc_start: 0.6504 (OUTLIER) cc_final: 0.6213 (t80) REVERT: 0c 112 MET cc_start: 0.4934 (ppp) cc_final: 0.2938 (mmp) REVERT: 0c 186 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7429 (m-80) REVERT: 0c 213 GLN cc_start: 0.7535 (tp40) cc_final: 0.7232 (tm-30) REVERT: 0d 22 ARG cc_start: 0.6462 (tpp-160) cc_final: 0.6217 (tpp-160) REVERT: 0d 100 TYR cc_start: 0.6512 (OUTLIER) cc_final: 0.5912 (t80) REVERT: 0d 153 ASN cc_start: 0.6379 (t0) cc_final: 0.6152 (t0) REVERT: 0e 30 TYR cc_start: 0.7122 (t80) cc_final: 0.6519 (t80) REVERT: 0e 112 MET cc_start: 0.5377 (ppp) cc_final: 0.4326 (ptt) REVERT: 0f 30 TYR cc_start: 0.7074 (t80) cc_final: 0.6650 (t80) REVERT: 0f 37 GLN cc_start: 0.7408 (pp30) cc_final: 0.7153 (tt0) REVERT: 0f 40 GLU cc_start: 0.5698 (mm-30) cc_final: 0.5439 (mt-10) REVERT: 0f 193 SER cc_start: 0.6618 (p) cc_final: 0.6371 (t) REVERT: 0f 213 GLN cc_start: 0.7712 (tp40) cc_final: 0.7382 (tp40) REVERT: 0f 221 MET cc_start: 0.6135 (tpp) cc_final: 0.5863 (tpp) REVERT: 0f 269 ASN cc_start: 0.7242 (t0) cc_final: 0.6915 (t0) REVERT: 0g 24 PHE cc_start: 0.4665 (p90) cc_final: 0.4390 (p90) REVERT: 0g 100 TYR cc_start: 0.6428 (OUTLIER) cc_final: 0.5802 (t80) REVERT: 0g 113 LYS cc_start: 0.4473 (mmtt) cc_final: 0.3306 (ttmm) REVERT: 0h 30 TYR cc_start: 0.6643 (t80) cc_final: 0.6313 (t80) REVERT: 0h 44 LEU cc_start: 0.7644 (mt) cc_final: 0.7338 (mt) REVERT: 0h 112 MET cc_start: 0.5259 (ppp) cc_final: 0.4213 (ptt) REVERT: 0h 185 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6745 (pt) REVERT: 0h 220 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6273 (mt-10) REVERT: 0i 30 TYR cc_start: 0.6617 (t80) cc_final: 0.5660 (t80) REVERT: 0i 100 TYR cc_start: 0.6668 (OUTLIER) cc_final: 0.6198 (t80) REVERT: 0i 112 MET cc_start: 0.4923 (ppp) cc_final: 0.3148 (mmp) REVERT: 0i 186 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.7270 (m-80) REVERT: 0i 213 GLN cc_start: 0.7654 (tp40) cc_final: 0.7395 (tp40) REVERT: 0j 18 GLN cc_start: 0.6671 (tp-100) cc_final: 0.6342 (tp-100) REVERT: 0j 22 ARG cc_start: 0.6746 (tpp-160) cc_final: 0.6284 (tpp-160) REVERT: 0j 100 TYR cc_start: 0.6514 (OUTLIER) cc_final: 0.6016 (t80) REVERT: 0k 30 TYR cc_start: 0.7263 (t80) cc_final: 0.6866 (t80) REVERT: 0k 44 LEU cc_start: 0.7438 (mt) cc_final: 0.7230 (mt) REVERT: 0k 112 MET cc_start: 0.5114 (ppp) cc_final: 0.4131 (ptt) REVERT: 0l 18 GLN cc_start: 0.6906 (tp-100) cc_final: 0.6566 (tp-100) REVERT: 0l 30 TYR cc_start: 0.6749 (t80) cc_final: 0.5994 (t80) REVERT: 0l 100 TYR cc_start: 0.6721 (OUTLIER) cc_final: 0.6240 (t80) REVERT: 0l 186 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6944 (m-80) REVERT: 0l 213 GLN cc_start: 0.7597 (tp40) cc_final: 0.7332 (tm-30) outliers start: 88 outliers final: 56 residues processed: 724 average time/residue: 0.1693 time to fit residues: 191.0290 Evaluate side-chains 660 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 594 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 52 PHE Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 141 LEU Chi-restraints excluded: chain 0a residue 170 SER Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0b residue 24 PHE Chi-restraints excluded: chain 0b residue 52 PHE Chi-restraints excluded: chain 0b residue 54 GLU Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 136 LEU Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0d residue 37 GLN Chi-restraints excluded: chain 0d residue 52 PHE Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 170 SER Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0d residue 217 VAL Chi-restraints excluded: chain 0e residue 24 PHE Chi-restraints excluded: chain 0e residue 52 PHE Chi-restraints excluded: chain 0e residue 54 GLU Chi-restraints excluded: chain 0e residue 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL Chi-restraints excluded: chain 0f residue 100 TYR Chi-restraints excluded: chain 0f residue 186 PHE Chi-restraints excluded: chain 0f residue 198 VAL Chi-restraints excluded: chain 0f residue 207 VAL Chi-restraints excluded: chain 0g residue 52 PHE Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 198 VAL Chi-restraints excluded: chain 0g residue 217 VAL Chi-restraints excluded: chain 0h residue 24 PHE Chi-restraints excluded: chain 0h residue 33 SER Chi-restraints excluded: chain 0h residue 52 PHE Chi-restraints excluded: chain 0h residue 100 TYR Chi-restraints excluded: chain 0h residue 185 ILE Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0i residue 37 GLN Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 170 SER Chi-restraints excluded: chain 0i residue 186 PHE Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0j residue 52 PHE Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 170 SER Chi-restraints excluded: chain 0j residue 186 PHE Chi-restraints excluded: chain 0j residue 198 VAL Chi-restraints excluded: chain 0k residue 24 PHE Chi-restraints excluded: chain 0k residue 33 SER Chi-restraints excluded: chain 0k residue 52 PHE Chi-restraints excluded: chain 0k residue 54 GLU Chi-restraints excluded: chain 0k residue 100 TYR Chi-restraints excluded: chain 0k residue 150 VAL Chi-restraints excluded: chain 0k residue 186 PHE Chi-restraints excluded: chain 0k residue 198 VAL Chi-restraints excluded: chain 0l residue 37 GLN Chi-restraints excluded: chain 0l residue 54 GLU Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 217 VAL Chi-restraints excluded: chain 0l residue 223 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 107 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 253 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 140 optimal weight: 0.0270 chunk 123 optimal weight: 0.7980 chunk 232 optimal weight: 0.9980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 59 GLN 0b 108 ASN ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 211 ASN 0c 49 ASN 0c 59 GLN ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 213 GLN ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 211 ASN ** 0f 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 59 GLN ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 151 ASN ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 211 ASN ** 0i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 123 ASN 0i 151 ASN ** 0j 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 59 GLN ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 152 GLN 0k 211 ASN ** 0l 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.215455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.203918 restraints weight = 49504.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.207452 restraints weight = 29340.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.209777 restraints weight = 18661.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.211183 restraints weight = 12530.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.212369 restraints weight = 8916.421| |-----------------------------------------------------------------------------| r_work (final): 0.4564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.7925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25728 Z= 0.152 Angle : 0.799 10.026 34860 Z= 0.425 Chirality : 0.048 0.231 3756 Planarity : 0.005 0.060 4548 Dihedral : 7.000 37.247 3348 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.40 % Allowed : 13.66 % Favored : 85.95 % Rotamer: Outliers : 3.03 % Allowed : 26.68 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.17), residues: 3024 helix: 0.45 (0.16), residues: 1080 sheet: -2.33 (0.27), residues: 420 loop : -2.04 (0.18), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG0j 281 TYR 0.019 0.001 TYR0h 36 PHE 0.028 0.002 PHE0e 65 TRP 0.011 0.001 TRP0d 218 HIS 0.002 0.000 HIS0h 26 Details of bonding type rmsd covalent geometry : bond 0.00342 (25728) covalent geometry : angle 0.79944 (34860) hydrogen bonds : bond 0.03580 ( 863) hydrogen bonds : angle 4.94524 ( 2481) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 620 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 24 PHE cc_start: 0.5031 (p90) cc_final: 0.4636 (p90) REVERT: 0a 40 GLU cc_start: 0.6485 (mm-30) cc_final: 0.5696 (mt-10) REVERT: 0a 213 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7842 (tm-30) REVERT: 0a 281 ARG cc_start: 0.7425 (mmm-85) cc_final: 0.7210 (mmm-85) REVERT: 0b 18 GLN cc_start: 0.7273 (tp-100) cc_final: 0.7069 (tp-100) REVERT: 0b 30 TYR cc_start: 0.6880 (t80) cc_final: 0.5639 (t80) REVERT: 0b 112 MET cc_start: 0.5542 (ppp) cc_final: 0.4837 (ptt) REVERT: 0c 20 ARG cc_start: 0.6327 (mmm160) cc_final: 0.5915 (mmp-170) REVERT: 0c 40 GLU cc_start: 0.6094 (mm-30) cc_final: 0.5552 (mt-10) REVERT: 0c 100 TYR cc_start: 0.6475 (OUTLIER) cc_final: 0.6118 (t80) REVERT: 0c 112 MET cc_start: 0.5270 (ppp) cc_final: 0.3139 (mmp) REVERT: 0c 186 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: 0c 213 GLN cc_start: 0.7978 (tp40) cc_final: 0.7626 (tm-30) REVERT: 0c 222 MET cc_start: 0.7871 (mmm) cc_final: 0.7539 (mmm) REVERT: 0c 225 LEU cc_start: 0.8223 (mt) cc_final: 0.7866 (mp) REVERT: 0d 112 MET cc_start: 0.5568 (ppp) cc_final: 0.4056 (ptt) REVERT: 0d 153 ASN cc_start: 0.7082 (t0) cc_final: 0.6721 (t0) REVERT: 0d 222 MET cc_start: 0.7661 (mpp) cc_final: 0.7105 (mpp) REVERT: 0e 30 TYR cc_start: 0.7358 (t80) cc_final: 0.6907 (t80) REVERT: 0e 112 MET cc_start: 0.5485 (ppp) cc_final: 0.4733 (ptt) REVERT: 0f 22 ARG cc_start: 0.7488 (ttm110) cc_final: 0.7137 (ptp-110) REVERT: 0f 40 GLU cc_start: 0.6179 (mm-30) cc_final: 0.5675 (mt-10) REVERT: 0f 112 MET cc_start: 0.5435 (ppp) cc_final: 0.3299 (mmp) REVERT: 0f 193 SER cc_start: 0.6830 (p) cc_final: 0.6489 (t) REVERT: 0f 213 GLN cc_start: 0.8081 (tp40) cc_final: 0.7696 (tp40) REVERT: 0f 221 MET cc_start: 0.6896 (tpp) cc_final: 0.6647 (tpp) REVERT: 0f 269 ASN cc_start: 0.7732 (t0) cc_final: 0.7350 (t0) REVERT: 0g 24 PHE cc_start: 0.5141 (p90) cc_final: 0.4779 (p90) REVERT: 0g 100 TYR cc_start: 0.6273 (OUTLIER) cc_final: 0.5820 (t80) REVERT: 0g 113 LYS cc_start: 0.4325 (mmtt) cc_final: 0.2912 (ttmm) REVERT: 0h 30 TYR cc_start: 0.6896 (t80) cc_final: 0.6581 (t80) REVERT: 0h 44 LEU cc_start: 0.7476 (mt) cc_final: 0.7121 (mt) REVERT: 0h 112 MET cc_start: 0.5319 (ppp) cc_final: 0.4402 (ptt) REVERT: 0h 185 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7464 (pt) REVERT: 0i 30 TYR cc_start: 0.6823 (t80) cc_final: 0.5865 (t80) REVERT: 0i 112 MET cc_start: 0.5114 (ppp) cc_final: 0.3270 (mmp) REVERT: 0i 186 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7312 (m-80) REVERT: 0i 213 GLN cc_start: 0.8095 (tp40) cc_final: 0.7766 (tm-30) REVERT: 0i 269 ASN cc_start: 0.7802 (t0) cc_final: 0.7453 (t0) REVERT: 0j 18 GLN cc_start: 0.7631 (tp-100) cc_final: 0.7100 (tp-100) REVERT: 0j 22 ARG cc_start: 0.7399 (tpp-160) cc_final: 0.6803 (tpp-160) REVERT: 0j 112 MET cc_start: 0.5412 (ppp) cc_final: 0.4137 (ptt) REVERT: 0j 153 ASN cc_start: 0.7093 (t0) cc_final: 0.6867 (t0) REVERT: 0j 172 LYS cc_start: 0.7199 (mmmt) cc_final: 0.6951 (pttp) REVERT: 0k 18 GLN cc_start: 0.7168 (tp-100) cc_final: 0.6960 (tp-100) REVERT: 0k 44 LEU cc_start: 0.7508 (mt) cc_final: 0.7264 (mt) REVERT: 0k 112 MET cc_start: 0.5191 (ppp) cc_final: 0.4913 (ppp) REVERT: 0l 20 ARG cc_start: 0.6452 (mmm160) cc_final: 0.6030 (mmp-170) REVERT: 0l 144 LEU cc_start: 0.7794 (mt) cc_final: 0.7533 (mt) REVERT: 0l 186 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.6853 (m-80) REVERT: 0l 213 GLN cc_start: 0.8183 (tp40) cc_final: 0.7694 (tm-30) REVERT: 0l 225 LEU cc_start: 0.8336 (mt) cc_final: 0.8128 (mp) outliers start: 83 outliers final: 56 residues processed: 678 average time/residue: 0.1695 time to fit residues: 177.7826 Evaluate side-chains 655 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 593 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 52 PHE Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 126 MET Chi-restraints excluded: chain 0a residue 141 LEU Chi-restraints excluded: chain 0a residue 170 SER Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0a residue 217 VAL Chi-restraints excluded: chain 0b residue 24 PHE Chi-restraints excluded: chain 0b residue 52 PHE Chi-restraints excluded: chain 0b residue 54 GLU Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0c residue 62 TYR Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0d residue 52 PHE Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 170 SER Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0d residue 217 VAL Chi-restraints excluded: chain 0e residue 24 PHE Chi-restraints excluded: chain 0e residue 52 PHE Chi-restraints excluded: chain 0e residue 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL Chi-restraints excluded: chain 0e residue 207 VAL Chi-restraints excluded: chain 0f residue 100 TYR Chi-restraints excluded: chain 0f residue 186 PHE Chi-restraints excluded: chain 0f residue 198 VAL Chi-restraints excluded: chain 0g residue 52 PHE Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 198 VAL Chi-restraints excluded: chain 0g residue 217 VAL Chi-restraints excluded: chain 0h residue 24 PHE Chi-restraints excluded: chain 0h residue 33 SER Chi-restraints excluded: chain 0h residue 52 PHE Chi-restraints excluded: chain 0h residue 185 ILE Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0i residue 24 PHE Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 170 SER Chi-restraints excluded: chain 0i residue 186 PHE Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 186 PHE Chi-restraints excluded: chain 0j residue 217 VAL Chi-restraints excluded: chain 0k residue 24 PHE Chi-restraints excluded: chain 0k residue 33 SER Chi-restraints excluded: chain 0k residue 52 PHE Chi-restraints excluded: chain 0k residue 54 GLU Chi-restraints excluded: chain 0k residue 186 PHE Chi-restraints excluded: chain 0k residue 198 VAL Chi-restraints excluded: chain 0l residue 37 GLN Chi-restraints excluded: chain 0l residue 54 GLU Chi-restraints excluded: chain 0l residue 62 TYR Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 217 VAL Chi-restraints excluded: chain 0l residue 223 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 201 optimal weight: 0.8980 chunk 205 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 208 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 174 optimal weight: 0.0040 chunk 101 optimal weight: 0.9990 chunk 202 optimal weight: 0.6980 chunk 135 optimal weight: 0.9980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 59 GLN ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 59 GLN ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 211 ASN ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 59 GLN ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 59 GLN ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 151 ASN ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 59 GLN ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 58 HIS ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.213024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.202343 restraints weight = 49345.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.205514 restraints weight = 29643.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.207632 restraints weight = 18745.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.209093 restraints weight = 12697.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.210234 restraints weight = 8939.388| |-----------------------------------------------------------------------------| r_work (final): 0.4563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5980 moved from start: 0.8131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25728 Z= 0.155 Angle : 0.816 10.696 34860 Z= 0.432 Chirality : 0.048 0.272 3756 Planarity : 0.005 0.061 4548 Dihedral : 6.986 37.149 3348 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.40 % Allowed : 13.89 % Favored : 85.71 % Rotamer: Outliers : 2.60 % Allowed : 27.81 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.17), residues: 3024 helix: 0.56 (0.16), residues: 1080 sheet: -2.30 (0.27), residues: 420 loop : -2.04 (0.18), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG0j 281 TYR 0.019 0.001 TYR0b 36 PHE 0.027 0.002 PHE0c 65 TRP 0.010 0.001 TRP0e 41 HIS 0.002 0.000 HIS0h 26 Details of bonding type rmsd covalent geometry : bond 0.00346 (25728) covalent geometry : angle 0.81588 (34860) hydrogen bonds : bond 0.03659 ( 863) hydrogen bonds : angle 4.92852 ( 2481) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 626 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 24 PHE cc_start: 0.5049 (p90) cc_final: 0.4632 (p90) REVERT: 0a 113 LYS cc_start: 0.4639 (mmtt) cc_final: 0.3620 (ttmm) REVERT: 0a 172 LYS cc_start: 0.7049 (mmmt) cc_final: 0.6775 (pttp) REVERT: 0a 281 ARG cc_start: 0.7428 (mmm-85) cc_final: 0.7145 (mmm-85) REVERT: 0b 112 MET cc_start: 0.5521 (ppp) cc_final: 0.4635 (ptt) REVERT: 0b 209 LYS cc_start: 0.8226 (mmtp) cc_final: 0.7770 (mmtm) REVERT: 0b 220 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6685 (mt-10) REVERT: 0c 20 ARG cc_start: 0.6491 (mmm160) cc_final: 0.6279 (mmp-170) REVERT: 0c 22 ARG cc_start: 0.7559 (ttm110) cc_final: 0.7253 (ptp-110) REVERT: 0c 100 TYR cc_start: 0.6581 (OUTLIER) cc_final: 0.6129 (t80) REVERT: 0c 112 MET cc_start: 0.5113 (ppp) cc_final: 0.3048 (mmp) REVERT: 0c 172 LYS cc_start: 0.7896 (mmmm) cc_final: 0.7370 (mmtm) REVERT: 0c 186 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.7224 (m-80) REVERT: 0c 213 GLN cc_start: 0.8182 (tp40) cc_final: 0.7706 (tm-30) REVERT: 0c 222 MET cc_start: 0.7864 (mmm) cc_final: 0.6997 (tpt) REVERT: 0d 112 MET cc_start: 0.5466 (ppp) cc_final: 0.4013 (ptt) REVERT: 0d 145 LYS cc_start: 0.7505 (tptp) cc_final: 0.7296 (tptp) REVERT: 0d 153 ASN cc_start: 0.7118 (t0) cc_final: 0.6784 (t0) REVERT: 0d 213 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7581 (tm-30) REVERT: 0d 222 MET cc_start: 0.7689 (mpp) cc_final: 0.7099 (mpp) REVERT: 0e 30 TYR cc_start: 0.7354 (t80) cc_final: 0.7003 (t80) REVERT: 0e 112 MET cc_start: 0.5502 (ppp) cc_final: 0.4705 (ptt) REVERT: 0f 20 ARG cc_start: 0.6536 (mmm160) cc_final: 0.6140 (mmp-170) REVERT: 0f 22 ARG cc_start: 0.7602 (ttm110) cc_final: 0.7175 (ptp-110) REVERT: 0f 112 MET cc_start: 0.5409 (ppp) cc_final: 0.3152 (mmp) REVERT: 0f 144 LEU cc_start: 0.8072 (tp) cc_final: 0.7611 (mt) REVERT: 0f 193 SER cc_start: 0.7013 (p) cc_final: 0.6688 (t) REVERT: 0f 213 GLN cc_start: 0.8202 (tp40) cc_final: 0.7873 (tm-30) REVERT: 0f 221 MET cc_start: 0.6911 (tpp) cc_final: 0.6665 (tpp) REVERT: 0f 269 ASN cc_start: 0.7807 (t0) cc_final: 0.7426 (t0) REVERT: 0g 24 PHE cc_start: 0.5022 (p90) cc_final: 0.4703 (p90) REVERT: 0g 222 MET cc_start: 0.7539 (mmm) cc_final: 0.7281 (mmm) REVERT: 0h 30 TYR cc_start: 0.6943 (t80) cc_final: 0.6601 (t80) REVERT: 0h 44 LEU cc_start: 0.7503 (mt) cc_final: 0.7174 (mt) REVERT: 0h 112 MET cc_start: 0.5196 (ppp) cc_final: 0.4287 (ptt) REVERT: 0h 144 LEU cc_start: 0.7638 (tp) cc_final: 0.7269 (tt) REVERT: 0h 185 ILE cc_start: 0.7534 (pt) cc_final: 0.7311 (pt) REVERT: 0i 22 ARG cc_start: 0.7610 (ttm110) cc_final: 0.7266 (ptp-110) REVERT: 0i 30 TYR cc_start: 0.6868 (t80) cc_final: 0.6034 (t80) REVERT: 0i 112 MET cc_start: 0.5070 (ppp) cc_final: 0.3283 (mmp) REVERT: 0i 128 PHE cc_start: 0.7606 (m-80) cc_final: 0.7160 (m-80) REVERT: 0i 186 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7370 (m-80) REVERT: 0i 213 GLN cc_start: 0.8174 (tp40) cc_final: 0.7817 (tm-30) REVERT: 0i 269 ASN cc_start: 0.7823 (t0) cc_final: 0.7481 (t0) REVERT: 0j 18 GLN cc_start: 0.7711 (tp-100) cc_final: 0.7233 (tp-100) REVERT: 0j 22 ARG cc_start: 0.7369 (tpp-160) cc_final: 0.6801 (tpp-160) REVERT: 0j 112 MET cc_start: 0.5399 (ppp) cc_final: 0.4266 (ptt) REVERT: 0j 137 PHE cc_start: 0.7352 (m-80) cc_final: 0.7068 (m-10) REVERT: 0k 44 LEU cc_start: 0.7538 (mt) cc_final: 0.7269 (mt) REVERT: 0k 112 MET cc_start: 0.5189 (ppp) cc_final: 0.4364 (ptt) REVERT: 0l 20 ARG cc_start: 0.6632 (mmm160) cc_final: 0.6424 (mmp-170) REVERT: 0l 117 MET cc_start: 0.6825 (ptm) cc_final: 0.6578 (ttp) REVERT: 0l 144 LEU cc_start: 0.7886 (mt) cc_final: 0.7628 (mt) REVERT: 0l 186 PHE cc_start: 0.7162 (OUTLIER) cc_final: 0.6671 (m-80) REVERT: 0l 213 GLN cc_start: 0.8154 (tp40) cc_final: 0.7619 (tm-30) REVERT: 0l 269 ASN cc_start: 0.7962 (t0) cc_final: 0.7643 (t0) outliers start: 71 outliers final: 55 residues processed: 681 average time/residue: 0.1773 time to fit residues: 185.8554 Evaluate side-chains 652 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 593 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 37 GLN Chi-restraints excluded: chain 0a residue 52 PHE Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 128 PHE Chi-restraints excluded: chain 0a residue 141 LEU Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0a residue 217 VAL Chi-restraints excluded: chain 0b residue 24 PHE Chi-restraints excluded: chain 0b residue 52 PHE Chi-restraints excluded: chain 0b residue 54 GLU Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 170 SER Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0d residue 276 VAL Chi-restraints excluded: chain 0e residue 24 PHE Chi-restraints excluded: chain 0e residue 52 PHE Chi-restraints excluded: chain 0e residue 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL Chi-restraints excluded: chain 0f residue 62 TYR Chi-restraints excluded: chain 0f residue 100 TYR Chi-restraints excluded: chain 0f residue 186 PHE Chi-restraints excluded: chain 0f residue 198 VAL Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 198 VAL Chi-restraints excluded: chain 0h residue 24 PHE Chi-restraints excluded: chain 0h residue 33 SER Chi-restraints excluded: chain 0h residue 52 PHE Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0i residue 24 PHE Chi-restraints excluded: chain 0i residue 62 TYR Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 170 SER Chi-restraints excluded: chain 0i residue 186 PHE Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0i residue 207 VAL Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 186 PHE Chi-restraints excluded: chain 0j residue 277 LYS Chi-restraints excluded: chain 0k residue 24 PHE Chi-restraints excluded: chain 0k residue 33 SER Chi-restraints excluded: chain 0k residue 52 PHE Chi-restraints excluded: chain 0k residue 54 GLU Chi-restraints excluded: chain 0k residue 186 PHE Chi-restraints excluded: chain 0k residue 198 VAL Chi-restraints excluded: chain 0l residue 37 GLN Chi-restraints excluded: chain 0l residue 54 GLU Chi-restraints excluded: chain 0l residue 62 TYR Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 217 VAL Chi-restraints excluded: chain 0l residue 223 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 99 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 253 optimal weight: 0.9980 chunk 277 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 59 GLN 0c 151 ASN ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 59 GLN ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 151 ASN ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 59 GLN ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 58 HIS ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 168 GLN 0k 32 GLN ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 151 ASN ** 0l 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 108 ASN ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.213048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.201594 restraints weight = 49444.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.204985 restraints weight = 29441.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.207268 restraints weight = 18884.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.208642 restraints weight = 12790.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.209865 restraints weight = 9255.125| |-----------------------------------------------------------------------------| r_work (final): 0.4571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.8254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25728 Z= 0.168 Angle : 0.833 10.820 34860 Z= 0.441 Chirality : 0.049 0.270 3756 Planarity : 0.005 0.069 4548 Dihedral : 7.045 36.946 3348 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.40 % Allowed : 14.81 % Favored : 84.79 % Rotamer: Outliers : 2.70 % Allowed : 28.33 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.17), residues: 3024 helix: 0.57 (0.16), residues: 1080 sheet: -2.24 (0.27), residues: 420 loop : -2.05 (0.18), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG0d 281 TYR 0.019 0.002 TYR0e 205 PHE 0.028 0.002 PHE0c 65 TRP 0.010 0.001 TRP0l 23 HIS 0.002 0.000 HIS0h 26 Details of bonding type rmsd covalent geometry : bond 0.00381 (25728) covalent geometry : angle 0.83344 (34860) hydrogen bonds : bond 0.03840 ( 863) hydrogen bonds : angle 4.99699 ( 2481) =============================================================================== Job complete usr+sys time: 4411.02 seconds wall clock time: 77 minutes 8.79 seconds (4628.79 seconds total)