Starting phenix.real_space_refine on Sat Jun 6 11:25:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ylv_73094/06_2026/9ylv_73094.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ylv_73094/06_2026/9ylv_73094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ylv_73094/06_2026/9ylv_73094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ylv_73094/06_2026/9ylv_73094.map" model { file = "/net/cci-nas-00/data/ceres_data/9ylv_73094/06_2026/9ylv_73094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ylv_73094/06_2026/9ylv_73094.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 132 5.16 5 C 17688 2.51 5 N 4980 2.21 5 O 5220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28020 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2335 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 278} Restraints were copied for chains: D, E, F, G, H, K, I, J, B, L, A Time building chain proxies: 3.09, per 1000 atoms: 0.11 Number of scatterers: 28020 At special positions: 0 Unit cell: (152.515, 166.793, 123.31, 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 132 16.00 O 5220 8.00 N 4980 7.00 C 17688 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: 2.21 Conformation dependent library (CDL) restraints added in 1.2 seconds 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6528 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 36 sheets defined 42.1% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'C' and resid 2 through 15 removed outlier: 5.760A pdb=" N ASN C 10 " --> pdb=" O ARG C 6 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'C' and resid 79 through 95 Processing helix chain 'C' and resid 153 through 161 removed outlier: 3.761A pdb=" N MET C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 Processing helix chain 'C' and resid 210 through 222 removed outlier: 3.657A pdb=" N THR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 241 through 257 Processing helix chain 'C' and resid 283 through 295 Processing helix chain 'D' and resid 3 through 15 removed outlier: 5.761A pdb=" N ASN D 10 " --> pdb=" O ARG D 6 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 79 through 95 Processing helix chain 'D' and resid 153 through 161 removed outlier: 3.761A pdb=" N MET D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 189 Processing helix chain 'D' and resid 210 through 222 removed outlier: 3.658A pdb=" N THR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 241 through 257 Processing helix chain 'D' and resid 283 through 295 Processing helix chain 'E' and resid 3 through 15 removed outlier: 5.760A pdb=" N ASN E 10 " --> pdb=" O ARG E 6 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TYR E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 79 through 95 Processing helix chain 'E' and resid 153 through 161 removed outlier: 3.762A pdb=" N MET E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 189 Processing helix chain 'E' and resid 210 through 222 removed outlier: 3.658A pdb=" N THR E 222 " --> pdb=" O LEU E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 232 Processing helix chain 'E' and resid 241 through 257 Processing helix chain 'E' and resid 283 through 295 Processing helix chain 'F' and resid 3 through 15 removed outlier: 5.761A pdb=" N ASN F 10 " --> pdb=" O ARG F 6 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TYR F 11 " --> pdb=" O LEU F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 79 through 95 Processing helix chain 'F' and resid 153 through 161 removed outlier: 3.761A pdb=" N MET F 161 " --> pdb=" O LEU F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 189 Processing helix chain 'F' and resid 210 through 222 removed outlier: 3.657A pdb=" N THR F 222 " --> pdb=" O LEU F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 232 Processing helix chain 'F' and resid 241 through 257 Processing helix chain 'F' and resid 283 through 295 Processing helix chain 'G' and resid 3 through 15 removed outlier: 5.761A pdb=" N ASN G 10 " --> pdb=" O ARG G 6 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR G 11 " --> pdb=" O LEU G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 46 Processing helix chain 'G' and resid 67 through 72 Processing helix chain 'G' and resid 79 through 95 Processing helix chain 'G' and resid 153 through 161 removed outlier: 3.761A pdb=" N MET G 161 " --> pdb=" O LEU G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 189 Processing helix chain 'G' and resid 210 through 222 removed outlier: 3.659A pdb=" N THR G 222 " --> pdb=" O LEU G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 232 Processing helix chain 'G' and resid 241 through 257 Processing helix chain 'G' and resid 283 through 295 Processing helix chain 'H' and resid 3 through 15 removed outlier: 5.761A pdb=" N ASN H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TYR H 11 " --> pdb=" O LEU H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 46 Processing helix chain 'H' and resid 67 through 72 Processing helix chain 'H' and resid 79 through 95 Processing helix chain 'H' and resid 153 through 161 removed outlier: 3.761A pdb=" N MET H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 189 Processing helix chain 'H' and resid 210 through 222 removed outlier: 3.657A pdb=" N THR H 222 " --> pdb=" O LEU H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 232 Processing helix chain 'H' and resid 241 through 257 Processing helix chain 'H' and resid 283 through 295 Processing helix chain 'K' and resid 3 through 15 removed outlier: 5.761A pdb=" N ASN K 10 " --> pdb=" O ARG K 6 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TYR K 11 " --> pdb=" O LEU K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 46 Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 79 through 95 Processing helix chain 'K' and resid 153 through 161 removed outlier: 3.760A pdb=" N MET K 161 " --> pdb=" O LEU K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 189 Processing helix chain 'K' and resid 210 through 222 removed outlier: 3.657A pdb=" N THR K 222 " --> pdb=" O LEU K 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 232 Processing helix chain 'K' and resid 241 through 257 Processing helix chain 'K' and resid 283 through 295 Processing helix chain 'I' and resid 3 through 15 removed outlier: 5.761A pdb=" N ASN I 10 " --> pdb=" O ARG I 6 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR I 11 " --> pdb=" O LEU I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 46 Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 79 through 95 Processing helix chain 'I' and resid 153 through 161 removed outlier: 3.762A pdb=" N MET I 161 " --> pdb=" O LEU I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 189 Processing helix chain 'I' and resid 210 through 222 removed outlier: 3.657A pdb=" N THR I 222 " --> pdb=" O LEU I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 232 Processing helix chain 'I' and resid 241 through 257 Processing helix chain 'I' and resid 283 through 295 Processing helix chain 'J' and resid 3 through 15 removed outlier: 5.761A pdb=" N ASN J 10 " --> pdb=" O ARG J 6 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR J 11 " --> pdb=" O LEU J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 46 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 79 through 95 Processing helix chain 'J' and resid 153 through 161 removed outlier: 3.761A pdb=" N MET J 161 " --> pdb=" O LEU J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 189 Processing helix chain 'J' and resid 210 through 222 removed outlier: 3.657A pdb=" N THR J 222 " --> pdb=" O LEU J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 232 Processing helix chain 'J' and resid 241 through 257 Processing helix chain 'J' and resid 283 through 295 Processing helix chain 'B' and resid 3 through 15 removed outlier: 5.762A pdb=" N ASN B 10 " --> pdb=" O ARG B 6 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TYR B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 79 through 95 Processing helix chain 'B' and resid 153 through 161 removed outlier: 3.761A pdb=" N MET B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 189 Processing helix chain 'B' and resid 210 through 222 removed outlier: 3.658A pdb=" N THR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 241 through 257 Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'L' and resid 3 through 15 removed outlier: 5.761A pdb=" N ASN L 10 " --> pdb=" O ARG L 6 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TYR L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 46 Processing helix chain 'L' and resid 67 through 72 Processing helix chain 'L' and resid 79 through 95 Processing helix chain 'L' and resid 153 through 161 removed outlier: 3.761A pdb=" N MET L 161 " --> pdb=" O LEU L 157 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 189 Processing helix chain 'L' and resid 210 through 222 removed outlier: 3.658A pdb=" N THR L 222 " --> pdb=" O LEU L 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 232 Processing helix chain 'L' and resid 241 through 257 Processing helix chain 'L' and resid 283 through 295 Processing helix chain 'A' and resid 3 through 15 removed outlier: 5.761A pdb=" N ASN A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TYR A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 79 through 95 Processing helix chain 'A' and resid 153 through 161 removed outlier: 3.760A pdb=" N MET A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 210 through 222 removed outlier: 3.658A pdb=" N THR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 Processing helix chain 'A' and resid 241 through 257 Processing helix chain 'A' and resid 283 through 295 Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 24 removed outlier: 6.445A pdb=" N ASP C 22 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 129 through 130 removed outlier: 4.042A pdb=" N ASP C 148 " --> pdb=" O ARG C 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 191 through 196 removed outlier: 7.010A pdb=" N ARG C 167 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU C 194 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS C 261 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE C 262 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL C 280 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ARG C 264 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 21 through 24 removed outlier: 6.444A pdb=" N ASP D 22 " --> pdb=" O ILE D 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 129 through 130 removed outlier: 4.042A pdb=" N ASP D 148 " --> pdb=" O ARG D 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 191 through 196 removed outlier: 7.011A pdb=" N ARG D 167 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU D 194 " --> pdb=" O ARG D 167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS D 261 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE D 262 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL D 280 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ARG D 264 " --> pdb=" O ALA D 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 21 through 24 removed outlier: 6.445A pdb=" N ASP E 22 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 129 through 130 removed outlier: 4.043A pdb=" N ASP E 148 " --> pdb=" O ARG E 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 191 through 196 removed outlier: 7.011A pdb=" N ARG E 167 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU E 194 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS E 261 " --> pdb=" O LEU E 234 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE E 262 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL E 280 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ARG E 264 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 21 through 24 removed outlier: 6.445A pdb=" N ASP F 22 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 129 through 130 removed outlier: 4.043A pdb=" N ASP F 148 " --> pdb=" O ARG F 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 191 through 196 removed outlier: 7.010A pdb=" N ARG F 167 " --> pdb=" O VAL F 192 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU F 194 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS F 261 " --> pdb=" O LEU F 234 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE F 262 " --> pdb=" O VAL F 280 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL F 280 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ARG F 264 " --> pdb=" O ALA F 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 21 through 24 removed outlier: 6.445A pdb=" N ASP G 22 " --> pdb=" O ILE G 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 129 through 130 removed outlier: 4.043A pdb=" N ASP G 148 " --> pdb=" O ARG G 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 191 through 196 removed outlier: 7.011A pdb=" N ARG G 167 " --> pdb=" O VAL G 192 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU G 194 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS G 261 " --> pdb=" O LEU G 234 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE G 262 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL G 280 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ARG G 264 " --> pdb=" O ALA G 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 21 through 24 removed outlier: 6.444A pdb=" N ASP H 22 " --> pdb=" O ILE H 54 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 129 through 130 removed outlier: 4.042A pdb=" N ASP H 148 " --> pdb=" O ARG H 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 191 through 196 removed outlier: 7.010A pdb=" N ARG H 167 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU H 194 " --> pdb=" O ARG H 167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS H 261 " --> pdb=" O LEU H 234 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE H 262 " --> pdb=" O VAL H 280 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL H 280 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ARG H 264 " --> pdb=" O ALA H 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 21 through 24 removed outlier: 6.445A pdb=" N ASP K 22 " --> pdb=" O ILE K 54 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 129 through 130 removed outlier: 4.042A pdb=" N ASP K 148 " --> pdb=" O ARG K 145 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 191 through 196 removed outlier: 7.011A pdb=" N ARG K 167 " --> pdb=" O VAL K 192 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU K 194 " --> pdb=" O ARG K 167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS K 261 " --> pdb=" O LEU K 234 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE K 262 " --> pdb=" O VAL K 280 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL K 280 " --> pdb=" O ILE K 262 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ARG K 264 " --> pdb=" O ALA K 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 21 through 24 removed outlier: 6.444A pdb=" N ASP I 22 " --> pdb=" O ILE I 54 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 129 through 130 removed outlier: 4.043A pdb=" N ASP I 148 " --> pdb=" O ARG I 145 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 191 through 196 removed outlier: 7.011A pdb=" N ARG I 167 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU I 194 " --> pdb=" O ARG I 167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS I 261 " --> pdb=" O LEU I 234 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE I 262 " --> pdb=" O VAL I 280 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL I 280 " --> pdb=" O ILE I 262 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ARG I 264 " --> pdb=" O ALA I 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 21 through 24 removed outlier: 6.445A pdb=" N ASP J 22 " --> pdb=" O ILE J 54 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 129 through 130 removed outlier: 4.042A pdb=" N ASP J 148 " --> pdb=" O ARG J 145 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 191 through 196 removed outlier: 7.011A pdb=" N ARG J 167 " --> pdb=" O VAL J 192 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU J 194 " --> pdb=" O ARG J 167 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS J 261 " --> pdb=" O LEU J 234 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE J 262 " --> pdb=" O VAL J 280 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL J 280 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ARG J 264 " --> pdb=" O ALA J 278 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 21 through 24 removed outlier: 6.445A pdb=" N ASP B 22 " --> pdb=" O ILE B 54 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 129 through 130 removed outlier: 4.043A pdb=" N ASP B 148 " --> pdb=" O ARG B 145 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 191 through 196 removed outlier: 7.012A pdb=" N ARG B 167 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU B 194 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS B 261 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE B 262 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL B 280 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ARG B 264 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 21 through 24 removed outlier: 6.444A pdb=" N ASP L 22 " --> pdb=" O ILE L 54 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 129 through 130 removed outlier: 4.043A pdb=" N ASP L 148 " --> pdb=" O ARG L 145 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 191 through 196 removed outlier: 7.011A pdb=" N ARG L 167 " --> pdb=" O VAL L 192 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU L 194 " --> pdb=" O ARG L 167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS L 261 " --> pdb=" O LEU L 234 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE L 262 " --> pdb=" O VAL L 280 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL L 280 " --> pdb=" O ILE L 262 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ARG L 264 " --> pdb=" O ALA L 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 21 through 24 removed outlier: 6.445A pdb=" N ASP A 22 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 129 through 130 removed outlier: 4.043A pdb=" N ASP A 148 " --> pdb=" O ARG A 145 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 191 through 196 removed outlier: 7.011A pdb=" N ARG A 167 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU A 194 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS A 261 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE A 262 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL A 280 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ARG A 264 " --> pdb=" O ALA A 278 " (cutoff:3.500A) 1297 hydrogen bonds defined for protein. 3783 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: 4.82 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9494 1.34 - 1.46: 4704 1.46 - 1.57: 14098 1.57 - 1.69: 0 1.69 - 1.81: 228 Bond restraints: 28524 Sorted by residual: bond pdb=" CB ASP F 79 " pdb=" CG ASP F 79 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.17e+00 bond pdb=" CB ASP K 79 " pdb=" CG ASP K 79 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.15e+00 bond pdb=" CB ASP J 79 " pdb=" CG ASP J 79 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.15e+00 bond pdb=" CB ASP G 79 " pdb=" CG ASP G 79 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.15e+00 bond pdb=" CB ASP L 79 " pdb=" CG ASP L 79 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.14e+00 ... (remaining 28519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 36676 1.04 - 2.09: 1520 2.09 - 3.13: 250 3.13 - 4.18: 134 4.18 - 5.22: 36 Bond angle restraints: 38616 Sorted by residual: angle pdb=" C ASP F 79 " pdb=" CA ASP F 79 " pdb=" CB ASP F 79 " ideal model delta sigma weight residual 110.22 115.03 -4.81 1.67e+00 3.59e-01 8.30e+00 angle pdb=" C ASP K 79 " pdb=" CA ASP K 79 " pdb=" CB ASP K 79 " ideal model delta sigma weight residual 110.22 115.02 -4.80 1.67e+00 3.59e-01 8.26e+00 angle pdb=" C ASP H 79 " pdb=" CA ASP H 79 " pdb=" CB ASP H 79 " ideal model delta sigma weight residual 110.22 115.01 -4.79 1.67e+00 3.59e-01 8.23e+00 angle pdb=" C ASP D 79 " pdb=" CA ASP D 79 " pdb=" CB ASP D 79 " ideal model delta sigma weight residual 110.22 115.01 -4.79 1.67e+00 3.59e-01 8.22e+00 angle pdb=" C ASP E 79 " pdb=" CA ASP E 79 " pdb=" CB ASP E 79 " ideal model delta sigma weight residual 110.22 115.00 -4.78 1.67e+00 3.59e-01 8.18e+00 ... (remaining 38611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 15495 17.58 - 35.15: 1533 35.15 - 52.73: 396 52.73 - 70.30: 36 70.30 - 87.88: 48 Dihedral angle restraints: 17508 sinusoidal: 7368 harmonic: 10140 Sorted by residual: dihedral pdb=" CA ASN K 96 " pdb=" C ASN K 96 " pdb=" N PRO K 97 " pdb=" CA PRO K 97 " ideal model delta harmonic sigma weight residual 180.00 163.91 16.09 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA ASN D 96 " pdb=" C ASN D 96 " pdb=" N PRO D 97 " pdb=" CA PRO D 97 " ideal model delta harmonic sigma weight residual 180.00 163.91 16.09 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA ASN L 96 " pdb=" C ASN L 96 " pdb=" N PRO L 97 " pdb=" CA PRO L 97 " ideal model delta harmonic sigma weight residual 180.00 163.93 16.07 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 17505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2741 0.028 - 0.056: 897 0.056 - 0.084: 307 0.084 - 0.112: 290 0.112 - 0.140: 133 Chirality restraints: 4368 Sorted by residual: chirality pdb=" CA ILE E 235 " pdb=" N ILE E 235 " pdb=" C ILE E 235 " pdb=" CB ILE E 235 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE B 235 " pdb=" N ILE B 235 " pdb=" C ILE B 235 " pdb=" CB ILE B 235 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE G 235 " pdb=" N ILE G 235 " pdb=" C ILE G 235 " pdb=" CB ILE G 235 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 4365 not shown) Planarity restraints: 5016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP J 79 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C ASP J 79 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP J 79 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU J 80 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 79 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.08e+00 pdb=" C ASP A 79 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP A 79 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 80 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 79 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C ASP B 79 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP B 79 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU B 80 " 0.011 2.00e-02 2.50e+03 ... (remaining 5013 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1274 2.73 - 3.28: 27850 3.28 - 3.82: 43739 3.82 - 4.36: 55770 4.36 - 4.90: 96001 Nonbonded interactions: 224634 Sorted by model distance: nonbonded pdb=" O ASP C 79 " pdb=" OD1 ASP C 79 " model vdw 2.194 3.040 nonbonded pdb=" O ASP H 79 " pdb=" OD1 ASP H 79 " model vdw 2.194 3.040 nonbonded pdb=" O ASP J 79 " pdb=" OD1 ASP J 79 " model vdw 2.194 3.040 nonbonded pdb=" O ASP E 79 " pdb=" OD1 ASP E 79 " model vdw 2.194 3.040 nonbonded pdb=" O ASP L 79 " pdb=" OD1 ASP L 79 " model vdw 2.194 3.040 ... (remaining 224629 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: 0.06 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'I' selection = chain 'J' selection = chain 'B' selection = chain 'L' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.180 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 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 : 0.003 0.028 28524 Z= 0.123 Angle : 0.543 5.221 38616 Z= 0.301 Chirality : 0.043 0.140 4368 Planarity : 0.004 0.034 5016 Dihedral : 15.218 87.879 10980 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.26 % Allowed : 12.24 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.14), residues: 3516 helix: 0.87 (0.13), residues: 1452 sheet: -0.72 (0.21), residues: 396 loop : 0.27 (0.17), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 145 TYR 0.012 0.001 TYR B 71 PHE 0.006 0.001 PHE K 172 TRP 0.005 0.001 TRP H 293 HIS 0.003 0.001 HIS C 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (28524) covalent geometry : angle 0.54266 / 0.30 (38616) hydrogen bonds : bond 0.20887 / 14.10 ( 1297) hydrogen bonds : angle 7.94322 / 5.70 ( 3783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 611 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 122 ARG cc_start: 0.8241 (tpp80) cc_final: 0.7690 (ttt90) REVERT: F 122 ARG cc_start: 0.8216 (tpp80) cc_final: 0.7607 (ttt90) REVERT: G 258 ARG cc_start: 0.6890 (ptp90) cc_final: 0.6278 (ptm-80) REVERT: H 258 ARG cc_start: 0.6908 (ptp90) cc_final: 0.6301 (ptm-80) REVERT: I 122 ARG cc_start: 0.8202 (tpp80) cc_final: 0.7683 (ttt90) REVERT: B 258 ARG cc_start: 0.6898 (ptp90) cc_final: 0.6278 (ptm-80) REVERT: L 122 ARG cc_start: 0.8192 (tpp80) cc_final: 0.7667 (ttt90) REVERT: A 258 ARG cc_start: 0.7036 (ptp90) cc_final: 0.6452 (ptm-80) outliers start: 8 outliers final: 0 residues processed: 617 average time/residue: 0.8355 time to fit residues: 582.9121 Evaluate side-chains 389 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 9.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN D 220 ASN E 89 GLN E 189 ASN E 220 ASN G 183 GLN H 183 GLN K 89 GLN K 220 ASN I 93 ASN B 174 GLN B 183 GLN A 183 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.186884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141270 restraints weight = 33684.722| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.53 r_work: 0.3594 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 28524 Z= 0.286 Angle : 0.724 6.154 38616 Z= 0.374 Chirality : 0.054 0.171 4368 Planarity : 0.007 0.055 5016 Dihedral : 4.967 18.930 3912 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.65 % Allowed : 18.16 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3516 helix: 0.90 (0.13), residues: 1452 sheet: -0.64 (0.18), residues: 540 loop : -0.02 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 144 TYR 0.029 0.003 TYR G 71 PHE 0.019 0.002 PHE B 150 TRP 0.012 0.002 TRP A 5 HIS 0.009 0.003 HIS J 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.29 (28524) covalent geometry : angle 0.72368 / 0.37 (38616) hydrogen bonds : bond 0.05013 / 3.38 ( 1297) hydrogen bonds : angle 5.65792 / 4.00 ( 3783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 405 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 LYS cc_start: 0.7857 (ttpt) cc_final: 0.7363 (mtmt) REVERT: C 7 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6731 (tt) REVERT: C 206 ASP cc_start: 0.6485 (OUTLIER) cc_final: 0.6216 (p0) REVERT: D 7 LEU cc_start: 0.7920 (tt) cc_final: 0.7684 (tt) REVERT: D 61 LYS cc_start: 0.7631 (mmpt) cc_final: 0.6869 (mmtp) REVERT: D 89 GLN cc_start: 0.7385 (tp40) cc_final: 0.6711 (mt0) REVERT: D 289 LYS cc_start: 0.7975 (pttt) cc_final: 0.7252 (mmtp) REVERT: E 7 LEU cc_start: 0.7865 (tt) cc_final: 0.7517 (tt) REVERT: E 28 GLU cc_start: 0.6162 (tp30) cc_final: 0.5901 (pm20) REVERT: E 61 LYS cc_start: 0.7652 (mmpt) cc_final: 0.6830 (mmtp) REVERT: E 89 GLN cc_start: 0.7444 (tp40) cc_final: 0.6741 (mt0) REVERT: E 265 MET cc_start: 0.7434 (mmm) cc_final: 0.7190 (mmm) REVERT: E 289 LYS cc_start: 0.7984 (pttt) cc_final: 0.7278 (mmtp) REVERT: F 7 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6629 (tt) REVERT: F 206 ASP cc_start: 0.6462 (OUTLIER) cc_final: 0.6195 (p0) REVERT: G 221 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7632 (tt0) REVERT: G 230 ARG cc_start: 0.8234 (mtm110) cc_final: 0.8022 (mtm110) REVERT: G 289 LYS cc_start: 0.7889 (tttp) cc_final: 0.7365 (mtpp) REVERT: H 216 LYS cc_start: 0.6889 (tppt) cc_final: 0.6646 (tppt) REVERT: H 221 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7565 (tt0) REVERT: H 289 LYS cc_start: 0.7844 (tttp) cc_final: 0.7357 (mtpp) REVERT: K 7 LEU cc_start: 0.7916 (tt) cc_final: 0.7686 (tt) REVERT: K 61 LYS cc_start: 0.7644 (mmpt) cc_final: 0.6898 (mmtp) REVERT: K 89 GLN cc_start: 0.7453 (tp40) cc_final: 0.6757 (mt0) REVERT: K 289 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7267 (mmtp) REVERT: I 7 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6715 (tt) REVERT: J 28 GLU cc_start: 0.6113 (tp30) cc_final: 0.5900 (pm20) REVERT: J 61 LYS cc_start: 0.7599 (mmpt) cc_final: 0.6855 (mmtp) REVERT: J 289 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7284 (mmtp) REVERT: B 89 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6888 (tt0) REVERT: B 93 ASN cc_start: 0.7318 (m-40) cc_final: 0.6979 (m110) REVERT: B 216 LYS cc_start: 0.6958 (tppt) cc_final: 0.6727 (tppt) REVERT: B 221 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7590 (tt0) REVERT: B 289 LYS cc_start: 0.7826 (tttp) cc_final: 0.7356 (mtpp) REVERT: L 7 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6718 (tt) REVERT: A 29 MET cc_start: 0.6399 (mmm) cc_final: 0.6187 (mmm) REVERT: A 55 ILE cc_start: 0.5879 (OUTLIER) cc_final: 0.5589 (mt) REVERT: A 93 ASN cc_start: 0.7370 (m-40) cc_final: 0.7055 (m110) REVERT: A 161 MET cc_start: 0.8230 (mtt) cc_final: 0.7581 (mtt) REVERT: A 221 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7585 (tt0) REVERT: A 289 LYS cc_start: 0.7923 (tttp) cc_final: 0.7423 (mtpp) outliers start: 112 outliers final: 13 residues processed: 467 average time/residue: 0.7758 time to fit residues: 413.9303 Evaluate side-chains 385 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 362 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 186 GLN Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 141 MET Chi-restraints excluded: chain K residue 206 ASP Chi-restraints excluded: chain K residue 289 LYS Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 276 GLU Chi-restraints excluded: chain J residue 206 ASP Chi-restraints excluded: chain J residue 289 LYS Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain A residue 55 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 266 optimal weight: 0.6980 chunk 236 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 chunk 181 optimal weight: 7.9990 chunk 293 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 346 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 282 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 ASN E 88 ASN E 189 ASN K 88 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.189578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.145035 restraints weight = 34219.701| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.58 r_work: 0.3669 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28524 Z= 0.122 Angle : 0.535 6.044 38616 Z= 0.280 Chirality : 0.047 0.174 4368 Planarity : 0.005 0.039 5016 Dihedral : 4.462 17.703 3912 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.47 % Allowed : 19.24 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3516 helix: 1.88 (0.14), residues: 1440 sheet: -0.36 (0.20), residues: 540 loop : -0.21 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 287 TYR 0.018 0.001 TYR H 71 PHE 0.014 0.001 PHE K 150 TRP 0.016 0.001 TRP C 5 HIS 0.004 0.001 HIS J 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (28524) covalent geometry : angle 0.53532 / 0.28 (38616) hydrogen bonds : bond 0.03593 / 2.42 ( 1297) hydrogen bonds : angle 4.98906 / 3.53 ( 3783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 387 time to evaluate : 1.120 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: C 3 LYS cc_start: 0.7857 (ttpt) cc_final: 0.7455 (mtmt) REVERT: D 7 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7493 (tt) REVERT: D 61 LYS cc_start: 0.7662 (mmpt) cc_final: 0.6958 (mmtp) REVERT: D 89 GLN cc_start: 0.7323 (tp40) cc_final: 0.6776 (mt0) REVERT: D 289 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7269 (mmtp) REVERT: E 7 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7588 (tt) REVERT: E 28 GLU cc_start: 0.6074 (tp30) cc_final: 0.5800 (pm20) REVERT: E 61 LYS cc_start: 0.7696 (mmpt) cc_final: 0.6986 (mmtp) REVERT: E 89 GLN cc_start: 0.7313 (tp40) cc_final: 0.6761 (mt0) REVERT: E 265 MET cc_start: 0.7292 (mmm) cc_final: 0.6949 (mmm) REVERT: E 289 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7220 (mmtp) REVERT: F 10 ASN cc_start: 0.7422 (OUTLIER) cc_final: 0.6625 (t0) REVERT: G 29 MET cc_start: 0.6649 (mmm) cc_final: 0.6388 (mmm) REVERT: G 55 ILE cc_start: 0.5773 (OUTLIER) cc_final: 0.5507 (mp) REVERT: G 289 LYS cc_start: 0.7784 (tttp) cc_final: 0.7407 (mtpp) REVERT: H 29 MET cc_start: 0.6538 (mmm) cc_final: 0.6291 (mmm) REVERT: H 289 LYS cc_start: 0.7784 (tttp) cc_final: 0.7449 (mtpp) REVERT: H 292 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6297 (mm-30) REVERT: K 7 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7489 (tt) REVERT: K 61 LYS cc_start: 0.7720 (mmpt) cc_final: 0.6980 (mmtp) REVERT: K 89 GLN cc_start: 0.7341 (tp40) cc_final: 0.6772 (mt0) REVERT: I 3 LYS cc_start: 0.8027 (tmmt) cc_final: 0.7535 (mtmt) REVERT: I 276 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6835 (pp20) REVERT: J 10 ASN cc_start: 0.5860 (t0) cc_final: 0.5639 (p0) REVERT: J 28 GLU cc_start: 0.6050 (tp30) cc_final: 0.5849 (pm20) REVERT: J 61 LYS cc_start: 0.7727 (mmpt) cc_final: 0.6969 (mmtp) REVERT: J 89 GLN cc_start: 0.7416 (tp-100) cc_final: 0.6641 (mt0) REVERT: B 29 MET cc_start: 0.6532 (mmm) cc_final: 0.6308 (mmm) REVERT: B 85 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.5938 (ttp-110) REVERT: B 221 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7467 (tt0) REVERT: B 289 LYS cc_start: 0.7752 (tttp) cc_final: 0.7453 (mtpp) REVERT: B 292 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6289 (mm-30) REVERT: L 3 LYS cc_start: 0.8036 (tmmt) cc_final: 0.7539 (mtmt) REVERT: A 16 ARG cc_start: 0.4759 (mtp85) cc_final: 0.4550 (mtm110) REVERT: A 29 MET cc_start: 0.6602 (mmm) cc_final: 0.6351 (mmm) REVERT: A 55 ILE cc_start: 0.5813 (OUTLIER) cc_final: 0.5504 (mp) REVERT: A 93 ASN cc_start: 0.7197 (m-40) cc_final: 0.6874 (m110) REVERT: A 221 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7500 (tt0) REVERT: A 289 LYS cc_start: 0.7778 (tttp) cc_final: 0.7426 (mtpp) outliers start: 76 outliers final: 8 residues processed: 439 average time/residue: 0.7781 time to fit residues: 388.7197 Evaluate side-chains 369 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 351 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 186 GLN Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 206 ASP Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 276 GLU Chi-restraints excluded: chain J residue 206 ASP Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain A residue 55 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 200 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 191 optimal weight: 0.0010 chunk 289 optimal weight: 0.8980 chunk 307 optimal weight: 0.0000 chunk 59 optimal weight: 7.9990 chunk 235 optimal weight: 4.9990 chunk 70 optimal weight: 0.0000 chunk 316 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 189 ASN E 189 ASN K 189 ASN J 88 ASN J 189 ASN B 253 GLN A 261 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.192045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.146935 restraints weight = 34278.451| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.69 r_work: 0.3684 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28524 Z= 0.099 Angle : 0.494 5.622 38616 Z= 0.256 Chirality : 0.046 0.161 4368 Planarity : 0.004 0.047 5016 Dihedral : 4.183 21.729 3912 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.57 % Allowed : 19.47 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.15), residues: 3516 helix: 2.35 (0.14), residues: 1440 sheet: -0.03 (0.24), residues: 420 loop : -0.13 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 16 TYR 0.018 0.001 TYR J 71 PHE 0.012 0.001 PHE K 150 TRP 0.017 0.001 TRP B 293 HIS 0.003 0.001 HIS J 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (28524) covalent geometry : angle 0.49360 / 0.26 (38616) hydrogen bonds : bond 0.03010 / 2.03 ( 1297) hydrogen bonds : angle 4.59175 / 3.25 ( 3783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 390 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 LYS cc_start: 0.7822 (ttpt) cc_final: 0.7463 (mtmt) REVERT: C 7 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6615 (tt) REVERT: C 122 ARG cc_start: 0.8409 (tpp80) cc_final: 0.7622 (ttt90) REVERT: D 7 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7555 (tt) REVERT: D 89 GLN cc_start: 0.7065 (tp40) cc_final: 0.6516 (mt0) REVERT: D 289 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7092 (mmtp) REVERT: E 7 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7495 (tt) REVERT: E 89 GLN cc_start: 0.7048 (tp40) cc_final: 0.6526 (mt0) REVERT: E 265 MET cc_start: 0.7250 (mmm) cc_final: 0.6810 (mmm) REVERT: E 289 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7079 (mmtp) REVERT: F 3 LYS cc_start: 0.7882 (tmmt) cc_final: 0.7423 (mtmt) REVERT: F 7 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6413 (tt) REVERT: F 10 ASN cc_start: 0.7301 (OUTLIER) cc_final: 0.6716 (t0) REVERT: G 29 MET cc_start: 0.6744 (mmm) cc_final: 0.6512 (mmm) REVERT: G 85 ARG cc_start: 0.6491 (OUTLIER) cc_final: 0.5877 (ttp-110) REVERT: G 289 LYS cc_start: 0.7635 (tttp) cc_final: 0.7390 (mtpp) REVERT: H 29 MET cc_start: 0.6647 (mmm) cc_final: 0.6357 (mmm) REVERT: H 85 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.5918 (ttp-110) REVERT: H 289 LYS cc_start: 0.7645 (tttp) cc_final: 0.7434 (mtpp) REVERT: H 292 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6230 (mm-30) REVERT: K 7 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7546 (tt) REVERT: K 61 LYS cc_start: 0.7841 (mmpt) cc_final: 0.7187 (mmtp) REVERT: K 89 GLN cc_start: 0.7086 (tp40) cc_final: 0.6530 (mt0) REVERT: I 3 LYS cc_start: 0.7962 (tmmt) cc_final: 0.7510 (mtmt) REVERT: I 7 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6463 (tt) REVERT: I 122 ARG cc_start: 0.8405 (tpp80) cc_final: 0.7632 (ttt90) REVERT: I 276 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6848 (pt0) REVERT: J 89 GLN cc_start: 0.7161 (tp-100) cc_final: 0.6469 (mt0) REVERT: J 213 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: B 29 MET cc_start: 0.6613 (mmm) cc_final: 0.6355 (mmm) REVERT: B 289 LYS cc_start: 0.7577 (tttp) cc_final: 0.7371 (mtpp) REVERT: B 292 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6183 (mm-30) REVERT: L 3 LYS cc_start: 0.7985 (tmmt) cc_final: 0.7511 (mtmt) REVERT: L 7 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6455 (tt) REVERT: L 122 ARG cc_start: 0.8391 (tpp80) cc_final: 0.7601 (ttt90) REVERT: A 16 ARG cc_start: 0.4710 (mtp85) cc_final: 0.4507 (mtm110) REVERT: A 29 MET cc_start: 0.6715 (mmm) cc_final: 0.6415 (mmm) REVERT: A 85 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.5971 (ttp-110) REVERT: A 289 LYS cc_start: 0.7579 (tttp) cc_final: 0.7325 (mtpp) outliers start: 79 outliers final: 2 residues processed: 445 average time/residue: 0.7675 time to fit residues: 388.6139 Evaluate side-chains 376 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 359 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 85 ARG Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 276 GLU Chi-restraints excluded: chain J residue 3 LYS Chi-restraints excluded: chain J residue 213 GLU Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain A residue 85 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 199 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 chunk 295 optimal weight: 7.9990 chunk 319 optimal weight: 5.9990 chunk 297 optimal weight: 0.0670 chunk 105 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 190 optimal weight: 0.7980 chunk 89 optimal weight: 0.0570 chunk 316 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 overall best weight: 1.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.191927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.152116 restraints weight = 32537.999| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.49 r_work: 0.3643 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28524 Z= 0.156 Angle : 0.569 7.478 38616 Z= 0.291 Chirality : 0.047 0.183 4368 Planarity : 0.005 0.051 5016 Dihedral : 4.479 26.062 3912 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.73 % Allowed : 19.92 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.15), residues: 3516 helix: 2.09 (0.14), residues: 1452 sheet: -0.03 (0.25), residues: 420 loop : -0.15 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 287 TYR 0.021 0.002 TYR H 71 PHE 0.016 0.001 PHE H 172 TRP 0.017 0.001 TRP G 293 HIS 0.004 0.001 HIS K 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (28524) covalent geometry : angle 0.56923 / 0.29 (38616) hydrogen bonds : bond 0.03592 / 2.41 ( 1297) hydrogen bonds : angle 4.80035 / 3.41 ( 3783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 371 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 LYS cc_start: 0.7894 (ttpt) cc_final: 0.7495 (mtmt) REVERT: C 7 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6758 (tt) REVERT: D 7 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7751 (tt) REVERT: D 61 LYS cc_start: 0.7932 (mmpt) cc_final: 0.7099 (mmtp) REVERT: D 258 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7523 (ptp-170) REVERT: D 289 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7328 (mmtp) REVERT: E 7 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7706 (tt) REVERT: E 61 LYS cc_start: 0.7976 (mmpt) cc_final: 0.7166 (mmtp) REVERT: E 258 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7523 (ptp-170) REVERT: E 265 MET cc_start: 0.7311 (mmm) cc_final: 0.7073 (mmm) REVERT: F 3 LYS cc_start: 0.7973 (tmmt) cc_final: 0.7495 (mtmt) REVERT: F 7 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6585 (tt) REVERT: F 10 ASN cc_start: 0.7286 (OUTLIER) cc_final: 0.6591 (t0) REVERT: G 29 MET cc_start: 0.6826 (mmm) cc_final: 0.6621 (mmm) REVERT: G 289 LYS cc_start: 0.7636 (tttp) cc_final: 0.7172 (mtpp) REVERT: H 29 MET cc_start: 0.6752 (mmm) cc_final: 0.6515 (mmm) REVERT: H 93 ASN cc_start: 0.7150 (m-40) cc_final: 0.6849 (m110) REVERT: H 289 LYS cc_start: 0.7659 (tttp) cc_final: 0.7209 (mtpp) REVERT: K 7 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7747 (tt) REVERT: K 258 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7484 (ptp-170) REVERT: I 3 LYS cc_start: 0.8059 (tmmt) cc_final: 0.7585 (mtmt) REVERT: I 7 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6657 (tt) REVERT: I 122 ARG cc_start: 0.8622 (tpp80) cc_final: 0.7736 (ttt90) REVERT: J 61 LYS cc_start: 0.7857 (mmpt) cc_final: 0.7019 (mmtp) REVERT: J 89 GLN cc_start: 0.7256 (tp-100) cc_final: 0.6483 (mt0) REVERT: J 213 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: J 258 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7481 (ptp-170) REVERT: B 29 MET cc_start: 0.6747 (mmm) cc_final: 0.6483 (mmm) REVERT: B 93 ASN cc_start: 0.7182 (m-40) cc_final: 0.6875 (m110) REVERT: B 289 LYS cc_start: 0.7626 (tttp) cc_final: 0.7174 (mtpp) REVERT: L 3 LYS cc_start: 0.8054 (tmmt) cc_final: 0.7575 (mtmt) REVERT: L 7 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6647 (tt) REVERT: A 16 ARG cc_start: 0.4850 (mtp85) cc_final: 0.4560 (mtm110) REVERT: A 93 ASN cc_start: 0.7262 (m-40) cc_final: 0.6945 (m110) REVERT: A 141 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.6798 (mmt) REVERT: A 289 LYS cc_start: 0.7645 (tttp) cc_final: 0.7387 (mtpp) outliers start: 84 outliers final: 13 residues processed: 425 average time/residue: 0.7914 time to fit residues: 381.7405 Evaluate side-chains 379 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 351 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 206 ASP Chi-restraints excluded: chain K residue 258 ARG Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 29 MET Chi-restraints excluded: chain I residue 276 GLU Chi-restraints excluded: chain J residue 3 LYS Chi-restraints excluded: chain J residue 206 ASP Chi-restraints excluded: chain J residue 213 GLU Chi-restraints excluded: chain J residue 258 ARG Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 141 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 178 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 chunk 286 optimal weight: 0.5980 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 chunk 288 optimal weight: 4.9990 chunk 335 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 345 optimal weight: 0.9990 chunk 343 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.191933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.147772 restraints weight = 32744.584| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.44 r_work: 0.3617 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28524 Z= 0.162 Angle : 0.575 8.483 38616 Z= 0.295 Chirality : 0.048 0.185 4368 Planarity : 0.005 0.052 5016 Dihedral : 4.549 28.590 3912 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.86 % Allowed : 20.38 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.15), residues: 3516 helix: 1.99 (0.14), residues: 1452 sheet: 0.03 (0.22), residues: 540 loop : -0.39 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 287 TYR 0.020 0.002 TYR H 71 PHE 0.015 0.001 PHE H 172 TRP 0.017 0.001 TRP G 293 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (28524) covalent geometry : angle 0.57488 / 0.29 (38616) hydrogen bonds : bond 0.03621 / 2.43 ( 1297) hydrogen bonds : angle 4.84013 / 3.44 ( 3783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 374 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 LYS cc_start: 0.7938 (ttpt) cc_final: 0.7531 (mtmt) REVERT: C 7 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6723 (tt) REVERT: D 7 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7712 (tt) REVERT: D 61 LYS cc_start: 0.7982 (mmpt) cc_final: 0.7148 (mmtp) REVERT: D 89 GLN cc_start: 0.7286 (tp-100) cc_final: 0.6464 (mt0) REVERT: D 258 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7602 (ptp-170) REVERT: D 289 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7332 (mmtp) REVERT: E 7 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7786 (tt) REVERT: E 26 GLU cc_start: 0.4706 (mm-30) cc_final: 0.4484 (mm-30) REVERT: E 61 LYS cc_start: 0.8005 (mmpt) cc_final: 0.7173 (mmtp) REVERT: E 89 GLN cc_start: 0.7274 (tp-100) cc_final: 0.6454 (mt0) REVERT: E 258 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7594 (ptp-170) REVERT: E 265 MET cc_start: 0.7325 (mmm) cc_final: 0.7102 (mmm) REVERT: E 289 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7323 (mmtp) REVERT: F 3 LYS cc_start: 0.8041 (tmmt) cc_final: 0.7576 (mtmt) REVERT: F 7 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6615 (tt) REVERT: F 10 ASN cc_start: 0.7323 (OUTLIER) cc_final: 0.6576 (t0) REVERT: G 29 MET cc_start: 0.6899 (mmm) cc_final: 0.6629 (mmm) REVERT: G 93 ASN cc_start: 0.7255 (m-40) cc_final: 0.6913 (m110) REVERT: G 292 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6222 (mm-30) REVERT: H 29 MET cc_start: 0.6811 (mmm) cc_final: 0.6548 (mmm) REVERT: H 93 ASN cc_start: 0.7176 (m-40) cc_final: 0.6828 (m110) REVERT: H 292 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6313 (mm-30) REVERT: K 7 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7821 (tt) REVERT: K 26 GLU cc_start: 0.4892 (mm-30) cc_final: 0.4616 (mm-30) REVERT: K 61 LYS cc_start: 0.8017 (mmpt) cc_final: 0.7223 (mmtp) REVERT: K 89 GLN cc_start: 0.7293 (tp-100) cc_final: 0.6464 (mt0) REVERT: K 258 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7597 (ptp-170) REVERT: I 3 LYS cc_start: 0.8089 (tmmt) cc_final: 0.7636 (mtmt) REVERT: I 7 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6658 (tt) REVERT: J 61 LYS cc_start: 0.7986 (mmpt) cc_final: 0.7132 (mmtp) REVERT: J 213 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: J 258 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7587 (ptp-170) REVERT: B 93 ASN cc_start: 0.7206 (m-40) cc_final: 0.6881 (m110) REVERT: B 139 LYS cc_start: 0.7137 (mtpt) cc_final: 0.6552 (mtpp) REVERT: B 292 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6333 (mm-30) REVERT: L 3 LYS cc_start: 0.8080 (tmmt) cc_final: 0.7626 (mtmt) REVERT: L 7 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6635 (tt) REVERT: A 16 ARG cc_start: 0.4910 (mtp85) cc_final: 0.4616 (mtm110) REVERT: A 29 MET cc_start: 0.6761 (mmm) cc_final: 0.6554 (mmm) REVERT: A 93 ASN cc_start: 0.7271 (m-40) cc_final: 0.6947 (m110) REVERT: A 141 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.6812 (mmt) REVERT: A 289 LYS cc_start: 0.7629 (tttp) cc_final: 0.7366 (mtpp) outliers start: 88 outliers final: 22 residues processed: 429 average time/residue: 0.8023 time to fit residues: 390.9490 Evaluate side-chains 390 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 352 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 206 ASP Chi-restraints excluded: chain K residue 258 ARG Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 29 MET Chi-restraints excluded: chain I residue 276 GLU Chi-restraints excluded: chain J residue 206 ASP Chi-restraints excluded: chain J residue 213 GLU Chi-restraints excluded: chain J residue 258 ARG Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 29 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 161 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 60 optimal weight: 0.5980 chunk 289 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 313 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 276 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.192384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.152354 restraints weight = 32674.862| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.61 r_work: 0.3622 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28524 Z= 0.138 Angle : 0.549 7.790 38616 Z= 0.281 Chirality : 0.047 0.177 4368 Planarity : 0.005 0.053 5016 Dihedral : 4.455 27.832 3912 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.86 % Allowed : 20.08 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.15), residues: 3516 helix: 2.10 (0.14), residues: 1452 sheet: 0.09 (0.26), residues: 420 loop : -0.34 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 287 TYR 0.019 0.002 TYR J 71 PHE 0.012 0.001 PHE G 172 TRP 0.016 0.001 TRP A 293 HIS 0.004 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (28524) covalent geometry : angle 0.54855 / 0.28 (38616) hydrogen bonds : bond 0.03413 / 2.28 ( 1297) hydrogen bonds : angle 4.78054 / 3.40 ( 3783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 366 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 LYS cc_start: 0.7904 (ttpt) cc_final: 0.7535 (mtmt) REVERT: C 7 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6646 (tt) REVERT: D 7 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7716 (tt) REVERT: D 61 LYS cc_start: 0.8059 (mmpt) cc_final: 0.7241 (mmtp) REVERT: D 89 GLN cc_start: 0.7133 (tp-100) cc_final: 0.6334 (mt0) REVERT: D 258 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7452 (ptp-170) REVERT: D 289 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7213 (mmtp) REVERT: D 291 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7902 (tt) REVERT: E 7 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7680 (tt) REVERT: E 61 LYS cc_start: 0.8118 (mmpt) cc_final: 0.7288 (mmtp) REVERT: E 89 GLN cc_start: 0.7124 (tp-100) cc_final: 0.6321 (mt0) REVERT: E 258 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7433 (ptp-170) REVERT: E 265 MET cc_start: 0.7260 (mmm) cc_final: 0.7050 (mmm) REVERT: E 289 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7245 (mmtp) REVERT: E 291 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.7928 (tt) REVERT: F 3 LYS cc_start: 0.8020 (tmmt) cc_final: 0.7588 (mtmt) REVERT: F 7 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6484 (tt) REVERT: F 10 ASN cc_start: 0.7296 (OUTLIER) cc_final: 0.6609 (t0) REVERT: G 29 MET cc_start: 0.6919 (mmm) cc_final: 0.6690 (mmm) REVERT: G 93 ASN cc_start: 0.7181 (m-40) cc_final: 0.6846 (m110) REVERT: G 292 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6251 (mm-30) REVERT: H 29 MET cc_start: 0.6872 (mmm) cc_final: 0.6660 (mmm) REVERT: H 93 ASN cc_start: 0.7152 (m-40) cc_final: 0.6830 (m110) REVERT: H 292 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6327 (mm-30) REVERT: K 7 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7781 (tt) REVERT: K 10 ASN cc_start: 0.6912 (p0) cc_final: 0.6598 (p0) REVERT: K 61 LYS cc_start: 0.8070 (mmpt) cc_final: 0.7238 (mmtp) REVERT: K 89 GLN cc_start: 0.7110 (tp-100) cc_final: 0.6308 (mt0) REVERT: K 258 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7430 (ptp-170) REVERT: I 3 LYS cc_start: 0.8058 (tmmt) cc_final: 0.7696 (mptt) REVERT: I 7 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6513 (tt) REVERT: I 122 ARG cc_start: 0.8506 (tpp80) cc_final: 0.7639 (ttt90) REVERT: J 61 LYS cc_start: 0.8082 (mmpt) cc_final: 0.7241 (mmtp) REVERT: J 89 GLN cc_start: 0.7164 (tp-100) cc_final: 0.6377 (mt0) REVERT: J 213 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: J 258 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7429 (ptp-170) REVERT: J 291 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7912 (tt) REVERT: B 93 ASN cc_start: 0.7171 (m-40) cc_final: 0.6834 (m110) REVERT: B 292 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6322 (mm-30) REVERT: L 3 LYS cc_start: 0.8064 (tmmt) cc_final: 0.7696 (mptt) REVERT: L 7 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6483 (tt) REVERT: A 93 ASN cc_start: 0.7200 (m-40) cc_final: 0.6890 (m110) REVERT: A 141 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.6679 (mmt) REVERT: A 289 LYS cc_start: 0.7583 (tttp) cc_final: 0.7367 (mtpp) outliers start: 88 outliers final: 24 residues processed: 428 average time/residue: 0.7917 time to fit residues: 385.3252 Evaluate side-chains 389 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 346 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 141 MET Chi-restraints excluded: chain K residue 206 ASP Chi-restraints excluded: chain K residue 258 ARG Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 141 MET Chi-restraints excluded: chain J residue 206 ASP Chi-restraints excluded: chain J residue 213 GLU Chi-restraints excluded: chain J residue 258 ARG Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 161 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 107 optimal weight: 0.0670 chunk 116 optimal weight: 10.0000 chunk 293 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 188 optimal weight: 0.9980 chunk 229 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 250 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 261 HIS J 186 GLN L 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.197808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.161163 restraints weight = 32618.928| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.23 r_work: 0.3744 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28524 Z= 0.106 Angle : 0.520 8.820 38616 Z= 0.266 Chirality : 0.045 0.175 4368 Planarity : 0.004 0.057 5016 Dihedral : 4.215 26.648 3912 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.28 % Allowed : 20.64 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.15), residues: 3516 helix: 2.38 (0.14), residues: 1452 sheet: 0.25 (0.26), residues: 420 loop : -0.27 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 287 TYR 0.019 0.001 TYR J 71 PHE 0.009 0.001 PHE J 150 TRP 0.022 0.001 TRP B 293 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (28524) covalent geometry : angle 0.51979 / 0.27 (38616) hydrogen bonds : bond 0.02988 / 2.00 ( 1297) hydrogen bonds : angle 4.54981 / 3.24 ( 3783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 380 time to evaluate : 1.150 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: C 3 LYS cc_start: 0.7944 (ttpt) cc_final: 0.7726 (mptt) REVERT: C 7 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.6886 (tt) REVERT: D 7 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7891 (tt) REVERT: D 61 LYS cc_start: 0.8044 (mmpt) cc_final: 0.7224 (mmtp) REVERT: D 89 GLN cc_start: 0.7322 (tp-100) cc_final: 0.6682 (mt0) REVERT: D 289 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7511 (mmtp) REVERT: E 7 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7872 (tt) REVERT: E 61 LYS cc_start: 0.8111 (mmpt) cc_final: 0.7332 (mmtp) REVERT: E 89 GLN cc_start: 0.7333 (tp-100) cc_final: 0.6662 (mt0) REVERT: E 265 MET cc_start: 0.7233 (mmm) cc_final: 0.6932 (mmm) REVERT: E 289 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7566 (mmtp) REVERT: F 3 LYS cc_start: 0.8033 (tmmt) cc_final: 0.7652 (mtmt) REVERT: F 7 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.6778 (tt) REVERT: F 10 ASN cc_start: 0.7331 (OUTLIER) cc_final: 0.6796 (t0) REVERT: F 88 ASN cc_start: 0.8194 (m-40) cc_final: 0.7905 (m-40) REVERT: G 35 LYS cc_start: 0.6819 (mmmm) cc_final: 0.6413 (mttp) REVERT: G 292 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6427 (mm-30) REVERT: H 35 LYS cc_start: 0.6781 (mmmm) cc_final: 0.6485 (mmtm) REVERT: H 93 ASN cc_start: 0.7251 (m-40) cc_final: 0.6975 (m110) REVERT: H 292 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6483 (mm-30) REVERT: K 7 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7950 (tt) REVERT: K 61 LYS cc_start: 0.8111 (mmpt) cc_final: 0.7306 (mmtp) REVERT: K 89 GLN cc_start: 0.7344 (tp-100) cc_final: 0.6665 (mt0) REVERT: I 3 LYS cc_start: 0.8114 (tmmt) cc_final: 0.7778 (mptt) REVERT: I 7 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.6814 (tt) REVERT: I 122 ARG cc_start: 0.8621 (tpp80) cc_final: 0.7890 (ttt90) REVERT: J 61 LYS cc_start: 0.8124 (mmpt) cc_final: 0.7301 (mmtp) REVERT: J 89 GLN cc_start: 0.7312 (tp-100) cc_final: 0.6642 (mt0) REVERT: J 213 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: B 35 LYS cc_start: 0.6786 (mmmm) cc_final: 0.6487 (mmtm) REVERT: B 93 ASN cc_start: 0.7233 (m-40) cc_final: 0.6984 (m110) REVERT: B 292 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6497 (mm-30) REVERT: L 3 LYS cc_start: 0.8122 (tmmt) cc_final: 0.7783 (mptt) REVERT: L 7 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.6831 (tt) REVERT: A 35 LYS cc_start: 0.6749 (mmmm) cc_final: 0.6503 (mmtm) REVERT: A 93 ASN cc_start: 0.7276 (m-40) cc_final: 0.6997 (m110) REVERT: A 141 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6867 (mmt) outliers start: 70 outliers final: 20 residues processed: 427 average time/residue: 0.7952 time to fit residues: 386.3537 Evaluate side-chains 385 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 353 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 281 ILE Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 186 GLN Chi-restraints excluded: chain J residue 206 ASP Chi-restraints excluded: chain J residue 213 GLU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 281 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 141 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 246 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 328 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 296 optimal weight: 0.0980 chunk 59 optimal weight: 0.6980 chunk 129 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 199 optimal weight: 0.5980 chunk 269 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 ASN J 88 ASN J 186 GLN L 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.199447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.165538 restraints weight = 32236.494| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.08 r_work: 0.3766 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28524 Z= 0.106 Angle : 0.519 7.912 38616 Z= 0.266 Chirality : 0.046 0.174 4368 Planarity : 0.005 0.058 5016 Dihedral : 4.188 25.907 3912 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.46 % Allowed : 21.78 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.15), residues: 3516 helix: 2.43 (0.14), residues: 1452 sheet: 0.37 (0.26), residues: 420 loop : -0.25 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 287 TYR 0.017 0.001 TYR H 71 PHE 0.009 0.001 PHE E 150 TRP 0.030 0.001 TRP B 293 HIS 0.003 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (28524) covalent geometry : angle 0.51897 / 0.27 (38616) hydrogen bonds : bond 0.02992 / 2.00 ( 1297) hydrogen bonds : angle 4.51127 / 3.21 ( 3783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 369 time to evaluate : 1.188 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: C 7 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7007 (tt) REVERT: C 122 ARG cc_start: 0.8627 (tpp80) cc_final: 0.8017 (ttt90) REVERT: D 7 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7970 (tt) REVERT: D 61 LYS cc_start: 0.8136 (mmpt) cc_final: 0.7326 (mmtp) REVERT: D 89 GLN cc_start: 0.7443 (tp-100) cc_final: 0.6896 (mt0) REVERT: D 258 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7524 (ptp-170) REVERT: D 289 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7706 (mmtp) REVERT: E 7 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7961 (tt) REVERT: E 61 LYS cc_start: 0.8127 (mmpt) cc_final: 0.7339 (mmtp) REVERT: E 89 GLN cc_start: 0.7424 (tp-100) cc_final: 0.6892 (mt0) REVERT: E 258 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7523 (ptp-170) REVERT: E 265 MET cc_start: 0.7134 (mmm) cc_final: 0.6809 (mmm) REVERT: E 289 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7719 (mmtp) REVERT: F 3 LYS cc_start: 0.7990 (tmmt) cc_final: 0.7765 (mptt) REVERT: F 10 ASN cc_start: 0.7340 (OUTLIER) cc_final: 0.6940 (t0) REVERT: F 88 ASN cc_start: 0.8256 (m-40) cc_final: 0.7995 (m-40) REVERT: G 187 TYR cc_start: 0.7627 (m-80) cc_final: 0.7413 (m-80) REVERT: G 292 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6522 (mm-30) REVERT: H 93 ASN cc_start: 0.7268 (m-40) cc_final: 0.7044 (m110) REVERT: H 187 TYR cc_start: 0.7637 (m-80) cc_final: 0.7437 (m-80) REVERT: H 292 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6611 (mm-30) REVERT: K 7 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8045 (tt) REVERT: K 61 LYS cc_start: 0.8146 (mmpt) cc_final: 0.7321 (mmtp) REVERT: K 89 GLN cc_start: 0.7392 (tp-100) cc_final: 0.6859 (mt0) REVERT: I 3 LYS cc_start: 0.8125 (tmmt) cc_final: 0.7863 (mptt) REVERT: I 122 ARG cc_start: 0.8569 (tpp80) cc_final: 0.7982 (ttt90) REVERT: J 61 LYS cc_start: 0.8105 (mmpt) cc_final: 0.7258 (mmtp) REVERT: J 89 GLN cc_start: 0.7372 (tp-100) cc_final: 0.6848 (mt0) REVERT: J 213 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: B 93 ASN cc_start: 0.7266 (m-40) cc_final: 0.7027 (m110) REVERT: B 292 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6566 (mm-30) REVERT: L 3 LYS cc_start: 0.8083 (tmmt) cc_final: 0.7869 (mptt) REVERT: L 113 LYS cc_start: 0.6547 (mttt) cc_final: 0.6302 (mtpt) REVERT: A 141 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6927 (mmt) REVERT: A 187 TYR cc_start: 0.7629 (m-80) cc_final: 0.7417 (m-80) outliers start: 45 outliers final: 19 residues processed: 405 average time/residue: 0.8090 time to fit residues: 370.8692 Evaluate side-chains 381 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 351 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain I residue 281 ILE Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 186 GLN Chi-restraints excluded: chain J residue 206 ASP Chi-restraints excluded: chain J residue 213 GLU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain L residue 281 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 141 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 325 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 338 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 125 optimal weight: 0.2980 chunk 312 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 ASN J 186 GLN L 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.197446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.163558 restraints weight = 32133.575| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.06 r_work: 0.3736 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28524 Z= 0.134 Angle : 0.558 10.035 38616 Z= 0.285 Chirality : 0.046 0.173 4368 Planarity : 0.005 0.058 5016 Dihedral : 4.354 25.963 3912 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.46 % Allowed : 21.94 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.15), residues: 3516 helix: 2.27 (0.14), residues: 1452 sheet: 0.36 (0.26), residues: 420 loop : -0.32 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 287 TYR 0.019 0.002 TYR H 71 PHE 0.012 0.001 PHE B 172 TRP 0.033 0.002 TRP B 293 HIS 0.004 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 (28524) covalent geometry : angle 0.55823 / 0.28 (38616) hydrogen bonds : bond 0.03273 / 2.19 ( 1297) hydrogen bonds : angle 4.64915 / 3.31 ( 3783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 359 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7039 (tt) REVERT: D 7 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8018 (tt) REVERT: D 61 LYS cc_start: 0.8155 (mmpt) cc_final: 0.7354 (mmtp) REVERT: D 258 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7516 (ptp-170) REVERT: E 7 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7984 (tt) REVERT: E 61 LYS cc_start: 0.8173 (mmpt) cc_final: 0.7394 (mmtp) REVERT: E 89 GLN cc_start: 0.7457 (tp-100) cc_final: 0.6885 (mt0) REVERT: E 258 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7512 (ptp-170) REVERT: E 265 MET cc_start: 0.7147 (mmm) cc_final: 0.6795 (mmm) REVERT: E 289 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7728 (mmtp) REVERT: F 3 LYS cc_start: 0.8023 (tmmt) cc_final: 0.7792 (mptt) REVERT: F 7 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.6953 (tt) REVERT: F 10 ASN cc_start: 0.7359 (OUTLIER) cc_final: 0.6892 (t0) REVERT: G 35 LYS cc_start: 0.6936 (mmmm) cc_final: 0.6628 (mmtp) REVERT: G 93 ASN cc_start: 0.7297 (m-40) cc_final: 0.7024 (m110) REVERT: G 139 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6717 (mtpp) REVERT: G 292 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6548 (mm-30) REVERT: H 35 LYS cc_start: 0.6909 (mmmm) cc_final: 0.6589 (mmtp) REVERT: H 93 ASN cc_start: 0.7257 (m-40) cc_final: 0.7038 (m110) REVERT: K 61 LYS cc_start: 0.8151 (mmpt) cc_final: 0.7332 (mmtp) REVERT: I 3 LYS cc_start: 0.8138 (tmmt) cc_final: 0.7879 (mptt) REVERT: I 7 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.6945 (tt) REVERT: J 89 GLN cc_start: 0.7452 (tp-100) cc_final: 0.6884 (mt0) REVERT: J 213 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: B 35 LYS cc_start: 0.7000 (mmmm) cc_final: 0.6683 (mmtp) REVERT: B 93 ASN cc_start: 0.7299 (m-40) cc_final: 0.7071 (m110) REVERT: B 258 ARG cc_start: 0.7724 (ptp90) cc_final: 0.6884 (ptm-80) REVERT: B 292 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6617 (mm-30) REVERT: L 3 LYS cc_start: 0.8133 (tmmt) cc_final: 0.7873 (mptt) REVERT: L 7 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.6960 (tt) REVERT: L 113 LYS cc_start: 0.6552 (mttt) cc_final: 0.6302 (mtpt) REVERT: A 35 LYS cc_start: 0.6948 (mmmm) cc_final: 0.6668 (mmtp) REVERT: A 93 ASN cc_start: 0.7301 (m-40) cc_final: 0.7062 (m110) REVERT: A 141 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.6967 (mmt) outliers start: 45 outliers final: 17 residues processed: 392 average time/residue: 0.8225 time to fit residues: 367.2079 Evaluate side-chains 382 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 352 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain K residue 206 ASP Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 281 ILE Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 186 GLN Chi-restraints excluded: chain J residue 206 ASP Chi-restraints excluded: chain J residue 213 GLU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 281 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 141 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 230 optimal weight: 0.0970 chunk 90 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 243 optimal weight: 6.9990 chunk 199 optimal weight: 0.6980 chunk 295 optimal weight: 2.9990 chunk 312 optimal weight: 2.9990 chunk 328 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 317 optimal weight: 0.9990 chunk 46 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 ASN F 93 ASN K 88 ASN I 186 GLN J 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.199742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.165770 restraints weight = 32156.744| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.02 r_work: 0.3780 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28524 Z= 0.107 Angle : 0.528 9.677 38616 Z= 0.270 Chirality : 0.045 0.172 4368 Planarity : 0.005 0.056 5016 Dihedral : 4.189 25.502 3912 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.43 % Allowed : 22.07 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.15), residues: 3516 helix: 2.44 (0.14), residues: 1452 sheet: 0.42 (0.26), residues: 420 loop : -0.29 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 287 TYR 0.017 0.001 TYR J 71 PHE 0.012 0.001 PHE B 241 TRP 0.033 0.002 TRP H 293 HIS 0.003 0.001 HIS G 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (28524) covalent geometry : angle 0.52833 / 0.27 (38616) hydrogen bonds : bond 0.02942 / 1.96 ( 1297) hydrogen bonds : angle 4.50437 / 3.21 ( 3783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12212.38 seconds wall clock time: 207 minutes 52.61 seconds (12472.61 seconds total)