Starting phenix.real_space_refine on Wed Mar 4 11:09:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i5t_4418/03_2026/6i5t_4418.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i5t_4418/03_2026/6i5t_4418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6i5t_4418/03_2026/6i5t_4418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i5t_4418/03_2026/6i5t_4418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6i5t_4418/03_2026/6i5t_4418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i5t_4418/03_2026/6i5t_4418.map" } resolution = 3.9 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= 0.006 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 78 5.16 5 C 8550 2.51 5 N 2286 2.21 5 O 2442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13356 Number of models: 1 Model: "" Number of chains: 1 Chain: "F" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Restraints were copied for chains: E, D, C, B, A Residues with excluded nonbonded symmetry interactions: 510 residue: pdb=" N ARG F 37 " occ=0.97 ... (9 atoms not shown) pdb=" NH2 ARG F 37 " occ=0.93 residue: pdb=" N ALA F 38 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA F 38 " occ=0.97 residue: pdb=" N VAL F 41 " occ=0.97 ... (5 atoms not shown) pdb=" CG2 VAL F 41 " occ=0.93 residue: pdb=" N GLN F 42 " occ=0.97 ... (7 atoms not shown) pdb=" NE2 GLN F 42 " occ=0.95 residue: pdb=" N ALA F 43 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA F 43 " occ=0.97 residue: pdb=" N VAL F 46 " occ=0.97 ... (5 atoms not shown) pdb=" CG2 VAL F 46 " occ=0.94 residue: pdb=" N ALA F 52 " occ=0.96 ... (3 atoms not shown) pdb=" CB ALA F 52 " occ=0.93 residue: pdb=" N LYS F 56 " occ=0.97 ... (7 atoms not shown) pdb=" NZ LYS F 56 " occ=0.94 residue: pdb=" N ALA F 57 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA F 57 " occ=0.97 residue: pdb=" N LEU F 60 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU F 60 " occ=0.80 residue: pdb=" N GLU F 63 " occ=0.97 ... (7 atoms not shown) pdb=" OE2 GLU F 63 " occ=0.80 residue: pdb=" N ALA F 64 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA F 64 " occ=0.97 ... (remaining 498 not shown) Time building chain proxies: 1.95, per 1000 atoms: 0.15 Number of scatterers: 13356 At special positions: 0 Unit cell: (118.15, 132.6, 130.9, 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 78 16.00 O 2442 8.00 N 2286 7.00 C 8550 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: 0.87 Conformation dependent library (CDL) restraints added in 476.2 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3156 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 21 sheets defined 24.6% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'F' and resid 53 through 66 removed outlier: 3.801A pdb=" N ALA F 57 " --> pdb=" O THR F 53 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU F 58 " --> pdb=" O LEU F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 108 removed outlier: 4.333A pdb=" N ARG F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ASP F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 127 removed outlier: 3.547A pdb=" N GLU F 119 " --> pdb=" O GLY F 115 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG F 120 " --> pdb=" O PRO F 116 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU F 121 " --> pdb=" O GLU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 173 Processing helix chain 'F' and resid 202 through 210 removed outlier: 3.915A pdb=" N ARG F 206 " --> pdb=" O MET F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 213 No H-bonds generated for 'chain 'F' and resid 211 through 213' Processing helix chain 'F' and resid 226 through 239 removed outlier: 4.432A pdb=" N ALA F 230 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 66 removed outlier: 3.801A pdb=" N ALA E 57 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 58 " --> pdb=" O LEU E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 108 removed outlier: 4.333A pdb=" N ARG E 100 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASP E 102 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 127 removed outlier: 3.547A pdb=" N GLU E 119 " --> pdb=" O GLY E 115 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG E 120 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 173 Processing helix chain 'E' and resid 202 through 210 removed outlier: 3.915A pdb=" N ARG E 206 " --> pdb=" O MET E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 213 No H-bonds generated for 'chain 'E' and resid 211 through 213' Processing helix chain 'E' and resid 226 through 239 removed outlier: 4.433A pdb=" N ALA E 230 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 66 removed outlier: 3.800A pdb=" N ALA D 57 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 108 removed outlier: 4.333A pdb=" N ARG D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ASP D 102 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 removed outlier: 3.547A pdb=" N GLU D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG D 120 " --> pdb=" O PRO D 116 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU D 121 " --> pdb=" O GLU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 173 Processing helix chain 'D' and resid 202 through 210 removed outlier: 3.915A pdb=" N ARG D 206 " --> pdb=" O MET D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 226 through 239 removed outlier: 4.433A pdb=" N ALA D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 66 removed outlier: 3.801A pdb=" N ALA C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 108 removed outlier: 4.333A pdb=" N ARG C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ASP C 102 " --> pdb=" O LYS C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.547A pdb=" N GLU C 119 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG C 120 " --> pdb=" O PRO C 116 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 202 through 210 removed outlier: 3.915A pdb=" N ARG C 206 " --> pdb=" O MET C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 213 No H-bonds generated for 'chain 'C' and resid 211 through 213' Processing helix chain 'C' and resid 226 through 239 removed outlier: 4.433A pdb=" N ALA C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS C 234 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.800A pdb=" N ALA B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 108 removed outlier: 4.334A pdb=" N ARG B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASP B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 127 removed outlier: 3.546A pdb=" N GLU B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG B 120 " --> pdb=" O PRO B 116 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 202 through 210 removed outlier: 3.915A pdb=" N ARG B 206 " --> pdb=" O MET B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 226 through 239 removed outlier: 4.433A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.801A pdb=" N ALA A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 108 removed outlier: 4.333A pdb=" N ARG A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ASP A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 127 removed outlier: 3.547A pdb=" N GLU A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG A 120 " --> pdb=" O PRO A 116 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 202 through 210 removed outlier: 3.915A pdb=" N ARG A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 226 through 239 removed outlier: 4.433A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 157 through 160 removed outlier: 7.243A pdb=" N PHE F 150 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL F 72 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU F 71 " --> pdb=" O ARG F 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 138 through 139 Processing sheet with id=AA3, first strand: chain 'F' and resid 186 through 187 removed outlier: 6.523A pdb=" N TYR F 217 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ALA F 246 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA F 219 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE F 283 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 330 through 334 removed outlier: 3.544A pdb=" N SER E 331 " --> pdb=" O ASN F 333 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER F 331 " --> pdb=" O ASN E 333 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N SER D 343 " --> pdb=" O PHE F 330 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU F 332 " --> pdb=" O SER D 343 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LYS D 345 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE F 334 " --> pdb=" O LYS D 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 157 through 160 removed outlier: 7.242A pdb=" N PHE E 150 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL E 72 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU E 71 " --> pdb=" O ARG E 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 138 through 139 Processing sheet with id=AA7, first strand: chain 'E' and resid 186 through 187 removed outlier: 6.523A pdb=" N TYR E 217 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ALA E 246 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA E 219 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE E 283 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 342 through 345 removed outlier: 3.537A pdb=" N SER C 331 " --> pdb=" O ASN D 333 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER D 331 " --> pdb=" O ASN C 333 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N SER B 343 " --> pdb=" O PHE D 330 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU D 332 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LYS B 345 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE D 334 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 157 through 160 removed outlier: 7.243A pdb=" N PHE D 150 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL D 72 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU D 71 " --> pdb=" O ARG D 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 138 through 139 Processing sheet with id=AB2, first strand: chain 'D' and resid 186 through 187 removed outlier: 6.522A pdb=" N TYR D 217 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ALA D 246 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA D 219 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE D 283 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 157 through 160 removed outlier: 7.243A pdb=" N PHE C 150 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL C 72 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU C 71 " --> pdb=" O ARG C 37 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 138 through 139 Processing sheet with id=AB5, first strand: chain 'C' and resid 186 through 187 removed outlier: 6.523A pdb=" N TYR C 217 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ALA C 246 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA C 219 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE C 283 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 342 through 345 removed outlier: 3.557A pdb=" N SER A 331 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 331 " --> pdb=" O ASN A 333 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 157 through 160 removed outlier: 7.242A pdb=" N PHE B 150 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 72 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 71 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AB9, first strand: chain 'B' and resid 186 through 187 removed outlier: 6.523A pdb=" N TYR B 217 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ALA B 246 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA B 219 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE B 283 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 157 through 160 removed outlier: 7.243A pdb=" N PHE A 150 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A 72 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 71 " --> pdb=" O ARG A 37 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AC3, first strand: chain 'A' and resid 186 through 187 removed outlier: 6.523A pdb=" N TYR A 217 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ALA A 246 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ALA A 219 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE A 283 " --> pdb=" O LEU A 291 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4295 1.34 - 1.46: 2618 1.46 - 1.57: 6629 1.57 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 13656 Sorted by residual: bond pdb=" CA HIS E 323 " pdb=" C HIS E 323 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.34e-02 5.57e+03 3.93e+00 bond pdb=" CA HIS B 323 " pdb=" C HIS B 323 " ideal model delta sigma weight residual 1.523 1.549 -0.026 1.34e-02 5.57e+03 3.70e+00 bond pdb=" CA HIS C 323 " pdb=" C HIS C 323 " ideal model delta sigma weight residual 1.523 1.549 -0.026 1.34e-02 5.57e+03 3.68e+00 bond pdb=" CA HIS A 323 " pdb=" C HIS A 323 " ideal model delta sigma weight residual 1.523 1.549 -0.025 1.34e-02 5.57e+03 3.58e+00 bond pdb=" CA HIS F 323 " pdb=" C HIS F 323 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.34e-02 5.57e+03 3.56e+00 ... (remaining 13651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 18241 3.40 - 6.81: 191 6.81 - 10.21: 34 10.21 - 13.61: 14 13.61 - 17.01: 6 Bond angle restraints: 18486 Sorted by residual: angle pdb=" C VAL E 320 " pdb=" N VAL E 321 " pdb=" CA VAL E 321 " ideal model delta sigma weight residual 121.97 130.89 -8.92 1.80e+00 3.09e-01 2.46e+01 angle pdb=" C VAL C 320 " pdb=" N VAL C 321 " pdb=" CA VAL C 321 " ideal model delta sigma weight residual 121.97 130.86 -8.89 1.80e+00 3.09e-01 2.44e+01 angle pdb=" C VAL A 320 " pdb=" N VAL A 321 " pdb=" CA VAL A 321 " ideal model delta sigma weight residual 121.97 130.86 -8.89 1.80e+00 3.09e-01 2.44e+01 angle pdb=" C VAL D 320 " pdb=" N VAL D 321 " pdb=" CA VAL D 321 " ideal model delta sigma weight residual 121.97 130.84 -8.87 1.80e+00 3.09e-01 2.43e+01 angle pdb=" N VAL D 321 " pdb=" CA VAL D 321 " pdb=" C VAL D 321 " ideal model delta sigma weight residual 109.34 119.58 -10.24 2.08e+00 2.31e-01 2.42e+01 ... (remaining 18481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.53: 7564 14.53 - 29.05: 434 29.05 - 43.58: 96 43.58 - 58.10: 6 58.10 - 72.63: 6 Dihedral angle restraints: 8106 sinusoidal: 3162 harmonic: 4944 Sorted by residual: dihedral pdb=" CA GLY B 322 " pdb=" C GLY B 322 " pdb=" N HIS B 323 " pdb=" CA HIS B 323 " ideal model delta harmonic sigma weight residual -180.00 -107.37 -72.63 0 5.00e+00 4.00e-02 2.11e+02 dihedral pdb=" CA GLY F 322 " pdb=" C GLY F 322 " pdb=" N HIS F 323 " pdb=" CA HIS F 323 " ideal model delta harmonic sigma weight residual -180.00 -107.40 -72.60 0 5.00e+00 4.00e-02 2.11e+02 dihedral pdb=" CA GLY A 322 " pdb=" C GLY A 322 " pdb=" N HIS A 323 " pdb=" CA HIS A 323 " ideal model delta harmonic sigma weight residual -180.00 -107.41 -72.59 0 5.00e+00 4.00e-02 2.11e+02 ... (remaining 8103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1591 0.066 - 0.132: 408 0.132 - 0.198: 29 0.198 - 0.265: 18 0.265 - 0.331: 12 Chirality restraints: 2058 Sorted by residual: chirality pdb=" CB VAL E 320 " pdb=" CA VAL E 320 " pdb=" CG1 VAL E 320 " pdb=" CG2 VAL E 320 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB VAL A 320 " pdb=" CA VAL A 320 " pdb=" CG1 VAL A 320 " pdb=" CG2 VAL A 320 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB VAL F 320 " pdb=" CA VAL F 320 " pdb=" CG1 VAL F 320 " pdb=" CG2 VAL F 320 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 2055 not shown) Planarity restraints: 2370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 187 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO F 188 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO F 188 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 188 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 187 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.50e+00 pdb=" N PRO A 188 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 187 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO C 188 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 188 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 188 " 0.029 5.00e-02 4.00e+02 ... (remaining 2367 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4687 2.87 - 3.38: 11187 3.38 - 3.88: 19763 3.88 - 4.39: 22052 4.39 - 4.90: 39536 Nonbonded interactions: 97225 Sorted by model distance: nonbonded pdb=" OE1 GLU A 89 " pdb=" OG1 THR A 96 " model vdw 2.362 3.040 nonbonded pdb=" OE1 GLU E 89 " pdb=" OG1 THR E 96 " model vdw 2.362 3.040 nonbonded pdb=" OE1 GLU F 89 " pdb=" OG1 THR F 96 " model vdw 2.362 3.040 nonbonded pdb=" OE1 GLU D 89 " pdb=" OG1 THR D 96 " model vdw 2.362 3.040 nonbonded pdb=" OE1 GLU C 89 " pdb=" OG1 THR C 96 " model vdw 2.363 3.040 ... (remaining 97220 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'E' selection = chain 'D' selection = chain 'C' selection = chain 'B' 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=0.50 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.560 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13656 Z= 0.273 Angle : 1.110 17.014 18486 Z= 0.584 Chirality : 0.064 0.331 2058 Planarity : 0.008 0.053 2370 Dihedral : 10.098 72.626 4950 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.70 % Allowed : 15.09 % Favored : 84.21 % Rotamer: Outliers : 0.43 % Allowed : 6.01 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.73 % 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: -5.80 (0.13), residues: 1710 helix: -3.89 (0.13), residues: 438 sheet: -4.21 (0.25), residues: 216 loop : -3.96 (0.13), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 206 TYR 0.030 0.003 TYR B 324 PHE 0.011 0.002 PHE C 316 TRP 0.022 0.003 TRP D 198 HIS 0.007 0.002 HIS F 234 Details of bonding type rmsd covalent geometry : bond 0.00608 (13656) covalent geometry : angle 1.10978 (18486) hydrogen bonds : bond 0.25207 ( 354) hydrogen bonds : angle 8.11915 ( 936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 436 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 138 GLU cc_start: 0.8759 (pt0) cc_final: 0.8275 (pt0) REVERT: F 162 ARG cc_start: 0.8582 (mtt180) cc_final: 0.8348 (mtt180) REVERT: F 221 THR cc_start: 0.9351 (t) cc_final: 0.8951 (m) REVERT: E 134 MET cc_start: 0.7090 (tpp) cc_final: 0.6817 (tpp) REVERT: D 89 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7266 (tt0) REVERT: D 138 GLU cc_start: 0.8764 (pt0) cc_final: 0.8254 (pt0) REVERT: D 221 THR cc_start: 0.9432 (t) cc_final: 0.9027 (m) REVERT: C 285 SER cc_start: 0.8506 (t) cc_final: 0.7628 (p) REVERT: B 138 GLU cc_start: 0.8746 (pt0) cc_final: 0.8078 (pt0) REVERT: B 221 THR cc_start: 0.9407 (t) cc_final: 0.8950 (m) REVERT: B 285 SER cc_start: 0.9045 (t) cc_final: 0.8192 (p) REVERT: B 315 LYS cc_start: 0.8751 (mtpp) cc_final: 0.8183 (tttt) REVERT: A 134 MET cc_start: 0.7057 (tpp) cc_final: 0.6848 (tpp) REVERT: A 167 THR cc_start: 0.8400 (p) cc_final: 0.8195 (m) outliers start: 6 outliers final: 1 residues processed: 436 average time/residue: 0.1456 time to fit residues: 86.4469 Evaluate side-chains 196 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 61 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.1980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 GLN F 154 GLN F 200 ASN F 295 ASN E 154 GLN E 200 ASN E 337 HIS D 200 ASN D 295 ASN C 200 ASN B 154 GLN B 200 ASN B 295 ASN A 200 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.110633 restraints weight = 21247.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.113267 restraints weight = 13758.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.115086 restraints weight = 10297.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116137 restraints weight = 8446.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.117046 restraints weight = 7428.259| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 91 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13656 Z= 0.175 Angle : 0.777 11.966 18486 Z= 0.393 Chirality : 0.049 0.173 2058 Planarity : 0.006 0.041 2370 Dihedral : 6.633 54.272 1904 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.88 % Allowed : 12.51 % Favored : 86.61 % Rotamer: Outliers : 4.15 % Allowed : 10.94 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.64 (0.16), residues: 1710 helix: -2.31 (0.22), residues: 402 sheet: -2.89 (0.27), residues: 312 loop : -3.65 (0.15), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 201 TYR 0.020 0.002 TYR D 128 PHE 0.010 0.001 PHE A 103 TRP 0.019 0.001 TRP B 198 HIS 0.010 0.002 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00411 (13656) covalent geometry : angle 0.77702 (18486) hydrogen bonds : bond 0.04237 ( 354) hydrogen bonds : angle 5.64704 ( 936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 209 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: F 127 LYS cc_start: 0.7523 (pttt) cc_final: 0.6327 (mtpp) REVERT: F 129 LYS cc_start: 0.7448 (mmtt) cc_final: 0.7087 (mmtm) REVERT: F 169 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8189 (tm) REVERT: F 221 THR cc_start: 0.9331 (t) cc_final: 0.8933 (m) REVERT: E 154 GLN cc_start: 0.7598 (mp-120) cc_final: 0.7391 (mp10) REVERT: D 67 ASN cc_start: 0.8547 (p0) cc_final: 0.8012 (t0) REVERT: D 127 LYS cc_start: 0.7559 (pttt) cc_final: 0.6646 (mtpp) REVERT: D 138 GLU cc_start: 0.9463 (pt0) cc_final: 0.9163 (pt0) REVERT: D 169 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8468 (tm) REVERT: D 221 THR cc_start: 0.9193 (t) cc_final: 0.8906 (m) REVERT: D 227 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8429 (m) REVERT: C 310 ASP cc_start: 0.8652 (t0) cc_final: 0.8343 (t0) REVERT: B 58 GLU cc_start: 0.7333 (tp30) cc_final: 0.7107 (tp30) REVERT: B 127 LYS cc_start: 0.7686 (pttt) cc_final: 0.6662 (mtpp) REVERT: B 138 GLU cc_start: 0.9540 (pt0) cc_final: 0.9306 (pt0) REVERT: B 221 THR cc_start: 0.9147 (t) cc_final: 0.8909 (m) REVERT: B 227 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8424 (m) REVERT: B 315 LYS cc_start: 0.8923 (mtpp) cc_final: 0.8516 (pttt) outliers start: 58 outliers final: 28 residues processed: 256 average time/residue: 0.1071 time to fit residues: 41.6768 Evaluate side-chains 202 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 289 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 26 optimal weight: 0.0010 chunk 115 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 overall best weight: 4.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 GLN F 295 ASN D 295 ASN C 295 ASN B 295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.110497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.091188 restraints weight = 22986.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.093384 restraints weight = 14798.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.094935 restraints weight = 11170.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.095965 restraints weight = 9290.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.096439 restraints weight = 8183.687| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 91 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 229 | |-----------------------------------------------------------------------------| r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13656 Z= 0.198 Angle : 0.782 12.142 18486 Z= 0.394 Chirality : 0.050 0.175 2058 Planarity : 0.006 0.040 2370 Dihedral : 6.575 55.325 1904 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.88 % Allowed : 13.04 % Favored : 86.08 % Rotamer: Outliers : 5.36 % Allowed : 11.37 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.29 (0.17), residues: 1710 helix: -1.82 (0.24), residues: 402 sheet: -2.32 (0.27), residues: 342 loop : -3.67 (0.15), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 162 TYR 0.016 0.002 TYR D 128 PHE 0.012 0.002 PHE F 157 TRP 0.013 0.001 TRP F 198 HIS 0.006 0.002 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00473 (13656) covalent geometry : angle 0.78223 (18486) hydrogen bonds : bond 0.04060 ( 354) hydrogen bonds : angle 5.54518 ( 936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 187 time to evaluate : 0.527 Fit side-chains REVERT: F 127 LYS cc_start: 0.7470 (pttt) cc_final: 0.6644 (mtpp) REVERT: F 169 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8331 (tm) REVERT: F 227 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8210 (m) REVERT: D 127 LYS cc_start: 0.7587 (pttt) cc_final: 0.6900 (mtpp) REVERT: D 169 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8543 (tm) REVERT: D 227 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8422 (m) REVERT: C 310 ASP cc_start: 0.9087 (t0) cc_final: 0.8779 (t0) REVERT: B 127 LYS cc_start: 0.7826 (pttt) cc_final: 0.6700 (mtpp) REVERT: B 221 THR cc_start: 0.9123 (t) cc_final: 0.8813 (m) REVERT: B 227 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8232 (m) outliers start: 75 outliers final: 42 residues processed: 244 average time/residue: 0.0966 time to fit residues: 37.1364 Evaluate side-chains 199 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 152 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 165 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 295 ASN E 295 ASN D 295 ASN C 295 ASN B 295 ASN A 295 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.096738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.080415 restraints weight = 24077.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.082203 restraints weight = 15653.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.083478 restraints weight = 11849.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.084297 restraints weight = 9864.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.084796 restraints weight = 8730.955| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 229 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 234 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 13656 Z= 0.191 Angle : 0.770 11.893 18486 Z= 0.388 Chirality : 0.049 0.184 2058 Planarity : 0.005 0.038 2370 Dihedral : 6.455 56.317 1904 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.88 % Allowed : 13.04 % Favored : 86.08 % Rotamer: Outliers : 5.79 % Allowed : 14.09 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.18), residues: 1710 helix: -1.58 (0.25), residues: 402 sheet: -2.10 (0.28), residues: 342 loop : -3.50 (0.16), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 162 TYR 0.014 0.001 TYR D 128 PHE 0.010 0.001 PHE A 103 TRP 0.009 0.001 TRP B 198 HIS 0.007 0.002 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00455 (13656) covalent geometry : angle 0.76966 (18486) hydrogen bonds : bond 0.03754 ( 354) hydrogen bonds : angle 5.44389 ( 936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 170 time to evaluate : 0.527 Fit side-chains REVERT: F 127 LYS cc_start: 0.7443 (pttt) cc_final: 0.6768 (mtpp) REVERT: F 169 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8281 (tm) REVERT: F 227 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8230 (m) REVERT: F 295 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8696 (p0) REVERT: E 134 MET cc_start: 0.7021 (tpp) cc_final: 0.6778 (tpp) REVERT: E 138 GLU cc_start: 0.9449 (tt0) cc_final: 0.9216 (tt0) REVERT: D 127 LYS cc_start: 0.7434 (pttt) cc_final: 0.6979 (mtpp) REVERT: D 169 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8505 (tm) REVERT: D 227 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8198 (m) REVERT: D 232 MET cc_start: 0.8690 (mmm) cc_final: 0.7764 (mmm) REVERT: C 310 ASP cc_start: 0.9088 (t0) cc_final: 0.8724 (t0) REVERT: B 127 LYS cc_start: 0.7828 (pttt) cc_final: 0.6854 (mtpp) REVERT: B 227 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8131 (m) REVERT: B 324 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.7695 (t80) REVERT: A 119 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8498 (mp0) REVERT: A 138 GLU cc_start: 0.9394 (tt0) cc_final: 0.9109 (tt0) outliers start: 81 outliers final: 52 residues processed: 235 average time/residue: 0.1061 time to fit residues: 38.1943 Evaluate side-chains 214 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 154 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 295 ASN Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 295 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 108 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 166 optimal weight: 0.3980 chunk 63 optimal weight: 0.1980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 295 ASN E 295 ASN D 295 ASN C 295 ASN B 295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.098331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.081614 restraints weight = 23885.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.083624 restraints weight = 14834.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.084876 restraints weight = 10921.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.085843 restraints weight = 8995.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.086384 restraints weight = 7869.963| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 234 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 252 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13656 Z= 0.155 Angle : 0.737 12.047 18486 Z= 0.369 Chirality : 0.048 0.195 2058 Planarity : 0.005 0.035 2370 Dihedral : 6.266 56.571 1904 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.76 % Allowed : 11.99 % Favored : 87.25 % Rotamer: Outliers : 5.65 % Allowed : 15.31 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.18), residues: 1710 helix: -1.34 (0.25), residues: 402 sheet: -1.93 (0.29), residues: 342 loop : -3.36 (0.16), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 162 TYR 0.015 0.001 TYR D 128 PHE 0.008 0.001 PHE A 103 TRP 0.007 0.001 TRP B 198 HIS 0.006 0.001 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00366 (13656) covalent geometry : angle 0.73655 (18486) hydrogen bonds : bond 0.03314 ( 354) hydrogen bonds : angle 5.26520 ( 936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 179 time to evaluate : 0.547 Fit side-chains REVERT: F 127 LYS cc_start: 0.7389 (pttt) cc_final: 0.6902 (mtpp) REVERT: F 169 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8294 (tm) REVERT: F 227 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8162 (m) REVERT: F 324 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7835 (t80) REVERT: E 144 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9013 (mt) REVERT: E 324 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.6579 (t80) REVERT: D 127 LYS cc_start: 0.7249 (pttt) cc_final: 0.6885 (mtpp) REVERT: D 169 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8513 (tm) REVERT: D 227 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8172 (m) REVERT: D 232 MET cc_start: 0.8716 (mmm) cc_final: 0.7770 (mmm) REVERT: D 324 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7609 (t80) REVERT: C 310 ASP cc_start: 0.9081 (t0) cc_final: 0.8724 (t0) REVERT: B 127 LYS cc_start: 0.7790 (pttt) cc_final: 0.6821 (mtpp) REVERT: B 227 THR cc_start: 0.8466 (OUTLIER) cc_final: 0.7992 (m) REVERT: B 324 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7758 (t80) REVERT: A 138 GLU cc_start: 0.9400 (OUTLIER) cc_final: 0.9132 (tt0) REVERT: A 324 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.6570 (t80) outliers start: 79 outliers final: 52 residues processed: 243 average time/residue: 0.0951 time to fit residues: 36.8692 Evaluate side-chains 226 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 162 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 324 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 153 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 104 optimal weight: 0.0670 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 295 ASN E 234 HIS E 295 ASN D 295 ASN C 295 ASN B 295 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.112901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.095346 restraints weight = 22154.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.097630 restraints weight = 13960.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.099147 restraints weight = 10356.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.100207 restraints weight = 8496.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.100836 restraints weight = 7425.309| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 252 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 290 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13656 Z= 0.115 Angle : 0.695 11.562 18486 Z= 0.345 Chirality : 0.046 0.176 2058 Planarity : 0.005 0.033 2370 Dihedral : 5.803 55.127 1904 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.70 % Allowed : 10.82 % Favored : 88.48 % Rotamer: Outliers : 4.51 % Allowed : 16.24 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.19), residues: 1710 helix: -1.04 (0.26), residues: 402 sheet: -1.64 (0.29), residues: 342 loop : -3.24 (0.16), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 201 TYR 0.015 0.001 TYR B 128 PHE 0.014 0.001 PHE C 330 TRP 0.008 0.001 TRP B 198 HIS 0.009 0.002 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00264 (13656) covalent geometry : angle 0.69471 (18486) hydrogen bonds : bond 0.02656 ( 354) hydrogen bonds : angle 4.89448 ( 936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 202 time to evaluate : 0.536 Fit side-chains REVERT: F 61 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8238 (tt) REVERT: F 127 LYS cc_start: 0.7192 (pttt) cc_final: 0.6930 (mtpp) REVERT: F 169 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8186 (tm) REVERT: F 227 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.7909 (m) REVERT: F 287 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8780 (mt) REVERT: F 324 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7893 (t80) REVERT: E 144 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8940 (mm) REVERT: E 324 TYR cc_start: 0.7615 (OUTLIER) cc_final: 0.6635 (t80) REVERT: D 127 LYS cc_start: 0.7139 (pttt) cc_final: 0.6902 (mtpp) REVERT: D 169 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8340 (tm) REVERT: D 215 GLU cc_start: 0.9322 (pt0) cc_final: 0.9071 (pt0) REVERT: D 232 MET cc_start: 0.8711 (mmm) cc_final: 0.7703 (mmm) REVERT: D 287 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8723 (mt) REVERT: D 324 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7847 (t80) REVERT: B 127 LYS cc_start: 0.7715 (pttt) cc_final: 0.7023 (mtpp) REVERT: B 324 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7675 (t80) REVERT: A 324 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.6665 (t80) outliers start: 63 outliers final: 30 residues processed: 252 average time/residue: 0.0949 time to fit residues: 37.6511 Evaluate side-chains 218 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 324 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 150 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 295 ASN D 295 ASN B 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.099363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.083546 restraints weight = 23793.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.085442 restraints weight = 15226.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.086746 restraints weight = 11372.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.087501 restraints weight = 9369.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.088154 restraints weight = 8293.856| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 290 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 299 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13656 Z= 0.141 Angle : 0.726 11.873 18486 Z= 0.358 Chirality : 0.047 0.191 2058 Planarity : 0.005 0.036 2370 Dihedral : 5.905 56.326 1904 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.82 % Allowed : 12.22 % Favored : 86.96 % Rotamer: Outliers : 4.65 % Allowed : 17.10 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.19), residues: 1710 helix: -0.97 (0.26), residues: 402 sheet: -1.46 (0.30), residues: 342 loop : -3.19 (0.16), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 171 TYR 0.015 0.001 TYR B 128 PHE 0.014 0.001 PHE C 330 TRP 0.006 0.001 TRP B 198 HIS 0.006 0.001 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00336 (13656) covalent geometry : angle 0.72578 (18486) hydrogen bonds : bond 0.03012 ( 354) hydrogen bonds : angle 4.95537 ( 936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 177 time to evaluate : 0.473 Fit side-chains REVERT: F 61 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8340 (tt) REVERT: F 127 LYS cc_start: 0.7559 (pttt) cc_final: 0.6754 (mtpp) REVERT: F 169 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8258 (tm) REVERT: F 227 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8070 (m) REVERT: F 324 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7899 (t80) REVERT: E 289 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7122 (mm) REVERT: E 324 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.6637 (t80) REVERT: D 169 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8431 (tm) REVERT: D 324 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7796 (t80) REVERT: C 310 ASP cc_start: 0.9011 (t0) cc_final: 0.8711 (t0) REVERT: B 127 LYS cc_start: 0.7804 (pttt) cc_final: 0.7051 (mtpp) REVERT: B 165 MET cc_start: 0.8064 (mtm) cc_final: 0.7843 (mtp) REVERT: B 324 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7755 (t80) REVERT: A 138 GLU cc_start: 0.9314 (tt0) cc_final: 0.9087 (tt0) REVERT: A 324 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.6707 (t80) outliers start: 65 outliers final: 43 residues processed: 227 average time/residue: 0.0963 time to fit residues: 34.4091 Evaluate side-chains 220 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 167 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 324 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 74 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 97 optimal weight: 0.3980 chunk 19 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 overall best weight: 5.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 295 ASN F 337 HIS E 295 ASN D 295 ASN D 337 HIS C 295 ASN B 295 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.095363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.079993 restraints weight = 23884.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.081585 restraints weight = 16382.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.082569 restraints weight = 12799.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.083371 restraints weight = 10924.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.083804 restraints weight = 9777.366| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 299 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 307 | |-----------------------------------------------------------------------------| r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 13656 Z= 0.233 Angle : 0.827 12.303 18486 Z= 0.413 Chirality : 0.051 0.205 2058 Planarity : 0.005 0.034 2370 Dihedral : 6.439 57.820 1904 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.88 % Allowed : 13.98 % Favored : 85.15 % Rotamer: Outliers : 4.65 % Allowed : 18.45 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.18), residues: 1710 helix: -1.51 (0.24), residues: 432 sheet: -1.62 (0.29), residues: 342 loop : -3.26 (0.17), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 171 TYR 0.022 0.002 TYR E 106 PHE 0.013 0.002 PHE A 330 TRP 0.009 0.001 TRP F 228 HIS 0.006 0.002 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00561 (13656) covalent geometry : angle 0.82656 (18486) hydrogen bonds : bond 0.03993 ( 354) hydrogen bonds : angle 5.39324 ( 936) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 160 time to evaluate : 0.450 Fit side-chains REVERT: F 61 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8508 (tt) REVERT: F 227 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8272 (m) REVERT: F 324 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.7894 (t80) REVERT: E 144 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9074 (mt) REVERT: E 324 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.6553 (t80) REVERT: D 169 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8630 (tm) REVERT: D 324 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.7695 (t80) REVERT: C 134 MET cc_start: 0.7922 (mmm) cc_final: 0.7658 (tpt) REVERT: B 127 LYS cc_start: 0.7848 (pttt) cc_final: 0.7164 (mtpp) REVERT: B 324 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.7938 (t80) REVERT: A 119 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8493 (mp0) REVERT: A 324 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.6692 (t80) outliers start: 65 outliers final: 44 residues processed: 210 average time/residue: 0.0943 time to fit residues: 31.2687 Evaluate side-chains 205 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 151 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 324 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 148 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 113 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 295 ASN E 295 ASN D 295 ASN B 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.104731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.086916 restraints weight = 22990.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.089080 restraints weight = 14614.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.090531 restraints weight = 10927.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.091470 restraints weight = 9048.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.091992 restraints weight = 7978.656| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 307 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 326 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13656 Z= 0.225 Angle : 0.817 11.922 18486 Z= 0.409 Chirality : 0.051 0.191 2058 Planarity : 0.005 0.038 2370 Dihedral : 6.469 57.541 1904 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.88 % Allowed : 13.45 % Favored : 85.67 % Rotamer: Outliers : 4.58 % Allowed : 18.53 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.18), residues: 1710 helix: -1.55 (0.24), residues: 432 sheet: -1.91 (0.28), residues: 342 loop : -3.30 (0.17), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 171 TYR 0.020 0.002 TYR E 106 PHE 0.014 0.002 PHE A 330 TRP 0.017 0.001 TRP F 228 HIS 0.005 0.001 HIS F 323 Details of bonding type rmsd covalent geometry : bond 0.00545 (13656) covalent geometry : angle 0.81664 (18486) hydrogen bonds : bond 0.03859 ( 354) hydrogen bonds : angle 5.42497 ( 936) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 157 time to evaluate : 0.886 Fit side-chains REVERT: F 61 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8440 (tt) REVERT: F 227 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8349 (m) REVERT: F 324 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7876 (t80) REVERT: E 144 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9064 (mt) REVERT: E 310 ASP cc_start: 0.8887 (t0) cc_final: 0.8617 (t0) REVERT: E 324 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.6573 (t80) REVERT: D 169 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8611 (tm) REVERT: D 324 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7739 (t80) REVERT: C 134 MET cc_start: 0.7952 (mmm) cc_final: 0.7711 (tpt) REVERT: B 55 ASP cc_start: 0.8740 (p0) cc_final: 0.8501 (p0) REVERT: B 127 LYS cc_start: 0.7847 (pttt) cc_final: 0.7235 (mtpp) REVERT: B 324 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7867 (t80) REVERT: A 119 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: A 324 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.6673 (t80) outliers start: 64 outliers final: 47 residues processed: 208 average time/residue: 0.0966 time to fit residues: 32.0642 Evaluate side-chains 212 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 155 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 324 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 143 optimal weight: 20.0000 chunk 87 optimal weight: 50.0000 chunk 102 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 295 ASN D 295 ASN C 337 HIS B 295 ASN A 337 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.106811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.089187 restraints weight = 22821.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.091394 restraints weight = 14320.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.092869 restraints weight = 10634.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.093769 restraints weight = 8752.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.094456 restraints weight = 7720.676| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 326 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 345 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13656 Z= 0.143 Angle : 0.751 12.102 18486 Z= 0.372 Chirality : 0.048 0.179 2058 Planarity : 0.005 0.036 2370 Dihedral : 6.078 56.184 1904 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.76 % Allowed : 11.70 % Favored : 87.54 % Rotamer: Outliers : 4.08 % Allowed : 18.88 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.18), residues: 1710 helix: -1.06 (0.26), residues: 402 sheet: -1.73 (0.28), residues: 342 loop : -3.22 (0.16), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 171 TYR 0.016 0.001 TYR E 106 PHE 0.013 0.001 PHE A 330 TRP 0.010 0.001 TRP B 198 HIS 0.007 0.001 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00341 (13656) covalent geometry : angle 0.75056 (18486) hydrogen bonds : bond 0.03154 ( 354) hydrogen bonds : angle 5.14528 ( 936) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 168 time to evaluate : 0.438 Fit side-chains REVERT: F 61 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8354 (tt) REVERT: F 227 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8150 (m) REVERT: F 324 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7959 (t80) REVERT: E 324 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.6565 (t80) REVERT: D 169 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8513 (tm) REVERT: D 324 TYR cc_start: 0.8330 (OUTLIER) cc_final: 0.7851 (t80) REVERT: B 127 LYS cc_start: 0.7860 (pttt) cc_final: 0.7273 (mtpp) REVERT: B 199 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8979 (mt-10) REVERT: B 324 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.7789 (t80) REVERT: A 310 ASP cc_start: 0.9143 (t0) cc_final: 0.8939 (t0) REVERT: A 324 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.6695 (t80) outliers start: 57 outliers final: 42 residues processed: 210 average time/residue: 0.0954 time to fit residues: 31.5914 Evaluate side-chains 211 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 324 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 92 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 165 optimal weight: 0.4980 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 295 ASN B 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.097675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.079699 restraints weight = 24349.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.081886 restraints weight = 14757.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.083278 restraints weight = 10751.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.084264 restraints weight = 8830.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.084955 restraints weight = 7716.251| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 345 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 345 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13656 Z= 0.188 Angle : 0.794 12.267 18486 Z= 0.394 Chirality : 0.049 0.195 2058 Planarity : 0.005 0.034 2370 Dihedral : 6.264 57.328 1904 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.88 % Allowed : 13.45 % Favored : 85.67 % Rotamer: Outliers : 4.29 % Allowed : 18.96 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.18), residues: 1710 helix: -1.11 (0.25), residues: 402 sheet: -1.69 (0.28), residues: 336 loop : -3.24 (0.16), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 171 TYR 0.017 0.001 TYR E 106 PHE 0.013 0.002 PHE A 330 TRP 0.008 0.001 TRP F 198 HIS 0.005 0.001 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00453 (13656) covalent geometry : angle 0.79375 (18486) hydrogen bonds : bond 0.03554 ( 354) hydrogen bonds : angle 5.26554 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2154.07 seconds wall clock time: 37 minutes 59.63 seconds (2279.63 seconds total)