Starting phenix.real_space_refine on Thu Mar 5 04:32:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rbg_4798/03_2026/6rbg_4798.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rbg_4798/03_2026/6rbg_4798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rbg_4798/03_2026/6rbg_4798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rbg_4798/03_2026/6rbg_4798.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rbg_4798/03_2026/6rbg_4798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rbg_4798/03_2026/6rbg_4798.map" } resolution = 3.0 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= 0.004 sd= 0.061 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 56 5.16 5 C 12216 2.51 5 N 3344 2.21 5 O 3720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s 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: 19336 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2417 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 297} Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 2.04, per 1000 atoms: 0.11 Number of scatterers: 19336 At special positions: 0 Unit cell: (111.3, 111.3, 166.42, 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 56 16.00 O 3720 8.00 N 3344 7.00 C 12216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 624.2 milliseconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4672 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 8 sheets defined 60.4% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.692A pdb=" N SER A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 40 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA A 85 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 160 removed outlier: 3.631A pdb=" N GLN A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.586A pdb=" N LYS A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 183 through 210 removed outlier: 3.631A pdb=" N VAL A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN A 205 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.707A pdb=" N LEU A 229 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 230 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 231 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 232 " --> pdb=" O LEU A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 232' Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 254 through 268 removed outlier: 3.602A pdb=" N LEU A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 265 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 324 removed outlier: 3.860A pdb=" N ALA A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 320 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 49 removed outlier: 3.692A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 40 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B 41 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 80 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA B 85 " --> pdb=" O GLY B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 removed outlier: 3.631A pdb=" N GLN B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 155 " --> pdb=" O TYR B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.587A pdb=" N LYS B 165 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 183 through 210 removed outlier: 3.632A pdb=" N VAL B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 189 " --> pdb=" O GLN B 185 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 198 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN B 205 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 removed outlier: 3.706A pdb=" N LEU B 229 " --> pdb=" O GLN B 226 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE B 230 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 231 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 232 " --> pdb=" O LEU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 232' Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 254 through 268 removed outlier: 3.603A pdb=" N LEU B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 324 removed outlier: 3.861A pdb=" N ALA B 302 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 313 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 320 " --> pdb=" O GLY B 316 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 31 through 49 removed outlier: 3.692A pdb=" N SER C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 40 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 80 Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA C 85 " --> pdb=" O GLY C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 160 removed outlier: 3.631A pdb=" N GLN C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 155 " --> pdb=" O TYR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.588A pdb=" N LYS C 165 " --> pdb=" O GLN C 161 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 180 Processing helix chain 'C' and resid 183 through 210 removed outlier: 3.633A pdb=" N VAL C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C 198 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN C 205 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN C 209 " --> pdb=" O GLN C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 232 removed outlier: 3.707A pdb=" N LEU C 229 " --> pdb=" O GLN C 226 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE C 230 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU C 231 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 232 " --> pdb=" O LEU C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 226 through 232' Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 254 through 268 removed outlier: 3.602A pdb=" N LEU C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 265 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 324 removed outlier: 3.861A pdb=" N ALA C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 313 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN C 318 " --> pdb=" O VAL C 314 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 320 " --> pdb=" O GLY C 316 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 31 through 49 removed outlier: 3.692A pdb=" N SER D 37 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 80 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA D 85 " --> pdb=" O GLY D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA D 102 " --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 160 removed outlier: 3.632A pdb=" N GLN D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 155 " --> pdb=" O TYR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 175 removed outlier: 3.587A pdb=" N LYS D 165 " --> pdb=" O GLN D 161 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU D 173 " --> pdb=" O ASP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 183 through 210 removed outlier: 3.632A pdb=" N VAL D 188 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA D 189 " --> pdb=" O GLN D 185 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 198 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN D 205 " --> pdb=" O GLN D 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN D 209 " --> pdb=" O GLN D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 232 removed outlier: 3.707A pdb=" N LEU D 229 " --> pdb=" O GLN D 226 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE D 230 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU D 231 " --> pdb=" O THR D 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 232 " --> pdb=" O LEU D 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 226 through 232' Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 254 through 268 removed outlier: 3.602A pdb=" N LEU D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE D 265 " --> pdb=" O ASN D 261 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 324 removed outlier: 3.860A pdb=" N ALA D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 313 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 320 " --> pdb=" O GLY D 316 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG D 321 " --> pdb=" O ARG D 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 31 through 49 removed outlier: 3.691A pdb=" N SER E 37 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA E 41 " --> pdb=" O SER E 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 80 Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA E 85 " --> pdb=" O GLY E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR E 94 " --> pdb=" O ASP E 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA E 102 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER E 104 " --> pdb=" O SER E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 160 removed outlier: 3.630A pdb=" N GLN E 153 " --> pdb=" O ALA E 149 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 175 removed outlier: 3.587A pdb=" N LYS E 165 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 180 Processing helix chain 'E' and resid 183 through 210 removed outlier: 3.632A pdb=" N VAL E 188 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG E 198 " --> pdb=" O ASP E 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN E 205 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN E 209 " --> pdb=" O GLN E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 232 removed outlier: 3.707A pdb=" N LEU E 229 " --> pdb=" O GLN E 226 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE E 230 " --> pdb=" O ASP E 227 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU E 231 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU E 232 " --> pdb=" O LEU E 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 226 through 232' Processing helix chain 'E' and resid 233 through 238 Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 254 through 268 removed outlier: 3.602A pdb=" N LEU E 262 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE E 265 " --> pdb=" O ASN E 261 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU E 268 " --> pdb=" O ASP E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 324 removed outlier: 3.861A pdb=" N ALA E 302 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU E 305 " --> pdb=" O LEU E 301 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E 313 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 320 " --> pdb=" O GLY E 316 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG E 321 " --> pdb=" O ARG E 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 31 through 49 removed outlier: 3.692A pdb=" N SER F 37 " --> pdb=" O THR F 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL F 40 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA F 41 " --> pdb=" O SER F 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 80 Processing helix chain 'F' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA F 85 " --> pdb=" O GLY F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA F 102 " --> pdb=" O ARG F 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER F 104 " --> pdb=" O SER F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 160 removed outlier: 3.632A pdb=" N GLN F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL F 155 " --> pdb=" O TYR F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 175 removed outlier: 3.587A pdb=" N LYS F 165 " --> pdb=" O GLN F 161 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 180 Processing helix chain 'F' and resid 183 through 210 removed outlier: 3.632A pdb=" N VAL F 188 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG F 198 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN F 205 " --> pdb=" O GLN F 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN F 209 " --> pdb=" O GLN F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 232 removed outlier: 3.706A pdb=" N LEU F 229 " --> pdb=" O GLN F 226 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE F 230 " --> pdb=" O ASP F 227 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU F 231 " --> pdb=" O THR F 228 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU F 232 " --> pdb=" O LEU F 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 226 through 232' Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 238 through 243 Processing helix chain 'F' and resid 254 through 268 removed outlier: 3.603A pdb=" N LEU F 262 " --> pdb=" O THR F 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE F 265 " --> pdb=" O ASN F 261 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU F 268 " --> pdb=" O ASP F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 324 removed outlier: 3.860A pdb=" N ALA F 302 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU F 305 " --> pdb=" O LEU F 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE F 313 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN F 318 " --> pdb=" O VAL F 314 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 320 " --> pdb=" O GLY F 316 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG F 321 " --> pdb=" O ARG F 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 30 Processing helix chain 'G' and resid 31 through 49 removed outlier: 3.692A pdb=" N SER G 37 " --> pdb=" O THR G 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL G 40 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA G 41 " --> pdb=" O SER G 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 80 Processing helix chain 'G' and resid 81 through 85 removed outlier: 3.936A pdb=" N ALA G 85 " --> pdb=" O GLY G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 96 removed outlier: 3.654A pdb=" N THR G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA G 102 " --> pdb=" O ARG G 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER G 104 " --> pdb=" O SER G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 160 removed outlier: 3.631A pdb=" N GLN G 153 " --> pdb=" O ALA G 149 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL G 155 " --> pdb=" O TYR G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 175 removed outlier: 3.587A pdb=" N LYS G 165 " --> pdb=" O GLN G 161 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP G 166 " --> pdb=" O GLU G 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 180 Processing helix chain 'G' and resid 183 through 210 removed outlier: 3.632A pdb=" N VAL G 188 " --> pdb=" O THR G 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG G 198 " --> pdb=" O ASP G 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN G 205 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN G 209 " --> pdb=" O GLN G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 232 removed outlier: 3.707A pdb=" N LEU G 229 " --> pdb=" O GLN G 226 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE G 230 " --> pdb=" O ASP G 227 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU G 231 " --> pdb=" O THR G 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU G 232 " --> pdb=" O LEU G 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 226 through 232' Processing helix chain 'G' and resid 233 through 238 Processing helix chain 'G' and resid 238 through 243 Processing helix chain 'G' and resid 254 through 268 removed outlier: 3.603A pdb=" N LEU G 262 " --> pdb=" O THR G 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE G 265 " --> pdb=" O ASN G 261 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU G 268 " --> pdb=" O ASP G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 324 removed outlier: 3.861A pdb=" N ALA G 302 " --> pdb=" O THR G 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU G 305 " --> pdb=" O LEU G 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE G 313 " --> pdb=" O VAL G 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN G 318 " --> pdb=" O VAL G 314 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU G 320 " --> pdb=" O GLY G 316 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG G 321 " --> pdb=" O ARG G 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 30 Processing helix chain 'H' and resid 31 through 49 removed outlier: 3.691A pdb=" N SER H 37 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA H 41 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 80 Processing helix chain 'H' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA H 85 " --> pdb=" O GLY H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR H 94 " --> pdb=" O ASP H 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA H 102 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER H 104 " --> pdb=" O SER H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 160 removed outlier: 3.631A pdb=" N GLN H 153 " --> pdb=" O ALA H 149 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL H 155 " --> pdb=" O TYR H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 175 removed outlier: 3.587A pdb=" N LYS H 165 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP H 166 " --> pdb=" O GLU H 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 180 Processing helix chain 'H' and resid 183 through 210 removed outlier: 3.632A pdb=" N VAL H 188 " --> pdb=" O THR H 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS H 193 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG H 198 " --> pdb=" O ASP H 194 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN H 205 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN H 209 " --> pdb=" O GLN H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 232 removed outlier: 3.707A pdb=" N LEU H 229 " --> pdb=" O GLN H 226 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE H 230 " --> pdb=" O ASP H 227 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU H 231 " --> pdb=" O THR H 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU H 232 " --> pdb=" O LEU H 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 226 through 232' Processing helix chain 'H' and resid 233 through 238 Processing helix chain 'H' and resid 238 through 243 Processing helix chain 'H' and resid 254 through 268 removed outlier: 3.603A pdb=" N LEU H 262 " --> pdb=" O THR H 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE H 265 " --> pdb=" O ASN H 261 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU H 268 " --> pdb=" O ASP H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 324 removed outlier: 3.860A pdb=" N ALA H 302 " --> pdb=" O THR H 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU H 305 " --> pdb=" O LEU H 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE H 313 " --> pdb=" O VAL H 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN H 318 " --> pdb=" O VAL H 314 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU H 320 " --> pdb=" O GLY H 316 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG H 321 " --> pdb=" O ARG H 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 123 removed outlier: 3.623A pdb=" N TYR A 136 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 61 " --> pdb=" O VAL A 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 119 through 123 removed outlier: 3.624A pdb=" N TYR B 136 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE B 61 " --> pdb=" O VAL B 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 119 through 123 removed outlier: 3.625A pdb=" N TYR C 136 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE C 61 " --> pdb=" O VAL C 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 119 through 123 removed outlier: 3.624A pdb=" N TYR D 136 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE D 61 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 119 through 123 removed outlier: 3.625A pdb=" N TYR E 136 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE E 61 " --> pdb=" O VAL E 281 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 119 through 123 removed outlier: 3.624A pdb=" N TYR F 136 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE F 61 " --> pdb=" O VAL F 281 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 119 through 123 removed outlier: 3.625A pdb=" N TYR G 136 " --> pdb=" O SER G 58 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE G 61 " --> pdb=" O VAL G 281 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.623A pdb=" N TYR H 136 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE H 61 " --> pdb=" O VAL H 281 " (cutoff:3.500A) 856 hydrogen bonds defined for protein. 2496 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: 2.96 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6528 1.34 - 1.46: 3625 1.46 - 1.58: 9311 1.58 - 1.70: 0 1.70 - 1.81: 112 Bond restraints: 19576 Sorted by residual: bond pdb=" N LYS B 31 " pdb=" CA LYS B 31 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.20e-02 6.94e+03 1.06e+01 bond pdb=" N LYS F 31 " pdb=" CA LYS F 31 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.20e-02 6.94e+03 1.06e+01 bond pdb=" N LYS H 31 " pdb=" CA LYS H 31 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.20e-02 6.94e+03 1.06e+01 bond pdb=" N LYS A 31 " pdb=" CA LYS A 31 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.20e-02 6.94e+03 1.05e+01 bond pdb=" N LYS C 31 " pdb=" CA LYS C 31 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.20e-02 6.94e+03 1.05e+01 ... (remaining 19571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 25401 1.93 - 3.86: 935 3.86 - 5.79: 88 5.79 - 7.73: 64 7.73 - 9.66: 24 Bond angle restraints: 26512 Sorted by residual: angle pdb=" N LEU E 27 " pdb=" CA LEU E 27 " pdb=" C LEU E 27 " ideal model delta sigma weight residual 111.07 102.19 8.88 1.07e+00 8.73e-01 6.89e+01 angle pdb=" N LEU C 27 " pdb=" CA LEU C 27 " pdb=" C LEU C 27 " ideal model delta sigma weight residual 111.07 102.20 8.87 1.07e+00 8.73e-01 6.88e+01 angle pdb=" N LEU G 27 " pdb=" CA LEU G 27 " pdb=" C LEU G 27 " ideal model delta sigma weight residual 111.07 102.20 8.87 1.07e+00 8.73e-01 6.87e+01 angle pdb=" N LEU A 27 " pdb=" CA LEU A 27 " pdb=" C LEU A 27 " ideal model delta sigma weight residual 111.07 102.21 8.86 1.07e+00 8.73e-01 6.85e+01 angle pdb=" N LEU B 27 " pdb=" CA LEU B 27 " pdb=" C LEU B 27 " ideal model delta sigma weight residual 111.07 102.21 8.86 1.07e+00 8.73e-01 6.85e+01 ... (remaining 26507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 10799 16.80 - 33.61: 1097 33.61 - 50.41: 200 50.41 - 67.21: 24 67.21 - 84.01: 40 Dihedral angle restraints: 12160 sinusoidal: 4944 harmonic: 7216 Sorted by residual: dihedral pdb=" CA TYR D 280 " pdb=" C TYR D 280 " pdb=" N VAL D 281 " pdb=" CA VAL D 281 " ideal model delta harmonic sigma weight residual 180.00 160.00 20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA TYR H 280 " pdb=" C TYR H 280 " pdb=" N VAL H 281 " pdb=" CA VAL H 281 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA TYR F 280 " pdb=" C TYR F 280 " pdb=" N VAL F 281 " pdb=" CA VAL F 281 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 12157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2327 0.052 - 0.104: 690 0.104 - 0.156: 111 0.156 - 0.207: 0 0.207 - 0.259: 16 Chirality restraints: 3144 Sorted by residual: chirality pdb=" CA GLN C 26 " pdb=" N GLN C 26 " pdb=" C GLN C 26 " pdb=" CB GLN C 26 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA GLN A 26 " pdb=" N GLN A 26 " pdb=" C GLN A 26 " pdb=" CB GLN A 26 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA GLN G 26 " pdb=" N GLN G 26 " pdb=" C GLN G 26 " pdb=" CB GLN G 26 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 3141 not shown) Planarity restraints: 3432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU H 24 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C LEU H 24 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU H 24 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL H 25 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 24 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C LEU A 24 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU A 24 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 25 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 24 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C LEU C 24 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU C 24 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 25 " 0.016 2.00e-02 2.50e+03 ... (remaining 3429 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 7024 2.91 - 3.40: 18140 3.40 - 3.90: 28989 3.90 - 4.40: 34530 4.40 - 4.90: 56348 Nonbonded interactions: 145031 Sorted by model distance: nonbonded pdb=" O LEU F 23 " pdb=" OE1 GLN F 26 " model vdw 2.407 3.040 nonbonded pdb=" O LEU G 23 " pdb=" OE1 GLN G 26 " model vdw 2.407 3.040 nonbonded pdb=" O LEU C 23 " pdb=" OE1 GLN C 26 " model vdw 2.407 3.040 nonbonded pdb=" O LEU E 23 " pdb=" OE1 GLN E 26 " model vdw 2.407 3.040 nonbonded pdb=" O LEU A 23 " pdb=" OE1 GLN A 26 " model vdw 2.407 3.040 ... (remaining 145026 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 13.430 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 : 0.004 0.050 19576 Z= 0.232 Angle : 0.890 9.658 26512 Z= 0.513 Chirality : 0.050 0.259 3144 Planarity : 0.005 0.038 3432 Dihedral : 14.499 84.014 7488 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.38 % Allowed : 5.04 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.39 (0.11), residues: 2448 helix: -5.01 (0.04), residues: 1496 sheet: -3.47 (0.31), residues: 200 loop : -1.98 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 198 TYR 0.010 0.001 TYR D 81 PHE 0.007 0.002 PHE A 103 TRP 0.013 0.002 TRP F 28 HIS 0.001 0.000 HIS C 243 Details of bonding type rmsd covalent geometry : bond 0.00437 (19576) covalent geometry : angle 0.88973 (26512) hydrogen bonds : bond 0.31548 ( 856) hydrogen bonds : angle 10.36168 ( 2496) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 339 time to evaluate : 0.471 Fit side-chains REVERT: A 32 MET cc_start: 0.6567 (ttp) cc_final: 0.6091 (tmm) REVERT: A 139 GLN cc_start: 0.8255 (mt0) cc_final: 0.8050 (mt0) REVERT: A 153 GLN cc_start: 0.7820 (tt0) cc_final: 0.7584 (tp-100) REVERT: A 176 LYS cc_start: 0.8065 (tptt) cc_final: 0.7809 (ttpt) REVERT: B 32 MET cc_start: 0.6349 (ttp) cc_final: 0.5782 (tmm) REVERT: B 77 MET cc_start: 0.8351 (mmm) cc_final: 0.8112 (mmp) REVERT: B 90 ASP cc_start: 0.8269 (t0) cc_final: 0.8030 (m-30) REVERT: B 146 MET cc_start: 0.7694 (ttm) cc_final: 0.7466 (ttt) REVERT: B 147 LYS cc_start: 0.8238 (tppt) cc_final: 0.8035 (tptm) REVERT: B 176 LYS cc_start: 0.8021 (tptt) cc_final: 0.7681 (ttpp) REVERT: B 202 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7255 (mm-30) REVERT: B 301 LEU cc_start: 0.8471 (mm) cc_final: 0.7997 (mm) REVERT: C 32 MET cc_start: 0.6603 (ttp) cc_final: 0.6166 (tmm) REVERT: C 139 GLN cc_start: 0.8272 (mt0) cc_final: 0.8061 (mt0) REVERT: C 146 MET cc_start: 0.7707 (ttm) cc_final: 0.7488 (ttt) REVERT: C 153 GLN cc_start: 0.7822 (tt0) cc_final: 0.7558 (tp-100) REVERT: C 176 LYS cc_start: 0.8093 (tptt) cc_final: 0.7792 (ttpt) REVERT: C 240 MET cc_start: 0.8721 (mtt) cc_final: 0.8510 (mtt) REVERT: D 32 MET cc_start: 0.6362 (ttp) cc_final: 0.5794 (tmm) REVERT: D 77 MET cc_start: 0.8359 (mmm) cc_final: 0.8121 (mmp) REVERT: D 90 ASP cc_start: 0.8270 (t0) cc_final: 0.8031 (m-30) REVERT: D 146 MET cc_start: 0.7696 (ttm) cc_final: 0.7476 (ttt) REVERT: D 147 LYS cc_start: 0.8239 (tppt) cc_final: 0.8026 (tptm) REVERT: D 176 LYS cc_start: 0.7981 (tptt) cc_final: 0.7633 (ttpp) REVERT: D 202 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7156 (mm-30) REVERT: D 301 LEU cc_start: 0.8480 (mm) cc_final: 0.8031 (mm) REVERT: E 32 MET cc_start: 0.6583 (ttp) cc_final: 0.6134 (tmm) REVERT: E 139 GLN cc_start: 0.8272 (mt0) cc_final: 0.8064 (mt0) REVERT: E 146 MET cc_start: 0.7727 (ttm) cc_final: 0.7512 (ttt) REVERT: E 153 GLN cc_start: 0.7823 (tt0) cc_final: 0.7554 (tp-100) REVERT: E 176 LYS cc_start: 0.8057 (tptt) cc_final: 0.7759 (ttpt) REVERT: F 32 MET cc_start: 0.6356 (ttp) cc_final: 0.5786 (tmm) REVERT: F 77 MET cc_start: 0.8391 (mmm) cc_final: 0.8156 (mmp) REVERT: F 90 ASP cc_start: 0.8271 (t0) cc_final: 0.8029 (m-30) REVERT: F 146 MET cc_start: 0.7702 (ttm) cc_final: 0.7482 (ttt) REVERT: F 147 LYS cc_start: 0.8242 (tppt) cc_final: 0.8006 (tptm) REVERT: F 176 LYS cc_start: 0.7979 (tptt) cc_final: 0.7626 (ttpp) REVERT: F 202 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7156 (mm-30) REVERT: F 301 LEU cc_start: 0.8475 (mm) cc_final: 0.7996 (mm) REVERT: G 32 MET cc_start: 0.6569 (ttp) cc_final: 0.6091 (tmm) REVERT: G 139 GLN cc_start: 0.8263 (mt0) cc_final: 0.8057 (mt0) REVERT: G 153 GLN cc_start: 0.7829 (tt0) cc_final: 0.7574 (tp-100) REVERT: G 176 LYS cc_start: 0.8122 (tptt) cc_final: 0.7810 (ttpt) REVERT: H 32 MET cc_start: 0.6346 (ttp) cc_final: 0.5775 (tmm) REVERT: H 77 MET cc_start: 0.8381 (mmm) cc_final: 0.8148 (mmp) REVERT: H 90 ASP cc_start: 0.8270 (t0) cc_final: 0.8031 (m-30) REVERT: H 146 MET cc_start: 0.7673 (ttm) cc_final: 0.7437 (ttt) REVERT: H 147 LYS cc_start: 0.8255 (tppt) cc_final: 0.8020 (tptm) REVERT: H 176 LYS cc_start: 0.8022 (tptt) cc_final: 0.7679 (ttpp) REVERT: H 202 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7165 (mm-30) REVERT: H 301 LEU cc_start: 0.8462 (mm) cc_final: 0.7979 (mm) outliers start: 8 outliers final: 8 residues processed: 347 average time/residue: 0.5881 time to fit residues: 229.3572 Evaluate side-chains 200 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 192 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain H residue 28 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN C 318 ASN ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 318 ASN E 318 ASN ** F 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 ASN G 318 ASN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 318 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.130305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.097224 restraints weight = 25628.592| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.35 r_work: 0.3069 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19576 Z= 0.144 Angle : 0.544 7.048 26512 Z= 0.285 Chirality : 0.037 0.117 3144 Planarity : 0.003 0.019 3432 Dihedral : 6.055 53.788 2672 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.33 % Allowed : 15.40 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.52 (0.13), residues: 2448 helix: -3.38 (0.08), residues: 1552 sheet: -2.32 (0.36), residues: 208 loop : -1.49 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.011 0.001 TYR E 206 PHE 0.006 0.001 PHE A 103 TRP 0.007 0.001 TRP B 56 HIS 0.001 0.000 HIS H 243 Details of bonding type rmsd covalent geometry : bond 0.00339 (19576) covalent geometry : angle 0.54445 (26512) hydrogen bonds : bond 0.04147 ( 856) hydrogen bonds : angle 4.56908 ( 2496) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 174 time to evaluate : 0.582 Fit side-chains REVERT: A 118 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7733 (ttmm) REVERT: A 139 GLN cc_start: 0.8733 (mt0) cc_final: 0.8514 (mt0) REVERT: A 176 LYS cc_start: 0.8181 (tptt) cc_final: 0.7897 (tttt) REVERT: A 202 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: A 291 ASP cc_start: 0.8601 (m-30) cc_final: 0.8348 (m-30) REVERT: B 147 LYS cc_start: 0.8308 (tppt) cc_final: 0.8094 (tptp) REVERT: B 176 LYS cc_start: 0.8092 (tptt) cc_final: 0.7857 (ttpp) REVERT: B 222 GLU cc_start: 0.8406 (tp30) cc_final: 0.7953 (mp0) REVERT: B 301 LEU cc_start: 0.8573 (mm) cc_final: 0.8219 (mm) REVERT: C 118 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7749 (ttmm) REVERT: C 139 GLN cc_start: 0.8751 (mt0) cc_final: 0.8537 (mt0) REVERT: C 176 LYS cc_start: 0.8154 (tptt) cc_final: 0.7874 (tttt) REVERT: C 202 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: C 240 MET cc_start: 0.9222 (mtt) cc_final: 0.9007 (mtt) REVERT: C 291 ASP cc_start: 0.8605 (m-30) cc_final: 0.8362 (m-30) REVERT: D 147 LYS cc_start: 0.8310 (tppt) cc_final: 0.8096 (tptp) REVERT: D 176 LYS cc_start: 0.8071 (tptt) cc_final: 0.7831 (ttpp) REVERT: D 222 GLU cc_start: 0.8418 (tp30) cc_final: 0.7963 (mp0) REVERT: D 301 LEU cc_start: 0.8574 (mm) cc_final: 0.8226 (mm) REVERT: E 118 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7738 (ttmm) REVERT: E 139 GLN cc_start: 0.8743 (mt0) cc_final: 0.8529 (mt0) REVERT: E 176 LYS cc_start: 0.8109 (tptt) cc_final: 0.7832 (tttt) REVERT: E 202 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: E 291 ASP cc_start: 0.8570 (m-30) cc_final: 0.8318 (m-30) REVERT: F 147 LYS cc_start: 0.8302 (tppt) cc_final: 0.8086 (tptp) REVERT: F 176 LYS cc_start: 0.8066 (tptt) cc_final: 0.7830 (ttpp) REVERT: F 301 LEU cc_start: 0.8564 (mm) cc_final: 0.8232 (mm) REVERT: G 118 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7722 (ttmm) REVERT: G 139 GLN cc_start: 0.8748 (mt0) cc_final: 0.8532 (mt0) REVERT: G 176 LYS cc_start: 0.8142 (tptt) cc_final: 0.7867 (tttt) REVERT: G 202 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: G 291 ASP cc_start: 0.8565 (m-30) cc_final: 0.8320 (m-30) REVERT: H 147 LYS cc_start: 0.8318 (tppt) cc_final: 0.8105 (tptp) REVERT: H 176 LYS cc_start: 0.8105 (tptt) cc_final: 0.7865 (ttpp) REVERT: H 301 LEU cc_start: 0.8568 (mm) cc_final: 0.8222 (mm) outliers start: 70 outliers final: 27 residues processed: 234 average time/residue: 0.5369 time to fit residues: 143.1492 Evaluate side-chains 186 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 225 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 88 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 225 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 146 optimal weight: 0.3980 chunk 156 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.096139 restraints weight = 25568.854| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.33 r_work: 0.3065 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19576 Z= 0.140 Angle : 0.509 7.563 26512 Z= 0.261 Chirality : 0.037 0.119 3144 Planarity : 0.002 0.013 3432 Dihedral : 5.612 54.303 2672 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.95 % Allowed : 18.63 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.16), residues: 2448 helix: -2.07 (0.12), residues: 1600 sheet: -1.76 (0.38), residues: 208 loop : -0.80 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 175 TYR 0.009 0.001 TYR H 256 PHE 0.007 0.001 PHE G 103 TRP 0.006 0.001 TRP H 56 HIS 0.001 0.000 HIS D 243 Details of bonding type rmsd covalent geometry : bond 0.00335 (19576) covalent geometry : angle 0.50883 (26512) hydrogen bonds : bond 0.03388 ( 856) hydrogen bonds : angle 3.68252 ( 2496) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 184 time to evaluate : 0.768 Fit side-chains REVERT: A 28 TRP cc_start: 0.9237 (OUTLIER) cc_final: 0.8385 (t60) REVERT: A 118 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7835 (ttmm) REVERT: A 139 GLN cc_start: 0.8711 (mt0) cc_final: 0.8318 (mt0) REVERT: A 176 LYS cc_start: 0.8441 (tptt) cc_final: 0.8146 (tttt) REVERT: A 202 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: B 28 TRP cc_start: 0.9252 (OUTLIER) cc_final: 0.8426 (t60) REVERT: B 222 GLU cc_start: 0.8387 (tp30) cc_final: 0.7762 (mp0) REVERT: B 301 LEU cc_start: 0.8349 (mm) cc_final: 0.7928 (mm) REVERT: C 28 TRP cc_start: 0.9266 (OUTLIER) cc_final: 0.8429 (t60) REVERT: C 118 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7850 (ttmm) REVERT: C 139 GLN cc_start: 0.8692 (mt0) cc_final: 0.8322 (mt0) REVERT: C 176 LYS cc_start: 0.8422 (tptt) cc_final: 0.8130 (tttt) REVERT: C 202 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: C 222 GLU cc_start: 0.8519 (tp30) cc_final: 0.7459 (mt-10) REVERT: D 28 TRP cc_start: 0.9256 (OUTLIER) cc_final: 0.8443 (t60) REVERT: D 222 GLU cc_start: 0.8387 (tp30) cc_final: 0.8090 (mp0) REVERT: D 301 LEU cc_start: 0.8342 (mm) cc_final: 0.7923 (mm) REVERT: D 308 MET cc_start: 0.7461 (mpt) cc_final: 0.7253 (mmp) REVERT: E 28 TRP cc_start: 0.9260 (OUTLIER) cc_final: 0.8445 (t60) REVERT: E 118 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7863 (ttmm) REVERT: E 139 GLN cc_start: 0.8693 (mt0) cc_final: 0.8323 (mt0) REVERT: E 176 LYS cc_start: 0.8397 (tptt) cc_final: 0.8097 (tttt) REVERT: E 202 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: F 28 TRP cc_start: 0.9244 (OUTLIER) cc_final: 0.8427 (t60) REVERT: F 301 LEU cc_start: 0.8339 (mm) cc_final: 0.7934 (mm) REVERT: G 28 TRP cc_start: 0.9243 (OUTLIER) cc_final: 0.8395 (t60) REVERT: G 118 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7866 (ttmm) REVERT: G 139 GLN cc_start: 0.8678 (mt0) cc_final: 0.8287 (mt0) REVERT: G 176 LYS cc_start: 0.8416 (tptt) cc_final: 0.8132 (tttt) REVERT: G 202 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: H 28 TRP cc_start: 0.9239 (OUTLIER) cc_final: 0.8457 (t60) REVERT: H 301 LEU cc_start: 0.8325 (mm) cc_final: 0.7915 (mm) outliers start: 62 outliers final: 23 residues processed: 229 average time/residue: 0.6923 time to fit residues: 176.0554 Evaluate side-chains 180 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 225 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 235 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 40 optimal weight: 0.0060 chunk 35 optimal weight: 0.2980 chunk 216 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 169 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.129804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.096840 restraints weight = 25661.220| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.29 r_work: 0.3053 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19576 Z= 0.113 Angle : 0.479 7.263 26512 Z= 0.241 Chirality : 0.036 0.116 3144 Planarity : 0.002 0.013 3432 Dihedral : 5.379 53.615 2672 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.52 % Allowed : 20.63 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.17), residues: 2448 helix: -1.35 (0.13), residues: 1600 sheet: -1.36 (0.39), residues: 208 loop : -0.44 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 259 TYR 0.007 0.001 TYR B 256 PHE 0.005 0.001 PHE E 103 TRP 0.004 0.001 TRP F 56 HIS 0.001 0.000 HIS H 243 Details of bonding type rmsd covalent geometry : bond 0.00270 (19576) covalent geometry : angle 0.47869 (26512) hydrogen bonds : bond 0.02736 ( 856) hydrogen bonds : angle 3.30251 ( 2496) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 173 time to evaluate : 0.695 Fit side-chains REVERT: A 28 TRP cc_start: 0.9222 (OUTLIER) cc_final: 0.8607 (t60) REVERT: A 115 GLU cc_start: 0.8352 (pm20) cc_final: 0.8004 (pm20) REVERT: A 130 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7998 (mt) REVERT: A 139 GLN cc_start: 0.8700 (mt0) cc_final: 0.8477 (mt0) REVERT: A 176 LYS cc_start: 0.8354 (tptt) cc_final: 0.8056 (tttt) REVERT: A 202 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: A 222 GLU cc_start: 0.8497 (tp30) cc_final: 0.7449 (mt-10) REVERT: B 28 TRP cc_start: 0.9243 (OUTLIER) cc_final: 0.8656 (t60) REVERT: B 77 MET cc_start: 0.8624 (mmm) cc_final: 0.8387 (mmp) REVERT: B 115 GLU cc_start: 0.8268 (pm20) cc_final: 0.8011 (pm20) REVERT: B 222 GLU cc_start: 0.8366 (tp30) cc_final: 0.7587 (mp0) REVERT: B 301 LEU cc_start: 0.8221 (mm) cc_final: 0.7791 (mm) REVERT: C 28 TRP cc_start: 0.9218 (OUTLIER) cc_final: 0.8603 (t60) REVERT: C 115 GLU cc_start: 0.8351 (pm20) cc_final: 0.8003 (pm20) REVERT: C 118 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7730 (ttmm) REVERT: C 139 GLN cc_start: 0.8688 (mt0) cc_final: 0.8249 (mt0) REVERT: C 176 LYS cc_start: 0.8338 (tptt) cc_final: 0.8042 (tttt) REVERT: C 202 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: C 218 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.7129 (mt0) REVERT: C 222 GLU cc_start: 0.8493 (tp30) cc_final: 0.7295 (mt-10) REVERT: C 301 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8030 (mm) REVERT: D 28 TRP cc_start: 0.9232 (OUTLIER) cc_final: 0.8653 (t60) REVERT: D 77 MET cc_start: 0.8644 (mmm) cc_final: 0.8412 (mmp) REVERT: D 115 GLU cc_start: 0.8260 (pm20) cc_final: 0.8009 (pm20) REVERT: D 222 GLU cc_start: 0.8314 (tp30) cc_final: 0.7917 (mp0) REVERT: D 301 LEU cc_start: 0.8220 (mm) cc_final: 0.7786 (mm) REVERT: E 28 TRP cc_start: 0.9220 (OUTLIER) cc_final: 0.8661 (t60) REVERT: E 115 GLU cc_start: 0.8315 (pm20) cc_final: 0.7973 (pm20) REVERT: E 118 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7734 (ttmm) REVERT: E 139 GLN cc_start: 0.8682 (mt0) cc_final: 0.8251 (mt0) REVERT: E 176 LYS cc_start: 0.8308 (tptt) cc_final: 0.8005 (tttt) REVERT: E 202 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: E 301 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8050 (mm) REVERT: F 28 TRP cc_start: 0.9224 (OUTLIER) cc_final: 0.8644 (t60) REVERT: F 77 MET cc_start: 0.8633 (mmm) cc_final: 0.8402 (mmp) REVERT: F 115 GLU cc_start: 0.8259 (pm20) cc_final: 0.7998 (pm20) REVERT: F 301 LEU cc_start: 0.8184 (mm) cc_final: 0.7740 (mm) REVERT: G 28 TRP cc_start: 0.9224 (OUTLIER) cc_final: 0.8615 (t60) REVERT: G 115 GLU cc_start: 0.8332 (pm20) cc_final: 0.7990 (pm20) REVERT: G 118 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7720 (ttmm) REVERT: G 130 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8000 (mt) REVERT: G 139 GLN cc_start: 0.8696 (mt0) cc_final: 0.8264 (mt0) REVERT: G 176 LYS cc_start: 0.8333 (tptt) cc_final: 0.8037 (tttt) REVERT: G 202 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: G 301 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8170 (mp) REVERT: H 28 TRP cc_start: 0.9230 (OUTLIER) cc_final: 0.8638 (t60) REVERT: H 77 MET cc_start: 0.8648 (mmm) cc_final: 0.8419 (mmp) REVERT: H 115 GLU cc_start: 0.8261 (pm20) cc_final: 0.8008 (pm20) REVERT: H 301 LEU cc_start: 0.8203 (mm) cc_final: 0.7761 (mm) outliers start: 74 outliers final: 30 residues processed: 227 average time/residue: 0.5930 time to fit residues: 151.5645 Evaluate side-chains 205 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 154 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 146 MET Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 225 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 81 optimal weight: 0.6980 chunk 231 optimal weight: 0.9990 chunk 221 optimal weight: 0.4980 chunk 184 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 HIS ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.128329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.095240 restraints weight = 25567.611| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.28 r_work: 0.3024 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 19576 Z= 0.146 Angle : 0.502 8.123 26512 Z= 0.252 Chirality : 0.037 0.118 3144 Planarity : 0.002 0.014 3432 Dihedral : 5.321 52.785 2672 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.94 % Allowed : 20.87 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.17), residues: 2448 helix: -0.91 (0.13), residues: 1600 sheet: -1.10 (0.39), residues: 208 loop : -0.28 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 259 TYR 0.008 0.001 TYR B 256 PHE 0.005 0.001 PHE H 251 TRP 0.007 0.001 TRP H 56 HIS 0.001 0.000 HIS D 243 Details of bonding type rmsd covalent geometry : bond 0.00354 (19576) covalent geometry : angle 0.50167 (26512) hydrogen bonds : bond 0.02924 ( 856) hydrogen bonds : angle 3.28076 ( 2496) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 164 time to evaluate : 0.673 Fit side-chains REVERT: A 28 TRP cc_start: 0.9220 (OUTLIER) cc_final: 0.8754 (t60) REVERT: A 115 GLU cc_start: 0.8302 (pm20) cc_final: 0.7916 (pm20) REVERT: A 176 LYS cc_start: 0.8335 (tptt) cc_final: 0.8042 (tttt) REVERT: A 202 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7981 (mm-30) REVERT: A 222 GLU cc_start: 0.8471 (tp30) cc_final: 0.7430 (mt-10) REVERT: A 223 ASP cc_start: 0.8361 (t0) cc_final: 0.8161 (t0) REVERT: B 28 TRP cc_start: 0.9274 (OUTLIER) cc_final: 0.8839 (t60) REVERT: B 32 MET cc_start: 0.7144 (tpp) cc_final: 0.6913 (tpp) REVERT: B 115 GLU cc_start: 0.8295 (pm20) cc_final: 0.8010 (pm20) REVERT: B 222 GLU cc_start: 0.8224 (tp30) cc_final: 0.7629 (mp0) REVERT: C 28 TRP cc_start: 0.9222 (OUTLIER) cc_final: 0.8778 (t60) REVERT: C 115 GLU cc_start: 0.8317 (pm20) cc_final: 0.7927 (pm20) REVERT: C 118 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7725 (ttmm) REVERT: C 139 GLN cc_start: 0.8719 (mt0) cc_final: 0.8272 (mt0) REVERT: C 176 LYS cc_start: 0.8320 (tptt) cc_final: 0.8018 (tttt) REVERT: C 202 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7990 (mm-30) REVERT: C 222 GLU cc_start: 0.8355 (tp30) cc_final: 0.7415 (mt-10) REVERT: C 301 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8031 (mm) REVERT: D 28 TRP cc_start: 0.9265 (OUTLIER) cc_final: 0.8841 (t60) REVERT: D 32 MET cc_start: 0.7174 (tpp) cc_final: 0.6946 (tpp) REVERT: D 115 GLU cc_start: 0.8281 (pm20) cc_final: 0.8003 (pm20) REVERT: D 222 GLU cc_start: 0.8223 (tp30) cc_final: 0.7649 (mp0) REVERT: D 291 ASP cc_start: 0.8719 (m-30) cc_final: 0.8246 (m-30) REVERT: D 301 LEU cc_start: 0.8130 (mm) cc_final: 0.7633 (mm) REVERT: E 28 TRP cc_start: 0.9224 (OUTLIER) cc_final: 0.8803 (t60) REVERT: E 115 GLU cc_start: 0.8331 (pm20) cc_final: 0.7924 (pm20) REVERT: E 118 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7720 (ttmm) REVERT: E 139 GLN cc_start: 0.8720 (mt0) cc_final: 0.8279 (mt0) REVERT: E 176 LYS cc_start: 0.8284 (tptt) cc_final: 0.7996 (tttt) REVERT: E 202 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7972 (mm-30) REVERT: E 222 GLU cc_start: 0.8113 (tp30) cc_final: 0.7475 (mt-10) REVERT: E 301 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8032 (mm) REVERT: F 28 TRP cc_start: 0.9262 (OUTLIER) cc_final: 0.8838 (t60) REVERT: F 32 MET cc_start: 0.7146 (tpp) cc_final: 0.6907 (tpp) REVERT: F 115 GLU cc_start: 0.8290 (pm20) cc_final: 0.7995 (pm20) REVERT: F 301 LEU cc_start: 0.8107 (mm) cc_final: 0.7608 (mm) REVERT: G 28 TRP cc_start: 0.9212 (OUTLIER) cc_final: 0.8793 (t60) REVERT: G 115 GLU cc_start: 0.8295 (pm20) cc_final: 0.7905 (pm20) REVERT: G 118 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7725 (ttmm) REVERT: G 139 GLN cc_start: 0.8706 (mt0) cc_final: 0.8255 (mt0) REVERT: G 176 LYS cc_start: 0.8318 (tptt) cc_final: 0.8032 (tttt) REVERT: G 202 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7990 (mm-30) REVERT: G 222 GLU cc_start: 0.8244 (tp30) cc_final: 0.7282 (mt-10) REVERT: G 301 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8014 (mm) REVERT: H 28 TRP cc_start: 0.9264 (OUTLIER) cc_final: 0.8827 (t60) REVERT: H 32 MET cc_start: 0.7137 (tpp) cc_final: 0.6906 (tpp) REVERT: H 115 GLU cc_start: 0.8296 (pm20) cc_final: 0.8006 (pm20) outliers start: 83 outliers final: 28 residues processed: 229 average time/residue: 0.5414 time to fit residues: 140.4188 Evaluate side-chains 200 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 308 MET Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 225 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.0170 chunk 135 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 0.0060 chunk 234 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 HIS ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 HIS ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.094645 restraints weight = 25517.287| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.27 r_work: 0.3007 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 19576 Z= 0.158 Angle : 0.514 9.255 26512 Z= 0.256 Chirality : 0.038 0.122 3144 Planarity : 0.002 0.014 3432 Dihedral : 5.288 52.160 2672 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.47 % Allowed : 22.67 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.17), residues: 2448 helix: -0.63 (0.13), residues: 1600 sheet: -0.94 (0.39), residues: 208 loop : -0.26 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 259 TYR 0.009 0.001 TYR F 256 PHE 0.006 0.001 PHE A 103 TRP 0.007 0.001 TRP B 56 HIS 0.002 0.000 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00386 (19576) covalent geometry : angle 0.51370 (26512) hydrogen bonds : bond 0.02893 ( 856) hydrogen bonds : angle 3.26150 ( 2496) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 158 time to evaluate : 0.764 Fit side-chains REVERT: A 28 TRP cc_start: 0.9225 (OUTLIER) cc_final: 0.8809 (t60) REVERT: A 115 GLU cc_start: 0.8301 (pm20) cc_final: 0.7914 (pm20) REVERT: A 176 LYS cc_start: 0.8350 (tptt) cc_final: 0.8051 (tttt) REVERT: A 202 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7993 (mm-30) REVERT: A 222 GLU cc_start: 0.8336 (tp30) cc_final: 0.7438 (mt-10) REVERT: A 301 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7760 (mm) REVERT: B 28 TRP cc_start: 0.9267 (OUTLIER) cc_final: 0.8863 (t60) REVERT: B 32 MET cc_start: 0.7236 (tpp) cc_final: 0.7026 (tpp) REVERT: B 115 GLU cc_start: 0.8317 (pm20) cc_final: 0.8066 (pm20) REVERT: B 222 GLU cc_start: 0.8280 (tp30) cc_final: 0.7724 (mp0) REVERT: B 291 ASP cc_start: 0.8717 (m-30) cc_final: 0.8247 (m-30) REVERT: C 28 TRP cc_start: 0.9218 (OUTLIER) cc_final: 0.8796 (t60) REVERT: C 115 GLU cc_start: 0.8287 (pm20) cc_final: 0.7891 (pm20) REVERT: C 118 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7732 (ttmm) REVERT: C 176 LYS cc_start: 0.8321 (tptt) cc_final: 0.8026 (tttt) REVERT: C 202 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.8005 (mm-30) REVERT: C 222 GLU cc_start: 0.8374 (tp30) cc_final: 0.7433 (mt-10) REVERT: C 301 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7911 (mm) REVERT: D 28 TRP cc_start: 0.9279 (OUTLIER) cc_final: 0.8890 (t60) REVERT: D 32 MET cc_start: 0.7243 (tpp) cc_final: 0.7034 (tpp) REVERT: D 222 GLU cc_start: 0.8278 (tp30) cc_final: 0.7834 (mp0) REVERT: E 28 TRP cc_start: 0.9222 (OUTLIER) cc_final: 0.8860 (t60) REVERT: E 115 GLU cc_start: 0.8294 (pm20) cc_final: 0.7906 (pm20) REVERT: E 118 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7765 (ttmm) REVERT: E 176 LYS cc_start: 0.8280 (tptt) cc_final: 0.7981 (tttt) REVERT: E 202 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7991 (mm-30) REVERT: E 222 GLU cc_start: 0.8122 (tp30) cc_final: 0.7507 (mp0) REVERT: F 28 TRP cc_start: 0.9266 (OUTLIER) cc_final: 0.8877 (t60) REVERT: F 32 MET cc_start: 0.7245 (tpp) cc_final: 0.7037 (tpp) REVERT: F 222 GLU cc_start: 0.7761 (mp0) cc_final: 0.7471 (mp0) REVERT: F 291 ASP cc_start: 0.8722 (m-30) cc_final: 0.8256 (m-30) REVERT: G 28 TRP cc_start: 0.9223 (OUTLIER) cc_final: 0.8813 (t60) REVERT: G 115 GLU cc_start: 0.8287 (pm20) cc_final: 0.7901 (pm20) REVERT: G 118 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7730 (ttmm) REVERT: G 139 GLN cc_start: 0.8735 (mt0) cc_final: 0.8286 (mt0) REVERT: G 176 LYS cc_start: 0.8323 (tptt) cc_final: 0.8032 (tttt) REVERT: G 202 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.8005 (mm-30) REVERT: G 222 GLU cc_start: 0.8212 (tp30) cc_final: 0.7502 (mp0) REVERT: H 28 TRP cc_start: 0.9259 (OUTLIER) cc_final: 0.8850 (t60) REVERT: H 32 MET cc_start: 0.7233 (tpp) cc_final: 0.7024 (tpp) REVERT: H 222 GLU cc_start: 0.7983 (mp0) cc_final: 0.7424 (mp0) outliers start: 73 outliers final: 34 residues processed: 213 average time/residue: 0.5349 time to fit residues: 128.9032 Evaluate side-chains 196 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 308 MET Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 225 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 33 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 214 optimal weight: 0.5980 chunk 131 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 142 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.096127 restraints weight = 25364.243| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.27 r_work: 0.3030 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19576 Z= 0.116 Angle : 0.489 10.189 26512 Z= 0.245 Chirality : 0.036 0.116 3144 Planarity : 0.002 0.013 3432 Dihedral : 5.131 51.628 2672 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.61 % Allowed : 23.05 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.18), residues: 2448 helix: -0.27 (0.14), residues: 1600 sheet: -0.68 (0.39), residues: 200 loop : -0.24 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 259 TYR 0.007 0.001 TYR H 256 PHE 0.006 0.001 PHE C 103 TRP 0.004 0.001 TRP B 56 HIS 0.001 0.000 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00282 (19576) covalent geometry : angle 0.48901 (26512) hydrogen bonds : bond 0.02584 ( 856) hydrogen bonds : angle 3.11673 ( 2496) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 164 time to evaluate : 0.506 Fit side-chains REVERT: A 28 TRP cc_start: 0.9178 (OUTLIER) cc_final: 0.8839 (t60) REVERT: A 115 GLU cc_start: 0.8311 (pm20) cc_final: 0.8017 (pm20) REVERT: A 139 GLN cc_start: 0.8723 (mt0) cc_final: 0.8303 (mt0) REVERT: A 176 LYS cc_start: 0.8489 (tptt) cc_final: 0.8214 (tttt) REVERT: A 222 GLU cc_start: 0.8309 (tp30) cc_final: 0.7508 (mt-10) REVERT: A 223 ASP cc_start: 0.8224 (t0) cc_final: 0.8023 (t0) REVERT: A 301 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7828 (mm) REVERT: B 28 TRP cc_start: 0.9210 (OUTLIER) cc_final: 0.8879 (t60) REVERT: B 77 MET cc_start: 0.8723 (mmm) cc_final: 0.8458 (mmp) REVERT: B 115 GLU cc_start: 0.8332 (pm20) cc_final: 0.8131 (pm20) REVERT: B 130 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8132 (mp) REVERT: B 222 GLU cc_start: 0.8263 (tp30) cc_final: 0.7766 (mp0) REVERT: B 291 ASP cc_start: 0.8678 (m-30) cc_final: 0.8223 (m-30) REVERT: C 28 TRP cc_start: 0.9179 (OUTLIER) cc_final: 0.8833 (t60) REVERT: C 115 GLU cc_start: 0.8322 (pm20) cc_final: 0.8029 (pm20) REVERT: C 139 GLN cc_start: 0.8699 (mt0) cc_final: 0.8278 (mt0) REVERT: C 176 LYS cc_start: 0.8458 (tptt) cc_final: 0.8201 (tttt) REVERT: C 222 GLU cc_start: 0.8306 (tp30) cc_final: 0.7577 (mt-10) REVERT: D 28 TRP cc_start: 0.9205 (OUTLIER) cc_final: 0.8880 (t60) REVERT: D 77 MET cc_start: 0.8731 (mmm) cc_final: 0.8482 (mmp) REVERT: D 130 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8134 (mp) REVERT: D 222 GLU cc_start: 0.8291 (tp30) cc_final: 0.7987 (mp0) REVERT: D 291 ASP cc_start: 0.8701 (m-30) cc_final: 0.8274 (m-30) REVERT: E 28 TRP cc_start: 0.9167 (OUTLIER) cc_final: 0.8834 (t60) REVERT: E 115 GLU cc_start: 0.8292 (pm20) cc_final: 0.7994 (pm20) REVERT: E 118 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7893 (ttmm) REVERT: E 139 GLN cc_start: 0.8709 (mt0) cc_final: 0.8291 (mt0) REVERT: E 176 LYS cc_start: 0.8429 (tptt) cc_final: 0.8173 (tttt) REVERT: E 222 GLU cc_start: 0.8088 (tp30) cc_final: 0.7583 (mp0) REVERT: E 301 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7945 (mm) REVERT: F 28 TRP cc_start: 0.9196 (OUTLIER) cc_final: 0.8872 (t60) REVERT: F 77 MET cc_start: 0.8736 (mmm) cc_final: 0.8491 (mmp) REVERT: F 130 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8138 (mp) REVERT: F 291 ASP cc_start: 0.8688 (m-30) cc_final: 0.8241 (m-30) REVERT: G 28 TRP cc_start: 0.9177 (OUTLIER) cc_final: 0.8825 (t60) REVERT: G 115 GLU cc_start: 0.8295 (pm20) cc_final: 0.8000 (pm20) REVERT: G 139 GLN cc_start: 0.8706 (mt0) cc_final: 0.8285 (mt0) REVERT: G 176 LYS cc_start: 0.8454 (tptt) cc_final: 0.8203 (tttt) REVERT: G 222 GLU cc_start: 0.8134 (tp30) cc_final: 0.7602 (mp0) REVERT: G 301 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7993 (mm) REVERT: H 28 TRP cc_start: 0.9209 (OUTLIER) cc_final: 0.8872 (t60) REVERT: H 32 MET cc_start: 0.7247 (tpp) cc_final: 0.7027 (tpp) REVERT: H 77 MET cc_start: 0.8734 (mmm) cc_final: 0.8490 (mmp) REVERT: H 130 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8137 (mp) REVERT: H 222 GLU cc_start: 0.7980 (mp0) cc_final: 0.7490 (mp0) REVERT: H 291 ASP cc_start: 0.8698 (m-30) cc_final: 0.8277 (m-30) outliers start: 76 outliers final: 37 residues processed: 219 average time/residue: 0.6040 time to fit residues: 148.3414 Evaluate side-chains 203 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 150 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 308 MET Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 146 MET Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 308 MET Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 225 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 82 optimal weight: 0.5980 chunk 100 optimal weight: 0.3980 chunk 61 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 215 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 55 optimal weight: 0.0370 chunk 135 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.129335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.096492 restraints weight = 25547.204| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.29 r_work: 0.3038 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19576 Z= 0.107 Angle : 0.503 11.052 26512 Z= 0.247 Chirality : 0.036 0.115 3144 Planarity : 0.002 0.019 3432 Dihedral : 5.024 51.265 2672 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.80 % Allowed : 23.81 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.18), residues: 2448 helix: 0.07 (0.14), residues: 1592 sheet: -0.52 (0.40), residues: 200 loop : -0.07 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 198 TYR 0.007 0.001 TYR H 256 PHE 0.005 0.001 PHE A 103 TRP 0.004 0.001 TRP B 56 HIS 0.001 0.000 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00258 (19576) covalent geometry : angle 0.50315 (26512) hydrogen bonds : bond 0.02487 ( 856) hydrogen bonds : angle 3.01782 ( 2496) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 161 time to evaluate : 0.756 Fit side-chains REVERT: A 28 TRP cc_start: 0.9221 (OUTLIER) cc_final: 0.8909 (t60) REVERT: A 115 GLU cc_start: 0.8262 (pm20) cc_final: 0.7883 (pm20) REVERT: A 139 GLN cc_start: 0.8704 (mt0) cc_final: 0.8233 (mt0) REVERT: A 176 LYS cc_start: 0.8367 (tptt) cc_final: 0.8048 (tttt) REVERT: A 222 GLU cc_start: 0.8321 (tp30) cc_final: 0.7440 (mt-10) REVERT: A 301 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7693 (mm) REVERT: B 28 TRP cc_start: 0.9251 (OUTLIER) cc_final: 0.8922 (t60) REVERT: B 77 MET cc_start: 0.8564 (mmm) cc_final: 0.8276 (mmp) REVERT: B 115 GLU cc_start: 0.8283 (pm20) cc_final: 0.8016 (pm20) REVERT: B 130 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8141 (mp) REVERT: B 222 GLU cc_start: 0.8285 (tp30) cc_final: 0.7700 (mp0) REVERT: B 291 ASP cc_start: 0.8636 (m-30) cc_final: 0.8147 (m-30) REVERT: C 28 TRP cc_start: 0.9227 (OUTLIER) cc_final: 0.8928 (t60) REVERT: C 115 GLU cc_start: 0.8277 (pm20) cc_final: 0.7909 (pm20) REVERT: C 139 GLN cc_start: 0.8693 (mt0) cc_final: 0.8229 (mt0) REVERT: C 176 LYS cc_start: 0.8326 (tptt) cc_final: 0.8021 (tttt) REVERT: C 222 GLU cc_start: 0.8391 (tp30) cc_final: 0.7562 (mt-10) REVERT: D 28 TRP cc_start: 0.9242 (OUTLIER) cc_final: 0.8921 (t60) REVERT: D 77 MET cc_start: 0.8558 (mmm) cc_final: 0.8322 (mmp) REVERT: D 130 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8142 (mp) REVERT: D 222 GLU cc_start: 0.8279 (tp30) cc_final: 0.7864 (mp0) REVERT: D 291 ASP cc_start: 0.8662 (m-30) cc_final: 0.8196 (m-30) REVERT: E 28 TRP cc_start: 0.9211 (OUTLIER) cc_final: 0.8889 (t60) REVERT: E 115 GLU cc_start: 0.8255 (pm20) cc_final: 0.7884 (pm20) REVERT: E 139 GLN cc_start: 0.8682 (mt0) cc_final: 0.8214 (mt0) REVERT: E 176 LYS cc_start: 0.8310 (tptt) cc_final: 0.7988 (tttt) REVERT: E 222 GLU cc_start: 0.8242 (tp30) cc_final: 0.7536 (mp0) REVERT: E 301 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7730 (mm) REVERT: F 28 TRP cc_start: 0.9238 (OUTLIER) cc_final: 0.8916 (t60) REVERT: F 77 MET cc_start: 0.8554 (mmm) cc_final: 0.8322 (mmp) REVERT: F 130 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8136 (mp) REVERT: F 222 GLU cc_start: 0.7971 (mp0) cc_final: 0.7404 (mp0) REVERT: F 291 ASP cc_start: 0.8643 (m-30) cc_final: 0.8159 (m-30) REVERT: G 28 TRP cc_start: 0.9212 (OUTLIER) cc_final: 0.8911 (t60) REVERT: G 115 GLU cc_start: 0.8242 (pm20) cc_final: 0.7854 (pm20) REVERT: G 139 GLN cc_start: 0.8683 (mt0) cc_final: 0.8215 (mt0) REVERT: G 176 LYS cc_start: 0.8337 (tptt) cc_final: 0.8027 (tttt) REVERT: G 222 GLU cc_start: 0.8149 (tp30) cc_final: 0.7492 (mp0) REVERT: H 28 TRP cc_start: 0.9239 (OUTLIER) cc_final: 0.8913 (t60) REVERT: H 77 MET cc_start: 0.8551 (mmm) cc_final: 0.8320 (mmp) REVERT: H 130 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8138 (mp) REVERT: H 222 GLU cc_start: 0.7887 (mp0) cc_final: 0.7420 (mp0) REVERT: H 291 ASP cc_start: 0.8621 (m-30) cc_final: 0.8146 (m-30) outliers start: 59 outliers final: 33 residues processed: 202 average time/residue: 0.5345 time to fit residues: 122.4022 Evaluate side-chains 198 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 308 MET Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 225 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 21 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 117 optimal weight: 0.0870 chunk 128 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 237 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 205 GLN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.129100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.096163 restraints weight = 25339.632| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.28 r_work: 0.3031 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19576 Z= 0.117 Angle : 0.520 11.715 26512 Z= 0.253 Chirality : 0.037 0.116 3144 Planarity : 0.002 0.017 3432 Dihedral : 4.983 50.667 2672 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.76 % Allowed : 24.05 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.18), residues: 2448 helix: 0.29 (0.14), residues: 1592 sheet: -0.62 (0.39), residues: 208 loop : -0.03 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 198 TYR 0.007 0.001 TYR F 256 PHE 0.005 0.001 PHE C 103 TRP 0.005 0.001 TRP D 56 HIS 0.001 0.000 HIS G 276 Details of bonding type rmsd covalent geometry : bond 0.00285 (19576) covalent geometry : angle 0.52049 (26512) hydrogen bonds : bond 0.02531 ( 856) hydrogen bonds : angle 3.01851 ( 2496) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 166 time to evaluate : 0.660 Fit side-chains REVERT: A 28 TRP cc_start: 0.9178 (OUTLIER) cc_final: 0.8860 (t60) REVERT: A 115 GLU cc_start: 0.8328 (pm20) cc_final: 0.8021 (pm20) REVERT: A 139 GLN cc_start: 0.8706 (mt0) cc_final: 0.8288 (mt0) REVERT: A 176 LYS cc_start: 0.8493 (tptt) cc_final: 0.8212 (tttt) REVERT: A 222 GLU cc_start: 0.8151 (tp30) cc_final: 0.7492 (mt-10) REVERT: B 28 TRP cc_start: 0.9178 (OUTLIER) cc_final: 0.8874 (t60) REVERT: B 130 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8176 (mp) REVERT: B 222 GLU cc_start: 0.8160 (tp30) cc_final: 0.7733 (mp0) REVERT: C 28 TRP cc_start: 0.9186 (OUTLIER) cc_final: 0.8885 (t60) REVERT: C 115 GLU cc_start: 0.8312 (pm20) cc_final: 0.8045 (pm20) REVERT: C 139 GLN cc_start: 0.8695 (mt0) cc_final: 0.8282 (mt0) REVERT: C 176 LYS cc_start: 0.8485 (tptt) cc_final: 0.8230 (tttt) REVERT: C 218 GLN cc_start: 0.7438 (mt0) cc_final: 0.7181 (mt0) REVERT: C 222 GLU cc_start: 0.8253 (tp30) cc_final: 0.7671 (mt-10) REVERT: D 28 TRP cc_start: 0.9174 (OUTLIER) cc_final: 0.8874 (t60) REVERT: D 130 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8185 (mp) REVERT: D 222 GLU cc_start: 0.8198 (tp30) cc_final: 0.7932 (mp0) REVERT: D 244 GLU cc_start: 0.8444 (tt0) cc_final: 0.8153 (pt0) REVERT: E 28 TRP cc_start: 0.9167 (OUTLIER) cc_final: 0.8879 (t60) REVERT: E 115 GLU cc_start: 0.8309 (pm20) cc_final: 0.8013 (pm20) REVERT: E 139 GLN cc_start: 0.8687 (mt0) cc_final: 0.8270 (mt0) REVERT: E 176 LYS cc_start: 0.8459 (tptt) cc_final: 0.8175 (tttt) REVERT: E 222 GLU cc_start: 0.8183 (tp30) cc_final: 0.7654 (mp0) REVERT: F 28 TRP cc_start: 0.9169 (OUTLIER) cc_final: 0.8881 (t60) REVERT: F 130 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8176 (mp) REVERT: F 222 GLU cc_start: 0.7872 (mp0) cc_final: 0.7455 (mp0) REVERT: G 28 TRP cc_start: 0.9173 (OUTLIER) cc_final: 0.8868 (t60) REVERT: G 115 GLU cc_start: 0.8287 (pm20) cc_final: 0.7991 (pm20) REVERT: G 139 GLN cc_start: 0.8677 (mt0) cc_final: 0.8262 (mt0) REVERT: G 176 LYS cc_start: 0.8468 (tptt) cc_final: 0.8199 (tttt) REVERT: G 222 GLU cc_start: 0.8175 (tp30) cc_final: 0.7561 (mp0) REVERT: H 28 TRP cc_start: 0.9172 (OUTLIER) cc_final: 0.8863 (t60) REVERT: H 130 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8176 (mp) REVERT: H 222 GLU cc_start: 0.7881 (mp0) cc_final: 0.7402 (mp0) outliers start: 58 outliers final: 34 residues processed: 206 average time/residue: 0.5398 time to fit residues: 126.0754 Evaluate side-chains 208 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 308 MET Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 308 MET Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 225 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 144 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 217 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 0.0770 chunk 19 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 193 optimal weight: 0.0980 chunk 182 optimal weight: 3.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.130440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.097574 restraints weight = 25388.333| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.29 r_work: 0.3056 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19576 Z= 0.099 Angle : 0.515 12.189 26512 Z= 0.251 Chirality : 0.036 0.114 3144 Planarity : 0.002 0.016 3432 Dihedral : 4.886 50.159 2672 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.00 % Allowed : 24.86 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.18), residues: 2448 helix: 0.50 (0.14), residues: 1592 sheet: -0.31 (0.40), residues: 200 loop : -0.05 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 116 TYR 0.006 0.001 TYR B 256 PHE 0.005 0.001 PHE A 103 TRP 0.003 0.001 TRP B 56 HIS 0.000 0.000 HIS F 243 Details of bonding type rmsd covalent geometry : bond 0.00237 (19576) covalent geometry : angle 0.51525 (26512) hydrogen bonds : bond 0.02361 ( 856) hydrogen bonds : angle 2.93939 ( 2496) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 0.712 Fit side-chains REVERT: A 28 TRP cc_start: 0.9196 (OUTLIER) cc_final: 0.8893 (t60) REVERT: A 115 GLU cc_start: 0.8229 (pm20) cc_final: 0.7890 (pm20) REVERT: A 139 GLN cc_start: 0.8710 (mt0) cc_final: 0.8253 (mt0) REVERT: A 176 LYS cc_start: 0.8369 (tptt) cc_final: 0.8026 (tttt) REVERT: A 222 GLU cc_start: 0.8243 (tp30) cc_final: 0.7474 (mt-10) REVERT: B 28 TRP cc_start: 0.9205 (OUTLIER) cc_final: 0.8909 (t60) REVERT: B 222 GLU cc_start: 0.8250 (tp30) cc_final: 0.7634 (mp0) REVERT: B 244 GLU cc_start: 0.8383 (tt0) cc_final: 0.8070 (pt0) REVERT: C 28 TRP cc_start: 0.9191 (OUTLIER) cc_final: 0.8907 (t60) REVERT: C 115 GLU cc_start: 0.8276 (pm20) cc_final: 0.7932 (pm20) REVERT: C 139 GLN cc_start: 0.8695 (mt0) cc_final: 0.8242 (mt0) REVERT: C 176 LYS cc_start: 0.8353 (tptt) cc_final: 0.8014 (tttt) REVERT: C 222 GLU cc_start: 0.8324 (tp30) cc_final: 0.7614 (mt-10) REVERT: D 28 TRP cc_start: 0.9196 (OUTLIER) cc_final: 0.8906 (t60) REVERT: D 77 MET cc_start: 0.8616 (mmm) cc_final: 0.8301 (mmp) REVERT: D 222 GLU cc_start: 0.8297 (tp30) cc_final: 0.7859 (mp0) REVERT: D 244 GLU cc_start: 0.8389 (tt0) cc_final: 0.8106 (pt0) REVERT: E 28 TRP cc_start: 0.9173 (OUTLIER) cc_final: 0.8870 (t60) REVERT: E 115 GLU cc_start: 0.8251 (pm20) cc_final: 0.7883 (pm20) REVERT: E 139 GLN cc_start: 0.8691 (mt0) cc_final: 0.8244 (mt0) REVERT: E 176 LYS cc_start: 0.8330 (tptt) cc_final: 0.7985 (tttt) REVERT: E 222 GLU cc_start: 0.8260 (tp30) cc_final: 0.7566 (mp0) REVERT: F 28 TRP cc_start: 0.9197 (OUTLIER) cc_final: 0.8871 (t60) REVERT: F 77 MET cc_start: 0.8623 (mmm) cc_final: 0.8313 (mmp) REVERT: F 222 GLU cc_start: 0.7981 (mp0) cc_final: 0.7499 (mp0) REVERT: F 244 GLU cc_start: 0.8360 (tt0) cc_final: 0.8047 (pt0) REVERT: G 28 TRP cc_start: 0.9188 (OUTLIER) cc_final: 0.8901 (t60) REVERT: G 115 GLU cc_start: 0.8236 (pm20) cc_final: 0.7872 (pm20) REVERT: G 139 GLN cc_start: 0.8688 (mt0) cc_final: 0.8232 (mt0) REVERT: G 176 LYS cc_start: 0.8348 (tptt) cc_final: 0.8007 (tttt) REVERT: G 222 GLU cc_start: 0.8186 (tp30) cc_final: 0.7437 (mp0) REVERT: H 28 TRP cc_start: 0.9200 (OUTLIER) cc_final: 0.8862 (t60) REVERT: H 77 MET cc_start: 0.8617 (mmm) cc_final: 0.8306 (mmp) REVERT: H 222 GLU cc_start: 0.7908 (mp0) cc_final: 0.7394 (mp0) REVERT: H 244 GLU cc_start: 0.8376 (tt0) cc_final: 0.8062 (pt0) outliers start: 42 outliers final: 26 residues processed: 209 average time/residue: 0.5504 time to fit residues: 130.8042 Evaluate side-chains 197 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 308 MET Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 308 MET Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 225 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 91 optimal weight: 0.2980 chunk 54 optimal weight: 0.5980 chunk 222 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 205 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 112 optimal weight: 0.0980 chunk 190 optimal weight: 0.0000 chunk 239 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 overall best weight: 0.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 205 GLN D 177 ASN F 177 ASN H 177 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.132368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.099516 restraints weight = 25229.192| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.34 r_work: 0.3072 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19576 Z= 0.082 Angle : 0.495 11.830 26512 Z= 0.242 Chirality : 0.035 0.111 3144 Planarity : 0.002 0.019 3432 Dihedral : 4.735 49.409 2672 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.57 % Allowed : 25.33 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 2448 helix: 0.79 (0.14), residues: 1592 sheet: -0.48 (0.40), residues: 208 loop : 0.06 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 279 TYR 0.004 0.001 TYR H 73 PHE 0.005 0.001 PHE A 103 TRP 0.003 0.000 TRP C 28 HIS 0.000 0.000 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00191 (19576) covalent geometry : angle 0.49481 (26512) hydrogen bonds : bond 0.02124 ( 856) hydrogen bonds : angle 2.81834 ( 2496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5287.76 seconds wall clock time: 92 minutes 17.68 seconds (5537.68 seconds total)