Starting phenix.real_space_refine on Sat Sep 12 02:10:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6o5b_0626/09_2026/6o5b_0626.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o5b_0626/09_2026/6o5b_0626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6o5b_0626/09_2026/6o5b_0626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o5b_0626/09_2026/6o5b_0626.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6o5b_0626/09_2026/6o5b_0626.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6o5b_0626/09_2026/6o5b_0626.cif" model { file = "/net/cci-nas-00/data/ceres_data/6o5b_0626/09_2026/6o5b_0626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o5b_0626/09_2026/6o5b_0626.cif" } resolution = 3.6 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= -0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 40 5.16 5 C 8472 2.51 5 N 2279 2.21 5 O 2377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13169 Number of models: 1 Model: "" Number of chains: 13 Chain: "J" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 723 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain: "K" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 723 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain: "E" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2226 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain: "F" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "C" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2211 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain: "D" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "A" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2254 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "B" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "L" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 723 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain: "I" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 723 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain: "G" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2069 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 9, 'TRANS': 240} Chain breaks: 1 Chain: "H" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 373 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.03, per 1000 atoms: 0.23 Number of scatterers: 13169 At special positions: 0 Unit cell: (103.32, 150.36, 136.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 40 16.00 O 2377 8.00 N 2279 7.00 C 8472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 523.9 milliseconds 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 17 sheets defined 53.8% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'J' and resid 107 through 112 Processing helix chain 'J' and resid 140 through 147 removed outlier: 4.519A pdb=" N ASP J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 119 removed outlier: 3.675A pdb=" N ARG K 113 " --> pdb=" O GLY K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 145 Processing helix chain 'E' and resid 107 through 119 removed outlier: 3.822A pdb=" N ARG E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 144 Processing helix chain 'E' and resid 169 through 190 removed outlier: 4.643A pdb=" N LEU E 176 " --> pdb=" O ASN E 172 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU E 182 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU E 190 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 253 removed outlier: 3.733A pdb=" N GLU E 200 " --> pdb=" O GLN E 196 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU E 208 " --> pdb=" O ILE E 204 " (cutoff:3.500A) Proline residue: E 216 - end of helix removed outlier: 4.317A pdb=" N LYS E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL E 220 " --> pdb=" O PRO E 216 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 224 " --> pdb=" O VAL E 220 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE E 249 " --> pdb=" O THR E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 285 removed outlier: 3.986A pdb=" N THR E 267 " --> pdb=" O MET E 263 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR E 268 " --> pdb=" O GLU E 264 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA E 275 " --> pdb=" O THR E 271 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE E 282 " --> pdb=" O MET E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 310 removed outlier: 3.912A pdb=" N ARG E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 328 removed outlier: 3.662A pdb=" N TYR E 317 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU E 320 " --> pdb=" O LYS E 316 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA E 325 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 335 Processing helix chain 'F' and resid 65 through 96 removed outlier: 3.732A pdb=" N PHE F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE F 73 " --> pdb=" O ARG F 69 " (cutoff:3.500A) Proline residue: F 76 - end of helix removed outlier: 4.103A pdb=" N SER F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE F 88 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA F 89 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA F 90 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU F 91 " --> pdb=" O ASN F 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 94 removed outlier: 3.550A pdb=" N ARG C 94 " --> pdb=" O PRO C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 91 through 94' Processing helix chain 'C' and resid 107 through 119 removed outlier: 3.691A pdb=" N PHE C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C 118 " --> pdb=" O GLN C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 178 through 190 removed outlier: 3.537A pdb=" N THR C 188 " --> pdb=" O GLN C 184 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 214 removed outlier: 3.503A pdb=" N HIS C 195 " --> pdb=" O CYS C 191 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE C 204 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 257 removed outlier: 3.661A pdb=" N ARG C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS C 230 " --> pdb=" O ARG C 226 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 250 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TRP C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TRP C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 284 removed outlier: 4.235A pdb=" N VAL C 266 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 282 " --> pdb=" O MET C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 311 removed outlier: 3.682A pdb=" N LYS C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 335 removed outlier: 3.799A pdb=" N ASN C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C 323 " --> pdb=" O GLN C 319 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN C 326 " --> pdb=" O ASP C 322 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 96 removed outlier: 3.947A pdb=" N ARG D 69 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE D 75 " --> pdb=" O PHE D 71 " (cutoff:3.500A) Proline residue: D 76 - end of helix removed outlier: 3.643A pdb=" N SER D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE D 88 " --> pdb=" O ILE D 84 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 118 removed outlier: 3.607A pdb=" N ARG A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 removed outlier: 3.601A pdb=" N LEU A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 174 removed outlier: 3.591A pdb=" N ALA A 174 " --> pdb=" O GLU A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 171 through 174' Processing helix chain 'A' and resid 175 through 192 removed outlier: 3.827A pdb=" N THR A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 215 removed outlier: 3.908A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 226 removed outlier: 3.898A pdb=" N ARG A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 256 removed outlier: 3.634A pdb=" N THR A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 285 removed outlier: 3.699A pdb=" N THR A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 282 " --> pdb=" O MET A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 310 removed outlier: 3.796A pdb=" N ARG A 295 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 340 removed outlier: 3.653A pdb=" N ALA A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Proline residue: A 337 - end of helix Processing helix chain 'B' and resid 66 through 71 removed outlier: 3.657A pdb=" N PHE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 96 removed outlier: 4.057A pdb=" N PHE B 77 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 119 removed outlier: 3.701A pdb=" N GLN L 116 " --> pdb=" O LEU L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 145 Processing helix chain 'I' and resid 107 through 117 removed outlier: 3.571A pdb=" N PHE I 111 " --> pdb=" O SER I 107 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU I 115 " --> pdb=" O PHE I 111 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN I 116 " --> pdb=" O LEU I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 144 Processing helix chain 'G' and resid 107 through 117 removed outlier: 3.549A pdb=" N PHE G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 145 Processing helix chain 'G' and resid 179 through 189 Processing helix chain 'G' and resid 192 through 257 removed outlier: 4.001A pdb=" N LEU G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG G 201 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU G 202 " --> pdb=" O ASN G 198 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS G 211 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) Proline residue: G 216 - end of helix removed outlier: 4.196A pdb=" N VAL G 220 " --> pdb=" O PRO G 216 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU G 223 " --> pdb=" O LYS G 219 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL G 235 " --> pdb=" O ARG G 231 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY G 238 " --> pdb=" O LEU G 234 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE G 247 " --> pdb=" O MET G 243 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY G 248 " --> pdb=" O ALA G 244 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU G 253 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP G 255 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 262 Processing helix chain 'G' and resid 263 through 286 removed outlier: 3.901A pdb=" N THR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET G 278 " --> pdb=" O SER G 274 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE G 282 " --> pdb=" O MET G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 305 removed outlier: 3.551A pdb=" N ARG G 295 " --> pdb=" O TYR G 291 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP G 296 " --> pdb=" O PRO G 292 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU G 300 " --> pdb=" O ASP G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 310 removed outlier: 3.673A pdb=" N LYS G 309 " --> pdb=" O LYS G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 334 removed outlier: 3.787A pdb=" N GLN G 319 " --> pdb=" O GLU G 315 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP G 322 " --> pdb=" O ASN G 318 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.783A pdb=" N ARG H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL H 74 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE H 75 " --> pdb=" O PHE H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 93 removed outlier: 3.661A pdb=" N GLY H 81 " --> pdb=" O PHE H 77 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE H 84 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER H 85 " --> pdb=" O GLY H 81 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU H 91 " --> pdb=" O ASN H 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 76 through 80 Processing sheet with id=AA2, first strand: chain 'J' and resid 125 through 128 removed outlier: 3.610A pdb=" N PHE J 149 " --> pdb=" O VAL J 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 134 through 135 removed outlier: 6.427A pdb=" N ARG J 134 " --> pdb=" O GLN I 98 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU I 95 " --> pdb=" O LEU I 90 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU I 90 " --> pdb=" O GLU I 95 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL I 78 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR I 76 " --> pdb=" O SER I 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 76 through 80 Processing sheet with id=AA5, first strand: chain 'K' and resid 126 through 128 removed outlier: 3.674A pdb=" N PHE K 149 " --> pdb=" O VAL K 160 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL K 160 " --> pdb=" O PHE K 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 76 through 80 removed outlier: 3.910A pdb=" N ARG G 134 " --> pdb=" O ARG E 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 125 through 127 Processing sheet with id=AA8, first strand: chain 'E' and resid 134 through 135 removed outlier: 6.569A pdb=" N ARG E 134 " --> pdb=" O GLN C 98 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N THR C 100 " --> pdb=" O ARG E 134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 128 removed outlier: 3.578A pdb=" N ILE C 153 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 134 through 135 removed outlier: 3.784A pdb=" N THR A 76 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AB3, first strand: chain 'L' and resid 78 through 80 removed outlier: 3.533A pdb=" N VAL L 78 " --> pdb=" O VAL L 85 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 87 through 90 removed outlier: 3.664A pdb=" N GLU L 95 " --> pdb=" O LEU L 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 125 through 128 Processing sheet with id=AB6, first strand: chain 'I' and resid 126 through 128 removed outlier: 3.556A pdb=" N ALA I 126 " --> pdb=" O VAL I 152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 86 through 88 removed outlier: 3.707A pdb=" N ILE G 86 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 125 through 128 644 hydrogen bonds defined for protein. 1830 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: 1.97 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4172 1.34 - 1.46: 2547 1.46 - 1.58: 6639 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 13426 Sorted by residual: bond pdb=" N ILE J 153 " pdb=" CA ILE J 153 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.29e-02 6.01e+03 7.22e+00 bond pdb=" N ILE C 153 " pdb=" CA ILE C 153 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.24e-02 6.50e+03 7.09e+00 bond pdb=" CA PRO C 162 " pdb=" C PRO C 162 " ideal model delta sigma weight residual 1.517 1.539 -0.022 9.30e-03 1.16e+04 5.78e+00 bond pdb=" N LEU G 101 " pdb=" CA LEU G 101 " ideal model delta sigma weight residual 1.457 1.485 -0.029 1.24e-02 6.50e+03 5.39e+00 bond pdb=" N ILE E 153 " pdb=" CA ILE E 153 " ideal model delta sigma weight residual 1.460 1.492 -0.033 1.42e-02 4.96e+03 5.25e+00 ... (remaining 13421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 17513 2.52 - 5.04: 529 5.04 - 7.56: 111 7.56 - 10.08: 35 10.08 - 12.61: 2 Bond angle restraints: 18190 Sorted by residual: angle pdb=" C ARG C 161 " pdb=" N PRO C 162 " pdb=" CA PRO C 162 " ideal model delta sigma weight residual 120.38 129.92 -9.54 1.03e+00 9.43e-01 8.58e+01 angle pdb=" N ASP J 155 " pdb=" CA ASP J 155 " pdb=" C ASP J 155 " ideal model delta sigma weight residual 113.16 123.39 -10.23 1.24e+00 6.50e-01 6.81e+01 angle pdb=" N ILE B 49 " pdb=" CA ILE B 49 " pdb=" C ILE B 49 " ideal model delta sigma weight residual 113.71 107.23 6.48 9.50e-01 1.11e+00 4.65e+01 angle pdb=" N ILE H 49 " pdb=" CA ILE H 49 " pdb=" C ILE H 49 " ideal model delta sigma weight residual 112.96 106.70 6.26 1.00e+00 1.00e+00 3.92e+01 angle pdb=" N ASP C 155 " pdb=" CA ASP C 155 " pdb=" C ASP C 155 " ideal model delta sigma weight residual 112.90 119.73 -6.83 1.31e+00 5.83e-01 2.72e+01 ... (remaining 18185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 7617 15.25 - 30.51: 434 30.51 - 45.76: 126 45.76 - 61.02: 6 61.02 - 76.27: 11 Dihedral angle restraints: 8194 sinusoidal: 3419 harmonic: 4775 Sorted by residual: dihedral pdb=" CA MET B 63 " pdb=" C MET B 63 " pdb=" N SER B 64 " pdb=" CA SER B 64 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ILE G 153 " pdb=" C ILE G 153 " pdb=" N ASN G 154 " pdb=" CA ASN G 154 " ideal model delta harmonic sigma weight residual 180.00 -151.81 -28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA LEU C 253 " pdb=" C LEU C 253 " pdb=" N THR C 254 " pdb=" CA THR C 254 " ideal model delta harmonic sigma weight residual 180.00 -152.60 -27.40 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 8191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1505 0.062 - 0.125: 465 0.125 - 0.187: 97 0.187 - 0.249: 23 0.249 - 0.311: 3 Chirality restraints: 2093 Sorted by residual: chirality pdb=" CA ASP J 155 " pdb=" N ASP J 155 " pdb=" C ASP J 155 " pdb=" CB ASP J 155 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB ILE E 122 " pdb=" CA ILE E 122 " pdb=" CG1 ILE E 122 " pdb=" CG2 ILE E 122 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB THR D 82 " pdb=" CA THR D 82 " pdb=" OG1 THR D 82 " pdb=" CG2 THR D 82 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 2090 not shown) Planarity restraints: 2309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 161 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.31e+00 pdb=" C ARG C 161 " 0.053 2.00e-02 2.50e+03 pdb=" O ARG C 161 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO C 162 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS G 102 " 0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO G 103 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO G 103 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 103 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 90 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO J 91 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO J 91 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO J 91 " 0.035 5.00e-02 4.00e+02 ... (remaining 2306 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3811 2.83 - 3.34: 11556 3.34 - 3.86: 20186 3.86 - 4.38: 22074 4.38 - 4.90: 38001 Nonbonded interactions: 95628 Sorted by model distance: nonbonded pdb=" O GLN E 185 " pdb=" OG1 THR E 189 " model vdw 2.307 3.040 nonbonded pdb=" NH1 ARG E 221 " pdb=" OH TYR E 317 " model vdw 2.378 3.120 nonbonded pdb=" OG SER E 138 " pdb=" NE2 GLN C 114 " model vdw 2.387 3.120 nonbonded pdb=" O TYR G 281 " pdb=" OG1 THR G 285 " model vdw 2.393 3.040 nonbonded pdb=" OE1 GLN C 196 " pdb=" NE2 GLN G 184 " model vdw 2.398 3.120 ... (remaining 95623 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'C' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'E' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'G' and resid 75 through 336) } ncs_group { reference = (chain 'B' and resid 48 through 95) selection = (chain 'D' and resid 48 through 95) selection = (chain 'F' and resid 48 through 95) selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.910 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 : 0.007 0.071 13426 Z= 0.288 Angle : 1.128 12.605 18190 Z= 0.614 Chirality : 0.064 0.311 2093 Planarity : 0.007 0.072 2309 Dihedral : 11.132 76.271 5098 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.41 % Allowed : 6.26 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.21 (0.17), residues: 1594 helix: -2.99 (0.12), residues: 840 sheet: -0.94 (0.37), residues: 175 loop : -2.80 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 297 TYR 0.027 0.002 TYR G 79 PHE 0.030 0.003 PHE I 149 TRP 0.024 0.003 TRP E 255 HIS 0.008 0.002 HIS H 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.29 (13426) covalent geometry : angle 1.12833 / 0.61 (18190) hydrogen bonds : bond 0.15037 / 9.95 ( 644) hydrogen bonds : angle 6.44168 / 4.47 ( 1830) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 335 time to evaluate : 0.564 Fit side-chains REVERT: J 105 SER cc_start: 0.6994 (p) cc_final: 0.6773 (p) REVERT: J 133 VAL cc_start: 0.8541 (m) cc_final: 0.8327 (m) REVERT: E 104 ILE cc_start: 0.7994 (pt) cc_final: 0.7637 (mp) REVERT: E 243 MET cc_start: 0.8082 (tpt) cc_final: 0.7786 (tpp) REVERT: C 148 ASP cc_start: 0.8022 (p0) cc_final: 0.7746 (m-30) REVERT: A 161 ARG cc_start: 0.7858 (ppp80) cc_final: 0.7604 (mtt90) REVERT: A 165 ARG cc_start: 0.7133 (tpt170) cc_final: 0.6830 (mtm-85) REVERT: A 177 ASN cc_start: 0.8106 (t160) cc_final: 0.7587 (p0) REVERT: A 278 MET cc_start: 0.8349 (mtt) cc_final: 0.8115 (mtm) REVERT: B 83 LEU cc_start: 0.8030 (tp) cc_final: 0.7695 (mp) REVERT: L 115 LEU cc_start: 0.6485 (mt) cc_final: 0.6272 (mp) REVERT: I 120 ARG cc_start: 0.7935 (pmm150) cc_final: 0.7556 (mtt90) outliers start: 6 outliers final: 1 residues processed: 340 average time/residue: 0.1518 time to fit residues: 68.9368 Evaluate side-chains 174 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 116 GLN K 116 GLN E 159 HIS E 184 GLN E 194 GLN F 95 HIS C 81 ASN C 114 GLN A 98 GLN A 177 ASN ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 GLN H 95 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.111656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.099333 restraints weight = 35080.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.101073 restraints weight = 19271.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.102240 restraints weight = 12589.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.102988 restraints weight = 9360.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.103445 restraints weight = 7628.125| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13426 Z= 0.143 Angle : 0.668 8.359 18190 Z= 0.343 Chirality : 0.045 0.169 2093 Planarity : 0.005 0.061 2309 Dihedral : 5.591 25.009 1812 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.03 % Allowed : 13.00 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.20), residues: 1594 helix: -1.29 (0.16), residues: 846 sheet: -0.34 (0.39), residues: 161 loop : -2.21 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 96 TYR 0.015 0.001 TYR K 79 PHE 0.024 0.002 PHE L 111 TRP 0.012 0.001 TRP E 255 HIS 0.006 0.001 HIS H 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (13426) covalent geometry : angle 0.66777 / 0.34 (18190) hydrogen bonds : bond 0.04668 / 3.11 ( 644) hydrogen bonds : angle 4.63496 / 3.26 ( 1830) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.501 Fit side-chains REVERT: J 164 LYS cc_start: 0.2342 (mttp) cc_final: 0.1805 (mtpt) REVERT: E 104 ILE cc_start: 0.7956 (pt) cc_final: 0.7635 (mp) REVERT: E 301 LEU cc_start: 0.8907 (tp) cc_final: 0.8694 (mt) REVERT: F 91 LEU cc_start: 0.7396 (tt) cc_final: 0.7173 (pp) REVERT: C 164 LYS cc_start: 0.7644 (pmtt) cc_final: 0.6971 (ptmm) REVERT: C 278 MET cc_start: 0.8410 (mtm) cc_final: 0.8209 (mtp) REVERT: A 161 ARG cc_start: 0.7855 (ppp80) cc_final: 0.7535 (mtt90) REVERT: A 165 ARG cc_start: 0.6997 (tpt170) cc_final: 0.6791 (mtm-85) REVERT: A 177 ASN cc_start: 0.7995 (t0) cc_final: 0.7570 (p0) REVERT: B 83 LEU cc_start: 0.8097 (tp) cc_final: 0.7812 (mp) REVERT: L 122 ILE cc_start: 0.4556 (OUTLIER) cc_final: 0.4202 (tt) REVERT: L 158 TYR cc_start: 0.5647 (m-80) cc_final: 0.5375 (m-80) REVERT: I 120 ARG cc_start: 0.7881 (pmm150) cc_final: 0.7425 (mtt90) REVERT: G 104 ILE cc_start: 0.6315 (OUTLIER) cc_final: 0.6077 (tp) outliers start: 44 outliers final: 21 residues processed: 230 average time/residue: 0.1172 time to fit residues: 38.8612 Evaluate side-chains 178 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 153 ILE Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 290 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 153 optimal weight: 0.0030 chunk 20 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 122 optimal weight: 0.0980 chunk 80 optimal weight: 4.9990 chunk 36 optimal weight: 0.0980 chunk 95 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 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 = 0.3694 r_free = 0.3694 target = 0.112785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.100324 restraints weight = 35604.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.102110 restraints weight = 19626.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.103299 restraints weight = 12813.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.104078 restraints weight = 9503.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.104485 restraints weight = 7722.083| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13426 Z= 0.119 Angle : 0.624 9.119 18190 Z= 0.312 Chirality : 0.044 0.211 2093 Planarity : 0.005 0.082 2309 Dihedral : 5.036 24.260 1812 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.51 % Allowed : 15.20 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.21), residues: 1594 helix: -0.39 (0.18), residues: 845 sheet: 0.11 (0.40), residues: 162 loop : -1.96 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 161 TYR 0.010 0.001 TYR G 79 PHE 0.022 0.001 PHE L 111 TRP 0.006 0.001 TRP E 255 HIS 0.005 0.001 HIS L 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (13426) covalent geometry : angle 0.62414 / 0.31 (18190) hydrogen bonds : bond 0.03928 / 2.61 ( 644) hydrogen bonds : angle 4.17925 / 2.95 ( 1830) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 0.564 Fit side-chains REVERT: J 118 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7243 (tp30) REVERT: J 133 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8220 (m) REVERT: J 164 LYS cc_start: 0.2518 (mttp) cc_final: 0.1588 (mtpt) REVERT: E 104 ILE cc_start: 0.8032 (pt) cc_final: 0.7698 (mp) REVERT: E 182 LEU cc_start: 0.8297 (tp) cc_final: 0.8090 (mt) REVERT: F 91 LEU cc_start: 0.7513 (tt) cc_final: 0.7164 (pp) REVERT: C 164 LYS cc_start: 0.7639 (pmtt) cc_final: 0.6948 (ptmm) REVERT: A 161 ARG cc_start: 0.7952 (ppp80) cc_final: 0.7713 (mtt90) REVERT: A 165 ARG cc_start: 0.7021 (tpt170) cc_final: 0.6818 (mtm-85) REVERT: A 177 ASN cc_start: 0.7941 (t0) cc_final: 0.7427 (p0) REVERT: B 83 LEU cc_start: 0.8100 (tp) cc_final: 0.7852 (mp) REVERT: L 158 TYR cc_start: 0.5493 (m-80) cc_final: 0.5277 (m-80) REVERT: I 120 ARG cc_start: 0.7795 (pmm150) cc_final: 0.7315 (mtt90) outliers start: 51 outliers final: 22 residues processed: 213 average time/residue: 0.1101 time to fit residues: 34.6727 Evaluate side-chains 179 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.110743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.098282 restraints weight = 35352.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.100016 restraints weight = 19731.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.101172 restraints weight = 13023.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.101878 restraints weight = 9696.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.102442 restraints weight = 7949.281| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13426 Z= 0.152 Angle : 0.643 9.087 18190 Z= 0.320 Chirality : 0.045 0.297 2093 Planarity : 0.005 0.063 2309 Dihedral : 4.923 22.338 1812 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.85 % Allowed : 16.57 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.21), residues: 1594 helix: 0.02 (0.18), residues: 843 sheet: 0.06 (0.38), residues: 172 loop : -1.81 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 96 TYR 0.016 0.001 TYR C 299 PHE 0.021 0.002 PHE L 111 TRP 0.009 0.001 TRP C 256 HIS 0.005 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (13426) covalent geometry : angle 0.64275 / 0.32 (18190) hydrogen bonds : bond 0.03993 / 2.65 ( 644) hydrogen bonds : angle 4.19208 / 2.95 ( 1830) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 160 time to evaluate : 0.540 Fit side-chains REVERT: J 118 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7406 (tp30) REVERT: J 164 LYS cc_start: 0.2606 (mttp) cc_final: 0.1822 (mtpt) REVERT: E 104 ILE cc_start: 0.8047 (pt) cc_final: 0.7720 (mp) REVERT: F 91 LEU cc_start: 0.7408 (tt) cc_final: 0.7128 (pp) REVERT: C 164 LYS cc_start: 0.7684 (pmtt) cc_final: 0.7007 (ptmm) REVERT: A 165 ARG cc_start: 0.7038 (tpt170) cc_final: 0.6805 (mtm-85) REVERT: A 177 ASN cc_start: 0.7869 (t0) cc_final: 0.7399 (p0) REVERT: B 83 LEU cc_start: 0.8059 (tp) cc_final: 0.7844 (mp) REVERT: I 120 ARG cc_start: 0.7935 (pmm150) cc_final: 0.7360 (mtt90) REVERT: G 153 ILE cc_start: 0.5587 (OUTLIER) cc_final: 0.5350 (mt) outliers start: 56 outliers final: 35 residues processed: 197 average time/residue: 0.1099 time to fit residues: 31.9625 Evaluate side-chains 187 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 40 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 152 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 172 ASN E 339 GLN A 114 GLN ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.109995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.097568 restraints weight = 35500.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.099298 restraints weight = 19787.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.100470 restraints weight = 13052.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.101169 restraints weight = 9701.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.101697 restraints weight = 7953.510| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13426 Z= 0.159 Angle : 0.644 8.122 18190 Z= 0.320 Chirality : 0.045 0.262 2093 Planarity : 0.005 0.061 2309 Dihedral : 4.902 24.236 1811 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.54 % Allowed : 16.44 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.21), residues: 1594 helix: 0.19 (0.18), residues: 845 sheet: 0.11 (0.39), residues: 172 loop : -1.72 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 120 TYR 0.017 0.001 TYR C 268 PHE 0.022 0.002 PHE L 111 TRP 0.008 0.001 TRP C 256 HIS 0.005 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (13426) covalent geometry : angle 0.64404 / 0.32 (18190) hydrogen bonds : bond 0.04012 / 2.67 ( 644) hydrogen bonds : angle 4.19875 / 2.95 ( 1830) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 148 time to evaluate : 0.533 Fit side-chains REVERT: J 118 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7501 (tp30) REVERT: J 164 LYS cc_start: 0.2844 (mttp) cc_final: 0.1935 (mtpt) REVERT: K 94 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.5791 (mtm180) REVERT: E 104 ILE cc_start: 0.8047 (pt) cc_final: 0.7723 (mp) REVERT: F 91 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7121 (pp) REVERT: C 164 LYS cc_start: 0.7752 (pmtt) cc_final: 0.7079 (ptmm) REVERT: A 165 ARG cc_start: 0.7054 (tpt170) cc_final: 0.6772 (mtm-85) REVERT: A 177 ASN cc_start: 0.7918 (t0) cc_final: 0.7424 (p0) REVERT: B 83 LEU cc_start: 0.8069 (tp) cc_final: 0.7786 (mp) REVERT: I 120 ARG cc_start: 0.7958 (pmm150) cc_final: 0.7364 (mtt90) REVERT: G 153 ILE cc_start: 0.5743 (OUTLIER) cc_final: 0.5493 (mt) outliers start: 66 outliers final: 44 residues processed: 194 average time/residue: 0.1123 time to fit residues: 31.7738 Evaluate side-chains 191 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 87 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 chunk 127 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 14 optimal weight: 0.0770 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.111622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.099236 restraints weight = 35193.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.100989 restraints weight = 19470.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.102143 restraints weight = 12740.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.102865 restraints weight = 9515.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.103407 restraints weight = 7783.030| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13426 Z= 0.116 Angle : 0.601 7.433 18190 Z= 0.298 Chirality : 0.044 0.268 2093 Planarity : 0.004 0.064 2309 Dihedral : 4.622 21.909 1811 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.65 % Allowed : 17.88 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.22), residues: 1594 helix: 0.53 (0.19), residues: 847 sheet: 0.23 (0.39), residues: 172 loop : -1.63 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 161 TYR 0.015 0.001 TYR C 268 PHE 0.023 0.001 PHE L 149 TRP 0.006 0.001 TRP C 256 HIS 0.005 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (13426) covalent geometry : angle 0.60074 / 0.30 (18190) hydrogen bonds : bond 0.03635 / 2.41 ( 644) hydrogen bonds : angle 3.96220 / 2.78 ( 1830) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 162 time to evaluate : 0.568 Fit side-chains REVERT: J 118 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7535 (tp30) REVERT: J 164 LYS cc_start: 0.2658 (mttp) cc_final: 0.1809 (tttm) REVERT: E 104 ILE cc_start: 0.8035 (pt) cc_final: 0.7705 (mp) REVERT: E 301 LEU cc_start: 0.8789 (mt) cc_final: 0.8579 (mt) REVERT: E 339 GLN cc_start: 0.6715 (OUTLIER) cc_final: 0.6303 (tm-30) REVERT: F 91 LEU cc_start: 0.7414 (tt) cc_final: 0.7149 (pp) REVERT: C 164 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7003 (ptmm) REVERT: A 177 ASN cc_start: 0.7798 (t0) cc_final: 0.7395 (p0) REVERT: B 83 LEU cc_start: 0.8089 (tp) cc_final: 0.7803 (mp) REVERT: L 158 TYR cc_start: 0.5668 (m-80) cc_final: 0.5369 (m-80) REVERT: I 120 ARG cc_start: 0.7884 (pmm150) cc_final: 0.7302 (mtt90) REVERT: G 153 ILE cc_start: 0.5616 (OUTLIER) cc_final: 0.5332 (mt) outliers start: 53 outliers final: 37 residues processed: 193 average time/residue: 0.1149 time to fit residues: 32.5495 Evaluate side-chains 189 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 339 GLN Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 153 ILE Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 71 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 143 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 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 = 0.3617 r_free = 0.3617 target = 0.107513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.094925 restraints weight = 35725.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.096697 restraints weight = 19481.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.097896 restraints weight = 12702.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.098652 restraints weight = 9376.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.099181 restraints weight = 7628.293| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 13426 Z= 0.241 Angle : 0.718 10.073 18190 Z= 0.359 Chirality : 0.048 0.254 2093 Planarity : 0.005 0.061 2309 Dihedral : 5.044 24.066 1811 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.20 % Allowed : 17.88 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.22), residues: 1594 helix: 0.31 (0.18), residues: 845 sheet: 0.14 (0.39), residues: 172 loop : -1.66 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 161 TYR 0.020 0.002 TYR C 258 PHE 0.025 0.002 PHE B 88 TRP 0.010 0.001 TRP C 256 HIS 0.006 0.001 HIS E 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.24 (13426) covalent geometry : angle 0.71788 / 0.36 (18190) hydrogen bonds : bond 0.04384 / 2.90 ( 644) hydrogen bonds : angle 4.41377 / 3.10 ( 1830) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 137 time to evaluate : 0.553 Fit side-chains REVERT: J 95 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7770 (pm20) REVERT: J 118 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7718 (tp30) REVERT: E 104 ILE cc_start: 0.8075 (pt) cc_final: 0.7745 (mp) REVERT: E 143 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8774 (tt) REVERT: E 320 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8429 (tt) REVERT: C 164 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7015 (ptmm) REVERT: A 161 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7770 (mtt90) REVERT: A 177 ASN cc_start: 0.7924 (t0) cc_final: 0.7490 (p0) REVERT: A 269 PHE cc_start: 0.8285 (m-10) cc_final: 0.7958 (m-80) REVERT: B 83 LEU cc_start: 0.8136 (tp) cc_final: 0.7840 (mp) REVERT: L 158 TYR cc_start: 0.5691 (m-80) cc_final: 0.5356 (m-80) REVERT: I 120 ARG cc_start: 0.8042 (pmm150) cc_final: 0.7397 (mtt90) REVERT: G 153 ILE cc_start: 0.5823 (OUTLIER) cc_final: 0.5560 (mt) outliers start: 61 outliers final: 47 residues processed: 179 average time/residue: 0.1104 time to fit residues: 29.5585 Evaluate side-chains 187 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 134 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 107 SER Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 91 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 77 optimal weight: 0.0470 chunk 88 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.111561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.099228 restraints weight = 35111.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.100963 restraints weight = 19439.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.102131 restraints weight = 12809.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.102882 restraints weight = 9536.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.103371 restraints weight = 7783.216| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13426 Z= 0.110 Angle : 0.597 7.109 18190 Z= 0.296 Chirality : 0.043 0.266 2093 Planarity : 0.004 0.065 2309 Dihedral : 4.546 22.124 1811 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.16 % Allowed : 19.53 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.22), residues: 1594 helix: 0.77 (0.19), residues: 846 sheet: 0.20 (0.41), residues: 161 loop : -1.52 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 161 TYR 0.013 0.001 TYR C 268 PHE 0.027 0.001 PHE L 149 TRP 0.007 0.001 TRP C 260 HIS 0.005 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (13426) covalent geometry : angle 0.59689 / 0.30 (18190) hydrogen bonds : bond 0.03504 / 2.33 ( 644) hydrogen bonds : angle 3.92858 / 2.76 ( 1830) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 0.558 Fit side-chains REVERT: J 95 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7830 (pm20) REVERT: J 118 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7574 (tp30) REVERT: J 133 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8288 (m) REVERT: E 104 ILE cc_start: 0.8035 (pt) cc_final: 0.7708 (mp) REVERT: E 320 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8395 (tt) REVERT: E 339 GLN cc_start: 0.6657 (tm-30) cc_final: 0.6443 (tm-30) REVERT: C 164 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.6983 (ptmm) REVERT: A 177 ASN cc_start: 0.7840 (t0) cc_final: 0.7445 (p0) REVERT: B 83 LEU cc_start: 0.8106 (tp) cc_final: 0.7885 (mp) REVERT: L 158 TYR cc_start: 0.5433 (m-80) cc_final: 0.5030 (m-80) REVERT: I 120 ARG cc_start: 0.7893 (pmm150) cc_final: 0.7310 (mtt90) REVERT: G 153 ILE cc_start: 0.5657 (OUTLIER) cc_final: 0.5364 (mt) REVERT: H 67 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7475 (tt) outliers start: 46 outliers final: 33 residues processed: 185 average time/residue: 0.1004 time to fit residues: 28.3259 Evaluate side-chains 179 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 107 SER Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 77 optimal weight: 0.2980 chunk 56 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 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 = 0.3656 r_free = 0.3656 target = 0.110146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.097683 restraints weight = 35840.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.099420 restraints weight = 19947.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.100568 restraints weight = 13161.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.101328 restraints weight = 9847.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.101795 restraints weight = 8034.444| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13426 Z= 0.139 Angle : 0.629 12.675 18190 Z= 0.311 Chirality : 0.045 0.259 2093 Planarity : 0.004 0.064 2309 Dihedral : 4.558 22.423 1811 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.71 % Allowed : 19.12 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.22), residues: 1594 helix: 0.79 (0.18), residues: 847 sheet: 0.24 (0.42), residues: 161 loop : -1.49 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 161 TYR 0.013 0.001 TYR C 268 PHE 0.023 0.001 PHE L 149 TRP 0.008 0.001 TRP C 256 HIS 0.005 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (13426) covalent geometry : angle 0.62924 / 0.31 (18190) hydrogen bonds : bond 0.03691 / 2.45 ( 644) hydrogen bonds : angle 3.97141 / 2.79 ( 1830) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 139 time to evaluate : 0.512 Fit side-chains REVERT: J 95 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7737 (pm20) REVERT: J 118 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7654 (tp30) REVERT: E 104 ILE cc_start: 0.8037 (pt) cc_final: 0.7703 (mp) REVERT: E 143 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8838 (tt) REVERT: E 320 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8335 (tt) REVERT: E 339 GLN cc_start: 0.6685 (tm-30) cc_final: 0.6426 (tm-30) REVERT: C 164 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7009 (ptmm) REVERT: C 258 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.4728 (t80) REVERT: A 177 ASN cc_start: 0.7911 (t0) cc_final: 0.7490 (p0) REVERT: A 223 GLU cc_start: 0.8020 (tt0) cc_final: 0.7748 (tm-30) REVERT: B 83 LEU cc_start: 0.8047 (tp) cc_final: 0.7798 (mp) REVERT: L 158 TYR cc_start: 0.5483 (m-80) cc_final: 0.5180 (m-80) REVERT: I 120 ARG cc_start: 0.7940 (pmm150) cc_final: 0.7333 (mtt90) REVERT: G 81 ASN cc_start: 0.6468 (p0) cc_final: 0.6192 (p0) REVERT: G 138 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7607 (p) REVERT: G 153 ILE cc_start: 0.5599 (OUTLIER) cc_final: 0.5290 (mt) REVERT: G 284 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8014 (mtp) outliers start: 54 outliers final: 40 residues processed: 178 average time/residue: 0.0986 time to fit residues: 26.7546 Evaluate side-chains 183 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 107 SER Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 144 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 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 = 0.3681 r_free = 0.3681 target = 0.111745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.099239 restraints weight = 35623.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.100961 restraints weight = 19769.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.102109 restraints weight = 13070.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.102893 restraints weight = 9756.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.103322 restraints weight = 7985.438| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13426 Z= 0.111 Angle : 0.605 11.997 18190 Z= 0.298 Chirality : 0.043 0.260 2093 Planarity : 0.004 0.066 2309 Dihedral : 4.420 23.620 1811 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.44 % Allowed : 19.46 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.22), residues: 1594 helix: 0.98 (0.19), residues: 845 sheet: 0.33 (0.41), residues: 161 loop : -1.46 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 124 TYR 0.012 0.001 TYR C 268 PHE 0.026 0.001 PHE L 149 TRP 0.006 0.001 TRP C 256 HIS 0.005 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (13426) covalent geometry : angle 0.60504 / 0.30 (18190) hydrogen bonds : bond 0.03446 / 2.29 ( 644) hydrogen bonds : angle 3.82297 / 2.69 ( 1830) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 144 time to evaluate : 0.567 Fit side-chains REVERT: J 95 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7645 (pm20) REVERT: J 118 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7660 (tp30) REVERT: J 164 LYS cc_start: 0.2906 (mttp) cc_final: 0.2076 (tttm) REVERT: E 104 ILE cc_start: 0.8023 (pt) cc_final: 0.7682 (mp) REVERT: E 320 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8449 (tt) REVERT: C 164 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.6256 (tmtt) REVERT: C 258 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.4677 (t80) REVERT: A 123 ASP cc_start: 0.6942 (p0) cc_final: 0.6605 (p0) REVERT: A 177 ASN cc_start: 0.7846 (t0) cc_final: 0.7458 (p0) REVERT: A 223 GLU cc_start: 0.8021 (tt0) cc_final: 0.7749 (tm-30) REVERT: B 83 LEU cc_start: 0.8038 (tp) cc_final: 0.7792 (mp) REVERT: I 120 ARG cc_start: 0.7897 (pmm150) cc_final: 0.7306 (mtt90) REVERT: G 81 ASN cc_start: 0.6386 (p0) cc_final: 0.6159 (p0) REVERT: G 138 SER cc_start: 0.8032 (OUTLIER) cc_final: 0.7593 (p) REVERT: G 153 ILE cc_start: 0.5464 (OUTLIER) cc_final: 0.5141 (mt) REVERT: G 284 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7942 (mtp) REVERT: H 67 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7441 (tt) outliers start: 50 outliers final: 39 residues processed: 181 average time/residue: 0.1076 time to fit residues: 29.4847 Evaluate side-chains 186 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 107 SER Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 125 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 152 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 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 = 0.3657 r_free = 0.3657 target = 0.110185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.097689 restraints weight = 35551.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.099424 restraints weight = 19934.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.100556 restraints weight = 13112.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.101297 restraints weight = 9820.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.101827 restraints weight = 8047.875| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13426 Z= 0.143 Angle : 0.628 11.869 18190 Z= 0.311 Chirality : 0.044 0.252 2093 Planarity : 0.005 0.102 2309 Dihedral : 4.497 21.298 1811 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.58 % Allowed : 19.46 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.22), residues: 1594 helix: 0.93 (0.18), residues: 846 sheet: 0.35 (0.42), residues: 161 loop : -1.41 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 161 TYR 0.011 0.001 TYR C 258 PHE 0.023 0.002 PHE L 149 TRP 0.008 0.001 TRP C 256 HIS 0.005 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (13426) covalent geometry : angle 0.62826 / 0.31 (18190) hydrogen bonds : bond 0.03656 / 2.43 ( 644) hydrogen bonds : angle 3.91418 / 2.75 ( 1830) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2283.11 seconds wall clock time: 40 minutes 2.65 seconds (2402.65 seconds total)