Starting phenix.real_space_refine on Sun Sep 13 03:04:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6o58_0625/09_2026/6o58_0625.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o58_0625/09_2026/6o58_0625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6o58_0625/09_2026/6o58_0625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o58_0625/09_2026/6o58_0625.map" model { file = "/net/cci-nas-00/data/ceres_data/6o58_0625/09_2026/6o58_0625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o58_0625/09_2026/6o58_0625.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6o58_0625/09_2026/6o58_0625.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6o58_0625/09_2026/6o58_0625.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 72 5.16 5 C 13272 2.51 5 N 3526 2.21 5 O 3682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 20554 Number of models: 1 Model: "" Number of chains: 18 Chain: "K" 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: "L" 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: "O" 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: "P" 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: "M" 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: "N" 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: "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: "I" 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: "J" 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: "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: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" 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: 4.65, per 1000 atoms: 0.23 Number of scatterers: 20554 At special positions: 0 Unit cell: (113.4, 215.88, 134.4, 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 2 19.99 S 72 16.00 O 3682 8.00 N 3526 7.00 C 13272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 844.2 milliseconds 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4816 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 16 sheets defined 64.8% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'K' and resid 91 through 94 removed outlier: 3.924A pdb=" N ARG K 94 " --> pdb=" O PRO K 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 91 through 94' Processing helix chain 'K' and resid 107 through 119 removed outlier: 3.707A pdb=" N LEU K 112 " --> pdb=" O VAL K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 145 Processing helix chain 'K' and resid 172 through 189 removed outlier: 3.620A pdb=" N VAL K 179 " --> pdb=" O THR K 175 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU K 182 " --> pdb=" O ASP K 178 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN K 185 " --> pdb=" O THR K 181 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR K 189 " --> pdb=" O GLN K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 215 removed outlier: 3.699A pdb=" N GLU K 208 " --> pdb=" O ILE K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 217 through 257 removed outlier: 3.627A pdb=" N ARG K 221 " --> pdb=" O LEU K 217 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU K 234 " --> pdb=" O LYS K 230 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL K 235 " --> pdb=" O ARG K 231 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU K 240 " --> pdb=" O LEU K 236 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET K 243 " --> pdb=" O GLY K 239 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY K 248 " --> pdb=" O ALA K 244 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU K 250 " --> pdb=" O GLN K 246 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG K 252 " --> pdb=" O GLY K 248 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU K 253 " --> pdb=" O ILE K 249 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP K 255 " --> pdb=" O ALA K 251 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TRP K 256 " --> pdb=" O ARG K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 286 removed outlier: 3.586A pdb=" N MET K 263 " --> pdb=" O SER K 259 " (cutoff:3.500A) Proline residue: K 265 - end of helix removed outlier: 3.566A pdb=" N PHE K 269 " --> pdb=" O PRO K 265 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA K 275 " --> pdb=" O THR K 271 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR K 279 " --> pdb=" O ALA K 275 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE K 282 " --> pdb=" O MET K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 310 removed outlier: 3.719A pdb=" N ARG K 295 " --> pdb=" O TYR K 291 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASP K 296 " --> pdb=" O PRO K 292 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG K 297 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS K 308 " --> pdb=" O HIS K 304 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS K 309 " --> pdb=" O LYS K 305 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 335 removed outlier: 3.534A pdb=" N GLN K 319 " --> pdb=" O GLU K 315 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP K 322 " --> pdb=" O ASN K 318 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA K 323 " --> pdb=" O GLN K 319 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE K 324 " --> pdb=" O LEU K 320 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA K 325 " --> pdb=" O LYS K 321 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG K 335 " --> pdb=" O LEU K 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 94 Proline residue: L 76 - end of helix removed outlier: 3.985A pdb=" N SER L 85 " --> pdb=" O GLY L 81 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN L 87 " --> pdb=" O LEU L 83 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE L 88 " --> pdb=" O ILE L 84 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU L 91 " --> pdb=" O ASN L 87 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 119 removed outlier: 3.993A pdb=" N ARG O 113 " --> pdb=" O GLY O 109 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU O 118 " --> pdb=" O GLN O 114 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP O 119 " --> pdb=" O LEU O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 188 Processing helix chain 'O' and resid 188 through 256 removed outlier: 3.698A pdb=" N ILE O 192 " --> pdb=" O THR O 188 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU O 193 " --> pdb=" O THR O 189 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLN O 194 " --> pdb=" O LEU O 190 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU O 197 " --> pdb=" O GLU O 193 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG O 201 " --> pdb=" O LEU O 197 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU O 202 " --> pdb=" O ASN O 198 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU O 205 " --> pdb=" O ARG O 201 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU O 210 " --> pdb=" O ARG O 206 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN O 213 " --> pdb=" O ASP O 209 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA O 215 " --> pdb=" O LYS O 211 " (cutoff:3.500A) Proline residue: O 216 - end of helix removed outlier: 3.691A pdb=" N GLU O 223 " --> pdb=" O LYS O 219 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG O 231 " --> pdb=" O LYS O 227 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU O 240 " --> pdb=" O LEU O 236 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE O 247 " --> pdb=" O MET O 243 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU O 253 " --> pdb=" O ILE O 249 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR O 254 " --> pdb=" O LEU O 250 " (cutoff:3.500A) Processing helix chain 'O' and resid 259 through 286 Proline residue: O 265 - end of helix removed outlier: 3.888A pdb=" N PHE O 269 " --> pdb=" O PRO O 265 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE O 270 " --> pdb=" O VAL O 266 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR O 271 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE O 282 " --> pdb=" O MET O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 309 removed outlier: 3.876A pdb=" N ASP O 296 " --> pdb=" O PRO O 292 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU O 300 " --> pdb=" O ASP O 296 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU O 301 " --> pdb=" O ARG O 297 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS O 305 " --> pdb=" O LEU O 301 " (cutoff:3.500A) Processing helix chain 'O' and resid 313 through 336 removed outlier: 3.570A pdb=" N TYR O 317 " --> pdb=" O ASP O 313 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN O 319 " --> pdb=" O GLU O 315 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG O 333 " --> pdb=" O MET O 329 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU O 334 " --> pdb=" O ASP O 330 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG O 335 " --> pdb=" O LEU O 331 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP O 336 " --> pdb=" O LYS O 332 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 95 removed outlier: 3.514A pdb=" N ARG P 69 " --> pdb=" O PHE P 65 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER P 72 " --> pdb=" O LEU P 68 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE P 73 " --> pdb=" O ARG P 69 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE P 75 " --> pdb=" O PHE P 71 " (cutoff:3.500A) Proline residue: P 76 - end of helix removed outlier: 3.609A pdb=" N THR P 82 " --> pdb=" O LEU P 78 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN P 87 " --> pdb=" O LEU P 83 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU P 91 " --> pdb=" O ASN P 87 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU P 92 " --> pdb=" O PHE P 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 119 removed outlier: 3.586A pdb=" N ARG M 113 " --> pdb=" O GLY M 109 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP M 119 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 144 Processing helix chain 'M' and resid 169 through 190 removed outlier: 3.510A pdb=" N ALA M 173 " --> pdb=" O SER M 169 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA M 174 " --> pdb=" O HIS M 170 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR M 175 " --> pdb=" O GLU M 171 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN M 184 " --> pdb=" O LYS M 180 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU M 190 " --> pdb=" O LEU M 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 246 removed outlier: 3.612A pdb=" N LYS M 199 " --> pdb=" O HIS M 195 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU M 200 " --> pdb=" O GLN M 196 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU M 208 " --> pdb=" O ILE M 204 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN M 213 " --> pdb=" O ASP M 209 " (cutoff:3.500A) Proline residue: M 216 - end of helix removed outlier: 3.721A pdb=" N LYS M 219 " --> pdb=" O ALA M 215 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS M 227 " --> pdb=" O GLU M 223 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL M 235 " --> pdb=" O ARG M 231 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA M 241 " --> pdb=" O TRP M 237 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN M 246 " --> pdb=" O TYR M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 254 removed outlier: 4.013A pdb=" N LEU M 250 " --> pdb=" O GLN M 246 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA M 251 " --> pdb=" O PHE M 247 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG M 252 " --> pdb=" O GLY M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 285 removed outlier: 4.060A pdb=" N THR M 267 " --> pdb=" O MET M 263 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA M 275 " --> pdb=" O THR M 271 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET M 276 " --> pdb=" O TYR M 272 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE M 282 " --> pdb=" O MET M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 290 through 310 removed outlier: 3.583A pdb=" N ARG M 297 " --> pdb=" O GLU M 293 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU M 300 " --> pdb=" O ASP M 296 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS M 304 " --> pdb=" O LEU M 300 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS M 305 " --> pdb=" O LEU M 301 " (cutoff:3.500A) Processing helix chain 'M' and resid 314 through 333 removed outlier: 3.772A pdb=" N LYS M 321 " --> pdb=" O TYR M 317 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 96 Proline residue: N 76 - end of helix removed outlier: 3.754A pdb=" N TYR N 79 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL N 80 " --> pdb=" O PRO N 76 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY N 81 " --> pdb=" O PHE N 77 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER N 85 " --> pdb=" O GLY N 81 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS N 86 " --> pdb=" O THR N 82 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU N 94 " --> pdb=" O ALA N 90 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS N 95 " --> pdb=" O LEU N 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 117 removed outlier: 3.994A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 145 removed outlier: 3.501A pdb=" N LEU G 144 " --> pdb=" O GLY G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 188 Processing helix chain 'G' and resid 188 through 256 removed outlier: 3.697A pdb=" N ILE G 192 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU G 193 " --> pdb=" O THR G 189 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLN G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG G 201 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU G 202 " --> pdb=" O ASN G 198 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLU G 205 " --> pdb=" O ARG G 201 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU G 210 " --> pdb=" O ARG G 206 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN G 213 " --> pdb=" O ASP G 209 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) Proline residue: G 216 - end of helix removed outlier: 3.689A pdb=" N GLU G 223 " --> pdb=" O LYS G 219 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU G 240 " --> pdb=" O LEU G 236 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE G 247 " --> pdb=" O MET G 243 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU G 253 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TRP G 255 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 286 Proline residue: G 265 - end of helix removed outlier: 3.822A pdb=" N PHE G 269 " --> pdb=" O PRO G 265 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE G 270 " --> pdb=" O VAL G 266 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE G 282 " --> pdb=" O MET G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 309 removed outlier: 3.897A pdb=" N ASP G 296 " --> pdb=" O PRO G 292 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU G 300 " --> pdb=" O ASP G 296 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU G 301 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS G 305 " --> pdb=" O LEU G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 336 removed outlier: 3.570A pdb=" N TYR G 317 " --> pdb=" O ASP G 313 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN G 319 " --> pdb=" O GLU G 315 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG G 333 " --> pdb=" O MET G 329 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU G 334 " --> pdb=" O ASP G 330 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG G 335 " --> pdb=" O LEU G 331 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP G 336 " --> pdb=" O LYS G 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 95 removed outlier: 3.508A pdb=" N ARG H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE H 75 " --> pdb=" O PHE H 71 " (cutoff:3.500A) Proline residue: H 76 - end of helix removed outlier: 3.863A pdb=" N SER H 85 " --> pdb=" O GLY H 81 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU H 91 " --> pdb=" O ASN H 87 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU H 92 " --> pdb=" O PHE H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 119 removed outlier: 4.122A pdb=" N ARG I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP I 119 " --> pdb=" O LEU I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 145 Processing helix chain 'I' and resid 172 through 191 removed outlier: 3.721A pdb=" N ASP I 178 " --> pdb=" O ALA I 174 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU I 190 " --> pdb=" O LEU I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 213 removed outlier: 3.866A pdb=" N HIS I 195 " --> pdb=" O CYS I 191 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU I 197 " --> pdb=" O GLU I 193 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU I 202 " --> pdb=" O ASN I 198 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU I 208 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP I 209 " --> pdb=" O GLU I 205 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU I 210 " --> pdb=" O ARG I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 250 removed outlier: 4.223A pdb=" N LEU I 217 " --> pdb=" O GLN I 213 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS I 219 " --> pdb=" O ALA I 215 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL I 220 " --> pdb=" O PRO I 216 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG I 221 " --> pdb=" O LEU I 217 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG I 231 " --> pdb=" O LYS I 227 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU I 234 " --> pdb=" O LYS I 230 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET I 243 " --> pdb=" O GLY I 239 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN I 246 " --> pdb=" O TYR I 242 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE I 247 " --> pdb=" O MET I 243 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU I 250 " --> pdb=" O GLN I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 256 Processing helix chain 'I' and resid 259 through 285 removed outlier: 3.565A pdb=" N MET I 263 " --> pdb=" O SER I 259 " (cutoff:3.500A) Proline residue: I 265 - end of helix removed outlier: 3.811A pdb=" N THR I 271 " --> pdb=" O THR I 267 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET I 276 " --> pdb=" O TYR I 272 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR I 281 " --> pdb=" O ALA I 277 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE I 282 " --> pdb=" O MET I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 293 Processing helix chain 'I' and resid 294 through 310 removed outlier: 3.985A pdb=" N LEU I 300 " --> pdb=" O ASP I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 340 removed outlier: 3.994A pdb=" N TYR I 317 " --> pdb=" O ASP I 313 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN I 319 " --> pdb=" O GLU I 315 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE I 324 " --> pdb=" O LEU I 320 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP I 336 " --> pdb=" O LYS I 332 " (cutoff:3.500A) Proline residue: I 337 - end of helix Processing helix chain 'J' and resid 67 through 75 removed outlier: 3.596A pdb=" N ILE J 75 " --> pdb=" O PHE J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 96 removed outlier: 3.764A pdb=" N TYR J 79 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU J 91 " --> pdb=" O ASN J 87 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS J 95 " --> pdb=" O LEU J 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 94 removed outlier: 3.699A 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: 3.686A pdb=" N LEU C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 172 through 189 removed outlier: 3.628A pdb=" N VAL C 179 " --> pdb=" O THR C 175 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 215 removed outlier: 3.693A pdb=" N GLU C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 257 removed outlier: 3.628A pdb=" N ARG C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU C 234 " --> pdb=" O LYS C 230 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET C 243 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 250 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU C 253 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TRP C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TRP C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 286 removed outlier: 3.592A pdb=" N MET C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) Proline residue: C 265 - end of helix removed outlier: 3.553A pdb=" N PHE C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE C 282 " --> pdb=" O MET C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 310 removed outlier: 3.717A pdb=" N ARG C 295 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASP C 296 " --> pdb=" O PRO C 292 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS C 308 " --> pdb=" O HIS C 304 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 335 removed outlier: 3.533A pdb=" N GLN C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA C 323 " --> pdb=" O GLN C 319 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA C 325 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 94 Proline residue: D 76 - end of helix removed outlier: 3.953A pdb=" N SER D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE D 88 " --> pdb=" O ILE D 84 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 119 removed outlier: 4.109A pdb=" N ARG A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 172 through 191 removed outlier: 3.718A pdb=" N ASP A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 213 removed outlier: 3.777A pdb=" N HIS A 195 " --> pdb=" O CYS A 191 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 250 removed outlier: 4.372A pdb=" N LEU A 217 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 246 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 263 through 285 removed outlier: 3.784A pdb=" N THR A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 282 " --> pdb=" O MET A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 310 removed outlier: 3.800A pdb=" N ARG A 295 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 334 removed outlier: 3.992A pdb=" N TYR A 317 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.901A pdb=" N LEU A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 75 through 96 removed outlier: 3.735A pdb=" N TYR B 79 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 119 removed outlier: 3.620A pdb=" N ARG E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.611A 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: 3.593A pdb=" N ALA E 174 " --> pdb=" O HIS E 170 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN E 184 " --> pdb=" O LYS E 180 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU E 190 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 246 removed outlier: 3.643A pdb=" N LYS E 199 " --> pdb=" O HIS E 195 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU E 200 " --> pdb=" O GLN E 196 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG E 201 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU E 208 " --> pdb=" O ILE E 204 " (cutoff:3.500A) Proline residue: E 216 - end of helix removed outlier: 3.659A pdb=" N LYS E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS E 227 " --> pdb=" O GLU E 223 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN E 246 " --> pdb=" O TYR E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 254 removed outlier: 4.044A pdb=" N LEU E 250 " --> pdb=" O GLN E 246 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA E 251 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG E 252 " --> pdb=" O GLY E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 285 removed outlier: 3.613A pdb=" N THR E 267 " --> pdb=" O MET E 263 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE E 270 " --> pdb=" O VAL E 266 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR E 271 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA E 275 " --> pdb=" O THR E 271 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET E 276 " --> pdb=" O TYR E 272 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE E 282 " --> pdb=" O MET E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 310 removed outlier: 3.583A pdb=" N ARG E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU E 300 " --> pdb=" O ASP E 296 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS E 305 " --> pdb=" O LEU E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 333 removed outlier: 3.726A pdb=" N LYS E 321 " --> pdb=" O TYR E 317 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA E 325 " --> pdb=" O LYS E 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 96 Proline residue: F 76 - end of helix removed outlier: 3.756A pdb=" N TYR F 79 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL F 80 " --> pdb=" O PRO F 76 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY F 81 " --> pdb=" O PHE F 77 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 76 through 80 Processing sheet with id=AA2, first strand: chain 'K' and resid 126 through 128 removed outlier: 3.585A pdb=" N PHE K 149 " --> pdb=" O VAL K 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 134 through 135 removed outlier: 3.796A pdb=" N THR I 76 " --> pdb=" O SER I 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 77 through 78 removed outlier: 3.614A pdb=" N VAL O 78 " --> pdb=" O VAL O 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'O' and resid 125 through 128 removed outlier: 3.588A pdb=" N PHE O 149 " --> pdb=" O VAL O 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'O' and resid 134 through 135 removed outlier: 6.982A pdb=" N ARG O 134 " --> pdb=" O GLN M 98 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N THR M 100 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR M 76 " --> pdb=" O SER M 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 126 through 127 Processing sheet with id=AA8, first strand: chain 'G' and resid 76 through 78 removed outlier: 4.634A pdb=" N THR G 76 " --> pdb=" O SER G 87 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER G 87 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL G 78 " --> pdb=" O VAL G 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 125 through 128 removed outlier: 3.597A pdb=" N PHE G 149 " --> pdb=" O VAL G 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 134 through 135 removed outlier: 6.982A pdb=" N ARG G 134 " --> pdb=" O GLN E 98 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N THR E 100 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR E 76 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 126 through 128 Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 80 Processing sheet with id=AB4, first strand: chain 'C' and resid 126 through 128 Processing sheet with id=AB5, first strand: chain 'C' and resid 134 through 135 removed outlier: 3.844A pdb=" N THR A 76 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AB7, first strand: chain 'E' and resid 126 through 127 1106 hydrogen bonds defined for protein. 3207 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 2.26 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: 6551 1.34 - 1.46: 4567 1.46 - 1.58: 9726 1.58 - 1.70: 0 1.70 - 1.82: 128 Bond restraints: 20972 Sorted by residual: bond pdb=" C ILE J 75 " pdb=" N PRO J 76 " ideal model delta sigma weight residual 1.336 1.400 -0.064 1.20e-02 6.94e+03 2.85e+01 bond pdb=" N GLU A 257 " pdb=" CA GLU A 257 " ideal model delta sigma weight residual 1.455 1.492 -0.036 1.09e-02 8.42e+03 1.12e+01 bond pdb=" C ALA M 215 " pdb=" N PRO M 216 " ideal model delta sigma weight residual 1.336 1.373 -0.037 1.20e-02 6.94e+03 9.44e+00 bond pdb=" N GLU M 257 " pdb=" CA GLU M 257 " ideal model delta sigma weight residual 1.455 1.496 -0.042 1.37e-02 5.33e+03 9.33e+00 bond pdb=" N GLU E 257 " pdb=" CA GLU E 257 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.37e-02 5.33e+03 9.08e+00 ... (remaining 20967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 27488 2.57 - 5.15: 687 5.15 - 7.72: 164 7.72 - 10.30: 48 10.30 - 12.87: 1 Bond angle restraints: 28388 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 120.38 112.08 8.30 1.03e+00 9.43e-01 6.49e+01 angle pdb=" CA TYR A 258 " pdb=" C TYR A 258 " pdb=" O TYR A 258 " ideal model delta sigma weight residual 120.51 111.83 8.68 1.43e+00 4.89e-01 3.69e+01 angle pdb=" N PRO K 162 " pdb=" CA PRO K 162 " pdb=" C PRO K 162 " ideal model delta sigma weight residual 110.70 117.89 -7.19 1.22e+00 6.72e-01 3.47e+01 angle pdb=" C ILE E 153 " pdb=" N ASN E 154 " pdb=" CA ASN E 154 " ideal model delta sigma weight residual 121.19 130.43 -9.24 1.59e+00 3.96e-01 3.37e+01 angle pdb=" CA PRO K 162 " pdb=" C PRO K 162 " pdb=" N PRO K 163 " ideal model delta sigma weight residual 117.93 124.63 -6.70 1.20e+00 6.94e-01 3.11e+01 ... (remaining 28383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.31: 11810 15.31 - 30.63: 685 30.63 - 45.94: 229 45.94 - 61.25: 11 61.25 - 76.57: 21 Dihedral angle restraints: 12756 sinusoidal: 5326 harmonic: 7430 Sorted by residual: dihedral pdb=" CA ARG K 161 " pdb=" C ARG K 161 " pdb=" N PRO K 162 " pdb=" CA PRO K 162 " ideal model delta harmonic sigma weight residual 180.00 150.06 29.94 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ILE E 153 " pdb=" C ILE E 153 " pdb=" N ASN E 154 " pdb=" CA ASN E 154 " ideal model delta harmonic sigma weight residual -180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ILE K 153 " pdb=" C ILE K 153 " pdb=" N ASN K 154 " pdb=" CA ASN K 154 " ideal model delta harmonic sigma weight residual -180.00 -151.82 -28.18 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 12753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2480 0.064 - 0.128: 639 0.128 - 0.192: 94 0.192 - 0.256: 16 0.256 - 0.321: 5 Chirality restraints: 3234 Sorted by residual: chirality pdb=" CB ILE K 86 " pdb=" CA ILE K 86 " pdb=" CG1 ILE K 86 " pdb=" CG2 ILE K 86 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB ILE M 122 " pdb=" CA ILE M 122 " pdb=" CG1 ILE M 122 " pdb=" CG2 ILE M 122 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.43e+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 2.35 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 3231 not shown) Planarity restraints: 3578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG K 161 " 0.069 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO K 162 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO K 162 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO K 162 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 258 " 0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C TYR A 258 " -0.058 2.00e-02 2.50e+03 pdb=" O TYR A 258 " 0.021 2.00e-02 2.50e+03 pdb=" N SER A 259 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP E 256 " 0.015 2.00e-02 2.50e+03 2.89e-02 8.36e+00 pdb=" C TRP E 256 " -0.050 2.00e-02 2.50e+03 pdb=" O TRP E 256 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU E 257 " 0.017 2.00e-02 2.50e+03 ... (remaining 3575 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4955 2.80 - 3.32: 18351 3.32 - 3.85: 32305 3.85 - 4.37: 35037 4.37 - 4.90: 60006 Nonbonded interactions: 150654 Sorted by model distance: nonbonded pdb=" OG SER A 259 " pdb=" N TRP A 260 " model vdw 2.271 3.120 nonbonded pdb=" O GLN E 185 " pdb=" OG1 THR E 189 " model vdw 2.282 3.040 nonbonded pdb=" O GLN M 185 " pdb=" OG1 THR M 189 " model vdw 2.285 3.040 nonbonded pdb=" OG SER E 225 " pdb=" OH TYR E 299 " model vdw 2.289 3.040 nonbonded pdb=" OE1 GLU E 218 " pdb=" OH TYR E 317 " model vdw 2.297 3.040 ... (remaining 150649 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: 0.01 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' selection = (chain 'I' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'K' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'M' and (resid 75 through 164 or resid 177 through 336)) selection = chain 'O' } 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' selection = (chain 'J' and resid 48 through 95) selection = (chain 'L' and resid 48 through 95) selection = (chain 'N' and resid 48 through 95) selection = chain 'P' } 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: 1.670 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: 0.000 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 17.570 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.005 0.077 20972 Z= 0.243 Angle : 1.074 12.875 28388 Z= 0.571 Chirality : 0.058 0.321 3234 Planarity : 0.007 0.102 3578 Dihedral : 11.586 76.565 7940 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.48 % Favored : 95.48 % Rotamer: Outliers : 0.31 % Allowed : 7.17 % Favored : 92.51 % 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: -3.97 (0.13), residues: 2476 helix: -2.63 (0.09), residues: 1498 sheet: -1.49 (0.34), residues: 196 loop : -2.49 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 297 TYR 0.023 0.002 TYR O 79 PHE 0.024 0.002 PHE C 312 TRP 0.019 0.002 TRP K 260 HIS 0.009 0.001 HIS E 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.24 (20972) covalent geometry : angle 1.07378 / 0.57 (28388) hydrogen bonds : bond 0.13883 / 9.09 ( 1106) hydrogen bonds : angle 6.04981 / 4.25 ( 3207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 394 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 243 MET cc_start: 0.8268 (mtm) cc_final: 0.7995 (ptm) REVERT: K 276 MET cc_start: 0.8299 (ttm) cc_final: 0.8063 (tpp) REVERT: K 329 MET cc_start: 0.8833 (tmm) cc_final: 0.8474 (tmm) REVERT: O 311 ARG cc_start: 0.6625 (mpt-90) cc_final: 0.6346 (ttp80) REVERT: O 316 LYS cc_start: 0.8452 (mtpm) cc_final: 0.7806 (tppt) REVERT: P 84 ILE cc_start: 0.7203 (pp) cc_final: 0.6736 (mm) REVERT: M 284 MET cc_start: 0.7910 (mtt) cc_final: 0.7668 (mtm) REVERT: G 263 MET cc_start: 0.7390 (ttt) cc_final: 0.7160 (tpt) REVERT: G 311 ARG cc_start: 0.6629 (mpt-90) cc_final: 0.6345 (ttp80) REVERT: G 316 LYS cc_start: 0.8464 (mtpm) cc_final: 0.7820 (tppt) REVERT: I 243 MET cc_start: 0.7349 (ttm) cc_final: 0.6808 (mtt) REVERT: C 276 MET cc_start: 0.8352 (ttm) cc_final: 0.8108 (tpp) REVERT: C 329 MET cc_start: 0.8804 (tmm) cc_final: 0.8442 (tmm) REVERT: A 243 MET cc_start: 0.7408 (ttm) cc_final: 0.6846 (mtt) REVERT: B 70 VAL cc_start: 0.8841 (t) cc_final: 0.8536 (p) REVERT: E 284 MET cc_start: 0.7912 (mtt) cc_final: 0.7669 (mtm) outliers start: 7 outliers final: 2 residues processed: 401 average time/residue: 0.1836 time to fit residues: 105.0682 Evaluate side-chains 164 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 258 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 114 GLN K 177 ASN K 194 GLN O 177 ASN O 196 GLN M 184 GLN N 87 ASN G 177 ASN G 196 GLN I 80 GLN I 177 ASN C 114 GLN C 159 HIS C 177 ASN C 194 GLN C 304 HIS A 80 GLN A 177 ASN E 184 GLN E 246 GLN E 339 GLN F 87 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.074479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.065239 restraints weight = 109526.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.066375 restraints weight = 62909.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.067139 restraints weight = 41900.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.067608 restraints weight = 30984.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.067977 restraints weight = 25281.108| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 20972 Z= 0.178 Angle : 0.690 8.785 28388 Z= 0.355 Chirality : 0.043 0.147 3234 Planarity : 0.006 0.103 3578 Dihedral : 5.657 71.172 2811 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.44 % Rotamer: Outliers : 2.85 % Allowed : 12.57 % Favored : 84.58 % 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: -1.88 (0.16), residues: 2476 helix: -0.82 (0.12), residues: 1510 sheet: -0.82 (0.34), residues: 216 loop : -1.97 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 297 TYR 0.021 0.002 TYR N 79 PHE 0.022 0.002 PHE M 312 TRP 0.011 0.001 TRP A 256 HIS 0.007 0.001 HIS K 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (20972) covalent geometry : angle 0.69011 / 0.35 (28388) hydrogen bonds : bond 0.04453 / 2.93 ( 1106) hydrogen bonds : angle 4.72524 / 3.29 ( 3207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 162 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 329 MET cc_start: 0.8748 (tmm) cc_final: 0.8538 (tmm) REVERT: O 311 ARG cc_start: 0.6727 (mpt-90) cc_final: 0.6296 (ttp80) REVERT: O 316 LYS cc_start: 0.8465 (mtpm) cc_final: 0.7784 (tppt) REVERT: G 311 ARG cc_start: 0.6662 (mpt-90) cc_final: 0.6269 (ttp80) REVERT: G 316 LYS cc_start: 0.8443 (mtpm) cc_final: 0.7792 (tppt) REVERT: C 276 MET cc_start: 0.8489 (ttm) cc_final: 0.8280 (tpp) REVERT: B 70 VAL cc_start: 0.8821 (t) cc_final: 0.8466 (p) outliers start: 64 outliers final: 23 residues processed: 215 average time/residue: 0.1337 time to fit residues: 46.7941 Evaluate side-chains 151 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain O residue 177 ASN Chi-restraints excluded: chain O residue 249 ILE Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 77 PHE Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain F residue 61 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 201 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 224 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 194 GLN O 184 GLN ** M 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 HIS G 184 GLN C 159 HIS C 194 GLN E 184 GLN E 246 GLN F 95 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.072515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.063228 restraints weight = 111834.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.064319 restraints weight = 65302.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.065027 restraints weight = 44064.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.065530 restraints weight = 33296.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.065798 restraints weight = 26981.765| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 20972 Z= 0.243 Angle : 0.732 9.074 28388 Z= 0.374 Chirality : 0.045 0.175 3234 Planarity : 0.006 0.099 3578 Dihedral : 5.413 28.020 2806 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.65 % Allowed : 14.75 % Favored : 81.60 % 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: -1.25 (0.16), residues: 2476 helix: -0.25 (0.13), residues: 1516 sheet: -0.82 (0.37), residues: 196 loop : -1.80 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 201 TYR 0.024 0.002 TYR K 268 PHE 0.022 0.002 PHE M 312 TRP 0.009 0.002 TRP I 237 HIS 0.011 0.002 HIS K 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 (20972) covalent geometry : angle 0.73207 / 0.37 (28388) hydrogen bonds : bond 0.04429 / 2.94 ( 1106) hydrogen bonds : angle 4.75998 / 3.31 ( 3207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 123 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 276 MET cc_start: 0.8329 (tpp) cc_final: 0.7637 (tpt) REVERT: K 329 MET cc_start: 0.8744 (tmm) cc_final: 0.8492 (tmm) REVERT: O 311 ARG cc_start: 0.6860 (mpt-90) cc_final: 0.6356 (ttp80) REVERT: O 316 LYS cc_start: 0.8589 (mtpm) cc_final: 0.7732 (tppt) REVERT: G 311 ARG cc_start: 0.6829 (mpt-90) cc_final: 0.6341 (ttp80) REVERT: G 316 LYS cc_start: 0.8571 (mtpm) cc_final: 0.7726 (tppt) REVERT: G 329 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7679 (tpt) REVERT: I 145 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8546 (mm) REVERT: I 243 MET cc_start: 0.7455 (ttt) cc_final: 0.6087 (ttt) REVERT: C 243 MET cc_start: 0.8610 (ptm) cc_final: 0.8047 (ptm) REVERT: C 276 MET cc_start: 0.8480 (ttm) cc_final: 0.8129 (tpt) REVERT: C 329 MET cc_start: 0.8745 (tmm) cc_final: 0.8498 (tmm) REVERT: A 145 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8575 (mm) REVERT: A 243 MET cc_start: 0.7408 (ttt) cc_final: 0.6013 (ttt) REVERT: B 70 VAL cc_start: 0.8797 (t) cc_final: 0.8470 (p) outliers start: 82 outliers final: 38 residues processed: 190 average time/residue: 0.1202 time to fit residues: 38.7819 Evaluate side-chains 158 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 191 CYS Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 172 ASN Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 191 CYS Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 61 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 167 optimal weight: 0.0270 chunk 191 optimal weight: 7.9990 chunk 112 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 60 optimal weight: 0.2980 chunk 11 optimal weight: 6.9990 overall best weight: 3.0644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 159 HIS K 194 GLN O 184 GLN ** M 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 246 GLN G 184 GLN C 159 HIS C 194 GLN A 195 HIS E 246 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.074046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.064743 restraints weight = 110564.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.065856 restraints weight = 64277.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.066608 restraints weight = 43271.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.067059 restraints weight = 32302.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.067422 restraints weight = 26470.084| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20972 Z= 0.131 Angle : 0.607 8.311 28388 Z= 0.305 Chirality : 0.041 0.211 3234 Planarity : 0.005 0.088 3578 Dihedral : 4.887 27.558 2806 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.90 % Allowed : 16.00 % Favored : 81.11 % 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: -0.45 (0.17), residues: 2476 helix: 0.43 (0.13), residues: 1516 sheet: -0.56 (0.38), residues: 196 loop : -1.57 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 297 TYR 0.016 0.001 TYR K 268 PHE 0.021 0.001 PHE M 312 TRP 0.010 0.001 TRP C 256 HIS 0.008 0.001 HIS K 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (20972) covalent geometry : angle 0.60716 / 0.30 (28388) hydrogen bonds : bond 0.03698 / 2.44 ( 1106) hydrogen bonds : angle 4.21301 / 2.94 ( 3207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 124 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 243 MET cc_start: 0.8424 (mtp) cc_final: 0.8034 (ptp) REVERT: K 276 MET cc_start: 0.8397 (tpp) cc_final: 0.7542 (tpt) REVERT: K 329 MET cc_start: 0.8705 (tmm) cc_final: 0.8498 (tmm) REVERT: O 311 ARG cc_start: 0.6758 (mpt-90) cc_final: 0.6317 (ttp80) REVERT: O 316 LYS cc_start: 0.8583 (mtpm) cc_final: 0.7772 (tppt) REVERT: M 300 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8678 (tt) REVERT: N 84 ILE cc_start: 0.7522 (tp) cc_final: 0.7298 (tp) REVERT: G 276 MET cc_start: 0.7644 (tpp) cc_final: 0.7279 (tpp) REVERT: G 311 ARG cc_start: 0.6745 (mpt-90) cc_final: 0.6311 (ttp80) REVERT: G 316 LYS cc_start: 0.8570 (mtpm) cc_final: 0.7773 (tppt) REVERT: G 329 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.6595 (tpt) REVERT: I 243 MET cc_start: 0.7215 (ttt) cc_final: 0.6085 (ttt) REVERT: C 243 MET cc_start: 0.8598 (ptm) cc_final: 0.8048 (ptm) REVERT: B 70 VAL cc_start: 0.8810 (t) cc_final: 0.8523 (p) outliers start: 65 outliers final: 30 residues processed: 180 average time/residue: 0.1281 time to fit residues: 38.2768 Evaluate side-chains 147 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 159 HIS Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain N residue 51 THR Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 191 CYS Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 230 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 188 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 218 optimal weight: 1.9990 chunk 240 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 158 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 194 GLN O 184 GLN ** M 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN C 159 HIS C 194 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.074123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.064810 restraints weight = 109919.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.065912 restraints weight = 64132.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.066650 restraints weight = 43195.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.067143 restraints weight = 32420.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.067432 restraints weight = 26392.170| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 20972 Z= 0.124 Angle : 0.596 7.757 28388 Z= 0.298 Chirality : 0.041 0.218 3234 Planarity : 0.004 0.089 3578 Dihedral : 4.696 28.182 2806 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.67 % Allowed : 16.89 % Favored : 80.44 % 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: -0.13 (0.17), residues: 2476 helix: 0.70 (0.14), residues: 1530 sheet: -0.46 (0.40), residues: 196 loop : -1.50 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 297 TYR 0.013 0.001 TYR F 79 PHE 0.021 0.001 PHE M 312 TRP 0.009 0.001 TRP C 256 HIS 0.016 0.001 HIS K 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (20972) covalent geometry : angle 0.59551 / 0.30 (28388) hydrogen bonds : bond 0.03593 / 2.37 ( 1106) hydrogen bonds : angle 4.08558 / 2.86 ( 3207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 121 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 243 MET cc_start: 0.8384 (mtp) cc_final: 0.8019 (ptp) REVERT: K 276 MET cc_start: 0.8406 (tpp) cc_final: 0.7529 (tpt) REVERT: K 329 MET cc_start: 0.8707 (tmm) cc_final: 0.8482 (tmm) REVERT: O 311 ARG cc_start: 0.6791 (mpt-90) cc_final: 0.6326 (ttp80) REVERT: O 316 LYS cc_start: 0.8604 (mtpm) cc_final: 0.7791 (tppt) REVERT: M 300 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8666 (tt) REVERT: G 311 ARG cc_start: 0.6771 (mpt-90) cc_final: 0.6315 (ttp80) REVERT: G 316 LYS cc_start: 0.8588 (mtpm) cc_final: 0.7788 (tppt) REVERT: I 243 MET cc_start: 0.7164 (ttt) cc_final: 0.6076 (ttt) REVERT: J 70 VAL cc_start: 0.8881 (t) cc_final: 0.8577 (p) REVERT: C 243 MET cc_start: 0.8524 (ptm) cc_final: 0.8318 (ptp) REVERT: B 70 VAL cc_start: 0.8874 (t) cc_final: 0.8544 (p) outliers start: 60 outliers final: 36 residues processed: 179 average time/residue: 0.1242 time to fit residues: 37.6143 Evaluate side-chains 149 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 191 CYS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain O residue 253 LEU Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 199 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 147 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 229 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 159 HIS K 194 GLN M 159 HIS M 184 GLN C 159 HIS C 194 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.073765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.064525 restraints weight = 109399.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.065587 restraints weight = 63088.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.066350 restraints weight = 42567.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.066866 restraints weight = 31911.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.067167 restraints weight = 25833.559| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20972 Z= 0.135 Angle : 0.593 7.740 28388 Z= 0.298 Chirality : 0.041 0.226 3234 Planarity : 0.004 0.089 3578 Dihedral : 4.599 28.047 2806 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.76 % Allowed : 18.14 % Favored : 79.10 % 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: 0.06 (0.18), residues: 2476 helix: 0.85 (0.14), residues: 1530 sheet: -0.39 (0.40), residues: 196 loop : -1.44 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 134 TYR 0.014 0.001 TYR M 268 PHE 0.021 0.001 PHE M 312 TRP 0.009 0.001 TRP C 256 HIS 0.007 0.001 HIS K 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (20972) covalent geometry : angle 0.59338 / 0.30 (28388) hydrogen bonds : bond 0.03573 / 2.36 ( 1106) hydrogen bonds : angle 4.07513 / 2.85 ( 3207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 115 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: K 243 MET cc_start: 0.8409 (mtp) cc_final: 0.8020 (ptp) REVERT: K 276 MET cc_start: 0.8448 (tpp) cc_final: 0.7590 (tpt) REVERT: K 329 MET cc_start: 0.8722 (tmm) cc_final: 0.8479 (tmm) REVERT: O 311 ARG cc_start: 0.6838 (mpt-90) cc_final: 0.6338 (ttp80) REVERT: M 300 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8706 (tt) REVERT: M 329 MET cc_start: 0.8708 (tpp) cc_final: 0.8426 (tpp) REVERT: G 311 ARG cc_start: 0.6810 (mpt-90) cc_final: 0.6324 (ttp80) REVERT: G 316 LYS cc_start: 0.8606 (mtpm) cc_final: 0.7774 (tppt) REVERT: G 329 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.6582 (tpt) REVERT: I 243 MET cc_start: 0.7112 (ttt) cc_final: 0.5915 (ttt) REVERT: J 70 VAL cc_start: 0.8897 (t) cc_final: 0.8603 (p) REVERT: B 70 VAL cc_start: 0.8965 (t) cc_final: 0.8615 (p) outliers start: 62 outliers final: 42 residues processed: 169 average time/residue: 0.1302 time to fit residues: 36.5600 Evaluate side-chains 154 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 110 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 159 HIS Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 191 CYS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain O residue 138 SER Chi-restraints excluded: chain O residue 253 LEU Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 88 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 235 optimal weight: 7.9990 chunk 238 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 159 HIS M 304 HIS C 159 HIS ** A 346 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 = 0.3589 r_free = 0.3589 target = 0.072570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.063492 restraints weight = 111447.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.064536 restraints weight = 65600.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.065235 restraints weight = 44571.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.065713 restraints weight = 33667.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.066036 restraints weight = 27460.154| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 20972 Z= 0.195 Angle : 0.651 11.395 28388 Z= 0.326 Chirality : 0.043 0.214 3234 Planarity : 0.005 0.088 3578 Dihedral : 4.727 27.977 2806 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.90 % Allowed : 18.98 % Favored : 78.12 % 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: -0.01 (0.17), residues: 2476 helix: 0.80 (0.14), residues: 1526 sheet: -0.42 (0.40), residues: 196 loop : -1.46 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 124 TYR 0.015 0.002 TYR G 317 PHE 0.021 0.002 PHE M 312 TRP 0.009 0.001 TRP C 256 HIS 0.012 0.001 HIS K 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (20972) covalent geometry : angle 0.65129 / 0.33 (28388) hydrogen bonds : bond 0.03825 / 2.54 ( 1106) hydrogen bonds : angle 4.27393 / 2.98 ( 3207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 106 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: K 243 MET cc_start: 0.8422 (mtp) cc_final: 0.8048 (ptp) REVERT: K 276 MET cc_start: 0.8397 (tpp) cc_final: 0.7601 (tpt) REVERT: K 329 MET cc_start: 0.8709 (tmm) cc_final: 0.8484 (tmm) REVERT: O 311 ARG cc_start: 0.6773 (mpt-90) cc_final: 0.6283 (ttp80) REVERT: O 329 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.6468 (tpt) REVERT: G 311 ARG cc_start: 0.6756 (mpt-90) cc_final: 0.6271 (ttp80) REVERT: G 329 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.6608 (tpt) REVERT: I 243 MET cc_start: 0.7185 (ttt) cc_final: 0.5977 (ttt) REVERT: B 70 VAL cc_start: 0.8977 (t) cc_final: 0.8639 (p) outliers start: 65 outliers final: 45 residues processed: 160 average time/residue: 0.1302 time to fit residues: 34.7336 Evaluate side-chains 152 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 159 HIS Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 191 CYS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain O residue 138 SER Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain O residue 329 MET Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 174 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 229 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.072403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.064107 restraints weight = 112374.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.064632 restraints weight = 60602.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.064985 restraints weight = 43832.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.065139 restraints weight = 38497.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.065221 restraints weight = 34175.302| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 20972 Z= 0.184 Angle : 0.656 11.907 28388 Z= 0.326 Chirality : 0.043 0.220 3234 Planarity : 0.005 0.088 3578 Dihedral : 4.782 28.306 2806 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.90 % Allowed : 19.30 % Favored : 77.81 % 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 (0.17), residues: 2476 helix: 0.77 (0.13), residues: 1530 sheet: -0.37 (0.40), residues: 196 loop : -1.43 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 94 TYR 0.014 0.002 TYR O 317 PHE 0.021 0.002 PHE M 312 TRP 0.011 0.001 TRP C 256 HIS 0.022 0.001 HIS K 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (20972) covalent geometry : angle 0.65566 / 0.33 (28388) hydrogen bonds : bond 0.03850 / 2.56 ( 1106) hydrogen bonds : angle 4.28471 / 2.99 ( 3207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 108 time to evaluate : 0.890 Fit side-chains REVERT: K 243 MET cc_start: 0.8484 (mtp) cc_final: 0.8020 (ptp) REVERT: K 276 MET cc_start: 0.8429 (tpp) cc_final: 0.7621 (tpt) REVERT: K 329 MET cc_start: 0.8738 (tmm) cc_final: 0.8503 (tmm) REVERT: O 311 ARG cc_start: 0.7111 (mpt-90) cc_final: 0.6470 (ttp80) REVERT: O 329 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.6427 (tpt) REVERT: M 329 MET cc_start: 0.8719 (tpp) cc_final: 0.8383 (tpp) REVERT: G 311 ARG cc_start: 0.7077 (mpt-90) cc_final: 0.6452 (ttp80) REVERT: G 329 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.6590 (tpt) REVERT: I 243 MET cc_start: 0.7229 (ttt) cc_final: 0.5974 (ttt) REVERT: B 70 VAL cc_start: 0.8955 (t) cc_final: 0.8631 (p) REVERT: E 205 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7732 (tm-30) outliers start: 65 outliers final: 45 residues processed: 164 average time/residue: 0.1213 time to fit residues: 33.9888 Evaluate side-chains 152 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 191 CYS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain O residue 138 SER Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain O residue 329 MET Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 177 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 124 optimal weight: 0.5980 chunk 126 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 159 HIS ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.073159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.064129 restraints weight = 111790.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.065286 restraints weight = 67153.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.066256 restraints weight = 40609.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.066338 restraints weight = 28127.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.066347 restraints weight = 27535.193| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 20972 Z= 0.137 Angle : 0.618 12.707 28388 Z= 0.303 Chirality : 0.041 0.231 3234 Planarity : 0.004 0.088 3578 Dihedral : 4.612 29.009 2806 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.27 % Allowed : 20.05 % Favored : 77.67 % 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: 0.24 (0.18), residues: 2476 helix: 0.98 (0.14), residues: 1524 sheet: -0.33 (0.39), residues: 202 loop : -1.30 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 94 TYR 0.012 0.001 TYR N 79 PHE 0.021 0.001 PHE M 312 TRP 0.013 0.001 TRP C 256 HIS 0.003 0.001 HIS M 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (20972) covalent geometry : angle 0.61810 / 0.30 (28388) hydrogen bonds : bond 0.03568 / 2.36 ( 1106) hydrogen bonds : angle 4.10030 / 2.87 ( 3207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 114 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: K 243 MET cc_start: 0.8357 (mtp) cc_final: 0.7876 (ptp) REVERT: K 276 MET cc_start: 0.8424 (tpp) cc_final: 0.7513 (tpt) REVERT: K 329 MET cc_start: 0.8738 (tmm) cc_final: 0.8504 (tmm) REVERT: O 150 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7756 (ptpp) REVERT: O 311 ARG cc_start: 0.6979 (mpt-90) cc_final: 0.6405 (ttp80) REVERT: O 329 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.6399 (tpt) REVERT: M 329 MET cc_start: 0.8707 (tpp) cc_final: 0.8401 (tpp) REVERT: G 311 ARG cc_start: 0.6949 (mpt-90) cc_final: 0.6388 (ttp80) REVERT: G 329 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.6601 (tpt) REVERT: I 243 MET cc_start: 0.7186 (ttt) cc_final: 0.6017 (ttt) REVERT: J 63 MET cc_start: 0.7622 (pmm) cc_final: 0.6933 (pmm) REVERT: A 276 MET cc_start: 0.7882 (mmm) cc_final: 0.7608 (mmt) REVERT: B 70 VAL cc_start: 0.8975 (t) cc_final: 0.8683 (p) REVERT: E 205 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7633 (tm-30) REVERT: E 329 MET cc_start: 0.8672 (tpp) cc_final: 0.8365 (tpp) outliers start: 51 outliers final: 42 residues processed: 156 average time/residue: 0.1304 time to fit residues: 33.9860 Evaluate side-chains 156 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 111 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 159 HIS Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 191 CYS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain O residue 138 SER Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain O residue 329 MET Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 98 optimal weight: 6.9990 chunk 6 optimal weight: 0.0770 chunk 115 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 218 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 chunk 241 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 overall best weight: 3.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 159 HIS ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.073108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.064125 restraints weight = 111661.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.065351 restraints weight = 67619.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.066217 restraints weight = 39997.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.066362 restraints weight = 28739.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.066372 restraints weight = 26467.860| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20972 Z= 0.135 Angle : 0.630 14.518 28388 Z= 0.306 Chirality : 0.041 0.233 3234 Planarity : 0.004 0.087 3578 Dihedral : 4.577 29.223 2806 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.32 % Allowed : 20.10 % Favored : 77.58 % 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: 0.32 (0.18), residues: 2476 helix: 1.03 (0.14), residues: 1524 sheet: -0.25 (0.40), residues: 202 loop : -1.27 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 94 TYR 0.013 0.001 TYR F 79 PHE 0.021 0.001 PHE M 312 TRP 0.013 0.001 TRP C 256 HIS 0.004 0.001 HIS K 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (20972) covalent geometry : angle 0.63005 / 0.31 (28388) hydrogen bonds : bond 0.03549 / 2.35 ( 1106) hydrogen bonds : angle 4.07799 / 2.86 ( 3207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 112 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: K 243 MET cc_start: 0.8341 (mtp) cc_final: 0.7871 (ptp) REVERT: K 276 MET cc_start: 0.8423 (tpp) cc_final: 0.7516 (tpt) REVERT: K 329 MET cc_start: 0.8738 (tmm) cc_final: 0.8506 (tmm) REVERT: O 150 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7732 (ptpp) REVERT: O 311 ARG cc_start: 0.6958 (mpt-90) cc_final: 0.6386 (ttp80) REVERT: O 329 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.6391 (tpt) REVERT: M 329 MET cc_start: 0.8702 (tpp) cc_final: 0.8411 (tpp) REVERT: G 311 ARG cc_start: 0.6941 (mpt-90) cc_final: 0.6376 (ttp80) REVERT: G 329 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.6581 (tpt) REVERT: I 243 MET cc_start: 0.7183 (ttt) cc_final: 0.6006 (ttt) REVERT: B 70 VAL cc_start: 0.8985 (t) cc_final: 0.8671 (p) REVERT: E 205 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7666 (tm-30) REVERT: E 329 MET cc_start: 0.8695 (tpp) cc_final: 0.8391 (tpp) outliers start: 52 outliers final: 44 residues processed: 155 average time/residue: 0.1300 time to fit residues: 34.0944 Evaluate side-chains 159 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 112 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 159 HIS Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 191 CYS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain O residue 138 SER Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain O residue 253 LEU Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain O residue 329 MET Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 211 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 237 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 159 HIS ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.073068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.064160 restraints weight = 111615.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.065548 restraints weight = 63426.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.066136 restraints weight = 35868.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.066270 restraints weight = 29058.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.066317 restraints weight = 26510.750| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20972 Z= 0.142 Angle : 0.621 12.484 28388 Z= 0.305 Chirality : 0.041 0.228 3234 Planarity : 0.004 0.087 3578 Dihedral : 4.568 29.256 2806 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.45 % Allowed : 19.96 % Favored : 77.58 % 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: 0.35 (0.18), residues: 2476 helix: 1.05 (0.14), residues: 1524 sheet: -0.25 (0.39), residues: 202 loop : -1.24 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 94 TYR 0.014 0.001 TYR N 79 PHE 0.021 0.001 PHE M 312 TRP 0.013 0.001 TRP C 256 HIS 0.004 0.001 HIS M 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (20972) covalent geometry : angle 0.62067 / 0.31 (28388) hydrogen bonds : bond 0.03556 / 2.35 ( 1106) hydrogen bonds : angle 4.09371 / 2.87 ( 3207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3259.64 seconds wall clock time: 57 minutes 18.87 seconds (3438.87 seconds total)