Starting phenix.real_space_refine on Fri Feb 6 12:51:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9efm_47976/02_2026/9efm_47976_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9efm_47976/02_2026/9efm_47976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9efm_47976/02_2026/9efm_47976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9efm_47976/02_2026/9efm_47976.map" model { file = "/net/cci-nas-00/data/ceres_data/9efm_47976/02_2026/9efm_47976_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9efm_47976/02_2026/9efm_47976_neut.cif" } resolution = 3.16 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= 0.006 sd= 0.023 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 Zn 3 6.06 5 S 141 5.16 5 C 15852 2.51 5 N 4271 2.21 5 O 4684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24951 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3271 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 8, 'TRANS': 400} Chain breaks: 1 Chain: "B" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3342 Classifications: {'peptide': 408} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 396} Chain breaks: 1 Chain: "C" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3216 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain: "D" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3241 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 9, 'TRANS': 395} Chain: "E" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2433 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "F" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2227 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 269} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1687 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain: "H" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1374 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain breaks: 1 Chain: "I" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 599 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "J" Number of atoms: 2813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2813 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 335} Chain breaks: 1 Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 745 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24495 SG CYS K 53 76.427 72.065 77.027 1.00 61.37 S ATOM 24518 SG CYS K 56 75.258 68.302 76.931 1.00 74.02 S ATOM 24602 SG CYS K 68 74.634 70.480 74.088 1.00 61.06 S ATOM 24409 SG CYS K 42 79.154 78.609 72.761 1.00 25.75 S ATOM 24428 SG CYS K 45 81.166 75.855 74.583 1.00 33.80 S ATOM 24723 SG CYS K 83 77.803 76.944 75.969 1.00 33.26 S ATOM 24652 SG CYS K 75 73.467 89.469 68.580 1.00 18.68 S ATOM 24819 SG CYS K 94 75.732 88.801 71.739 1.00 20.08 S Time building chain proxies: 5.17, per 1000 atoms: 0.21 Number of scatterers: 24951 At special positions: 0 Unit cell: (136.757, 171.995, 207.233, 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) Zn 3 29.99 S 141 16.00 O 4684 8.00 N 4271 7.00 C 15852 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" ND1 HIS K 82 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 68 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 53 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 56 " pdb=" ZN K 202 " pdb="ZN ZN K 202 " - pdb=" ND1 HIS K 80 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 83 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 45 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 42 " pdb=" ZN K 203 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 94 " pdb="ZN ZN K 203 " - pdb=" ND1 HIS K 77 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 75 " Number of angles added : 6 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5962 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 13 sheets defined 65.8% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 52 through 55 removed outlier: 4.032A pdb=" N MET A 55 " --> pdb=" O SER A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 55' Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 70 through 79 removed outlier: 3.887A pdb=" N ALA A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.763A pdb=" N ILE A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 removed outlier: 4.202A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 155 removed outlier: 4.023A pdb=" N ALA A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR A 134 " --> pdb=" O TRP A 130 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU A 139 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A 141 " --> pdb=" O LYS A 137 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 176 removed outlier: 3.709A pdb=" N HIS A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 176 " --> pdb=" O TYR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 191 removed outlier: 3.668A pdb=" N LEU A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 188 " --> pdb=" O CYS A 184 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.790A pdb=" N ASN A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET A 201 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASN A 204 " --> pdb=" O ASN A 200 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 205 " --> pdb=" O MET A 201 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 206 " --> pdb=" O CYS A 202 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 210 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 228 removed outlier: 3.523A pdb=" N SER A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA A 225 " --> pdb=" O TYR A 221 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 5.430A pdb=" N ARG A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 260 removed outlier: 3.777A pdb=" N LYS A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 255 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 269 Processing helix chain 'A' and resid 274 through 278 removed outlier: 4.009A pdb=" N HIS A 277 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.503A pdb=" N ILE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 316 through 323 removed outlier: 3.878A pdb=" N LEU A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 323 " --> pdb=" O PHE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.723A pdb=" N ARG A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 353 removed outlier: 3.648A pdb=" N CYS A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 379 removed outlier: 4.763A pdb=" N ARG A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 393 Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.840A pdb=" N GLN A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 410 " --> pdb=" O GLN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 462 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.657A pdb=" N SER B 39 " --> pdb=" O GLN B 35 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B 40 " --> pdb=" O TYR B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 removed outlier: 4.032A pdb=" N LYS B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 82 removed outlier: 3.857A pdb=" N PHE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 87 through 96 removed outlier: 3.685A pdb=" N GLN B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 119 removed outlier: 3.652A pdb=" N SER B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 124 through 143 removed outlier: 3.679A pdb=" N GLU B 133 " --> pdb=" O GLN B 129 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 162 removed outlier: 3.581A pdb=" N PHE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 177 removed outlier: 3.964A pdb=" N ILE B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 208 removed outlier: 3.516A pdb=" N ILE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA B 207 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 223 removed outlier: 3.647A pdb=" N ALA B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N HIS B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 Processing helix chain 'B' and resid 236 through 249 Processing helix chain 'B' and resid 251 through 268 removed outlier: 3.774A pdb=" N HIS B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 286 removed outlier: 3.793A pdb=" N CYS B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LYS B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.844A pdb=" N SER B 296 " --> pdb=" O PRO B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 removed outlier: 4.177A pdb=" N ASN B 304 " --> pdb=" O PRO B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 322 through 333 removed outlier: 3.611A pdb=" N PHE B 326 " --> pdb=" O ASP B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 345 Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' Processing helix chain 'B' and resid 352 through 363 Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 418 through 440 removed outlier: 3.791A pdb=" N THR B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 436 " --> pdb=" O ASN B 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 16 removed outlier: 3.552A pdb=" N ASN C 10 " --> pdb=" O GLU C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 29 removed outlier: 3.509A pdb=" N ILE C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 38 No H-bonds generated for 'chain 'C' and resid 36 through 38' Processing helix chain 'C' and resid 39 through 47 removed outlier: 4.201A pdb=" N THR C 44 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N VAL C 45 " --> pdb=" O HIS C 41 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY C 47 " --> pdb=" O ASP C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 63 removed outlier: 3.836A pdb=" N LEU C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL C 61 " --> pdb=" O GLY C 57 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 88 removed outlier: 3.579A pdb=" N GLN C 80 " --> pdb=" O THR C 76 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 86 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 97 removed outlier: 3.754A pdb=" N THR C 97 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 114 removed outlier: 3.519A pdb=" N GLY C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 132 Processing helix chain 'C' and resid 141 through 152 Processing helix chain 'C' and resid 155 through 162 Proline residue: C 160 - end of helix Processing helix chain 'C' and resid 177 through 195 removed outlier: 4.047A pdb=" N PHE C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY C 189 " --> pdb=" O TYR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 removed outlier: 3.727A pdb=" N TYR C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 235 removed outlier: 3.748A pdb=" N GLU C 222 " --> pdb=" O HIS C 218 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER C 223 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 224 " --> pdb=" O MET C 220 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LYS C 226 " --> pdb=" O GLU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 252 removed outlier: 4.190A pdb=" N GLY C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 4.031A pdb=" N LEU C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 267 Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 295 through 311 removed outlier: 3.650A pdb=" N TYR C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 326 removed outlier: 4.006A pdb=" N SER C 324 " --> pdb=" O GLN C 320 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG C 325 " --> pdb=" O ASP C 321 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL C 326 " --> pdb=" O MET C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 345 Processing helix chain 'C' and resid 369 through 399 removed outlier: 3.597A pdb=" N ILE C 397 " --> pdb=" O MET C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 406 removed outlier: 4.080A pdb=" N GLN C 405 " --> pdb=" O PRO C 401 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS C 406 " --> pdb=" O GLN C 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 14 removed outlier: 3.783A pdb=" N LEU D 9 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA D 10 " --> pdb=" O ARG D 6 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 24 through 34 removed outlier: 4.130A pdb=" N GLN D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 29 " --> pdb=" O LYS D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 51 removed outlier: 3.869A pdb=" N LEU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA D 44 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 71 Processing helix chain 'D' and resid 77 through 93 removed outlier: 4.208A pdb=" N GLU D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 101 through 117 Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.934A pdb=" N ILE D 130 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 Processing helix chain 'D' and resid 160 through 172 Processing helix chain 'D' and resid 180 through 198 Processing helix chain 'D' and resid 200 through 212 Processing helix chain 'D' and resid 218 through 236 Processing helix chain 'D' and resid 239 through 252 removed outlier: 3.705A pdb=" N ASP D 252 " --> pdb=" O THR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 259 removed outlier: 3.573A pdb=" N LEU D 258 " --> pdb=" O CYS D 255 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ALA D 259 " --> pdb=" O GLN D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 removed outlier: 3.560A pdb=" N LEU D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 283 removed outlier: 3.810A pdb=" N ALA D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.867A pdb=" N ALA D 291 " --> pdb=" O HIS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 313 removed outlier: 5.045A pdb=" N ILE D 305 " --> pdb=" O ASP D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 328 removed outlier: 3.739A pdb=" N LEU D 327 " --> pdb=" O GLU D 323 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 343 removed outlier: 3.728A pdb=" N LYS D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 392 Processing helix chain 'D' and resid 392 through 403 removed outlier: 3.552A pdb=" N GLN D 398 " --> pdb=" O GLU D 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 18 removed outlier: 4.047A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA E 16 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN E 17 " --> pdb=" O TRP E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 removed outlier: 4.197A pdb=" N ILE E 28 " --> pdb=" O ILE E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 43 Processing helix chain 'E' and resid 59 through 72 Processing helix chain 'E' and resid 112 through 127 removed outlier: 3.812A pdb=" N ALA E 118 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL E 127 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 162 removed outlier: 3.754A pdb=" N PHE E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 206 through 214 Processing helix chain 'E' and resid 217 through 219 No H-bonds generated for 'chain 'E' and resid 217 through 219' Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 246 through 251 Processing helix chain 'E' and resid 258 through 282 removed outlier: 4.157A pdb=" N ARG E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 329 removed outlier: 3.677A pdb=" N LYS E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 63 Processing helix chain 'F' and resid 101 through 114 removed outlier: 3.989A pdb=" N TYR F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 144 removed outlier: 3.668A pdb=" N GLU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 206 Processing helix chain 'F' and resid 216 through 248 removed outlier: 4.458A pdb=" N ILE F 222 " --> pdb=" O ALA F 218 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 266 Processing helix chain 'F' and resid 272 through 311 removed outlier: 4.389A pdb=" N GLY F 293 " --> pdb=" O MET F 289 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N THR F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL F 311 " --> pdb=" O ASN F 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 19 removed outlier: 3.723A pdb=" N PHE G 15 " --> pdb=" O LEU G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 37 Processing helix chain 'G' and resid 44 through 48 removed outlier: 3.545A pdb=" N GLU G 48 " --> pdb=" O GLU G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 54 removed outlier: 3.566A pdb=" N GLN G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 72 removed outlier: 3.570A pdb=" N LEU G 64 " --> pdb=" O ASN G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 81 removed outlier: 4.048A pdb=" N ASN G 81 " --> pdb=" O ASP G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 108 Processing helix chain 'G' and resid 113 through 120 Processing helix chain 'G' and resid 124 through 138 Processing helix chain 'G' and resid 166 through 220 removed outlier: 3.513A pdb=" N ILE G 216 " --> pdb=" O GLU G 212 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU G 220 " --> pdb=" O ILE G 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 26 removed outlier: 3.653A pdb=" N LEU H 16 " --> pdb=" O SER H 12 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP H 18 " --> pdb=" O LYS H 14 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN H 19 " --> pdb=" O LYS H 15 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS H 20 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU H 21 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN H 22 " --> pdb=" O ASP H 18 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLN H 23 " --> pdb=" O GLN H 19 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU H 24 " --> pdb=" O CYS H 20 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU H 25 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU H 26 " --> pdb=" O ASN H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 47 Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 61 through 68 Processing helix chain 'H' and resid 68 through 83 removed outlier: 4.055A pdb=" N GLY H 72 " --> pdb=" O ASN H 68 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 96 removed outlier: 4.027A pdb=" N TYR H 90 " --> pdb=" O PHE H 86 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR H 91 " --> pdb=" O PRO H 87 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN H 94 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N HIS H 96 " --> pdb=" O THR H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 124 removed outlier: 3.509A pdb=" N MET H 106 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'H' and resid 142 through 150 removed outlier: 3.547A pdb=" N LYS H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE H 148 " --> pdb=" O ALA H 144 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU H 149 " --> pdb=" O VAL H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 208 Processing helix chain 'I' and resid 22 through 34 Processing helix chain 'I' and resid 37 through 41 Processing helix chain 'J' and resid 418 through 431 Processing helix chain 'J' and resid 438 through 454 removed outlier: 3.609A pdb=" N GLU J 443 " --> pdb=" O GLU J 439 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP J 444 " --> pdb=" O ALA J 440 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS J 454 " --> pdb=" O MET J 450 " (cutoff:3.500A) Processing helix chain 'J' and resid 459 through 476 removed outlier: 3.856A pdb=" N GLN J 463 " --> pdb=" O LYS J 459 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS J 464 " --> pdb=" O ASP J 460 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE J 465 " --> pdb=" O VAL J 461 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS J 468 " --> pdb=" O LYS J 464 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS J 476 " --> pdb=" O LYS J 472 " (cutoff:3.500A) Processing helix chain 'J' and resid 481 through 497 removed outlier: 3.548A pdb=" N GLN J 494 " --> pdb=" O SER J 490 " (cutoff:3.500A) Processing helix chain 'J' and resid 497 through 527 removed outlier: 3.547A pdb=" N THR J 501 " --> pdb=" O GLY J 497 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYS J 503 " --> pdb=" O GLU J 499 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU J 504 " --> pdb=" O TYR J 500 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU J 519 " --> pdb=" O LYS J 515 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN J 527 " --> pdb=" O LYS J 523 " (cutoff:3.500A) Processing helix chain 'J' and resid 556 through 559 Processing helix chain 'J' and resid 560 through 573 removed outlier: 3.535A pdb=" N ARG J 573 " --> pdb=" O PHE J 569 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 585 Processing helix chain 'J' and resid 605 through 614 removed outlier: 3.906A pdb=" N TYR J 614 " --> pdb=" O ILE J 610 " (cutoff:3.500A) Processing helix chain 'J' and resid 622 through 630 removed outlier: 3.717A pdb=" N SER J 628 " --> pdb=" O GLN J 624 " (cutoff:3.500A) Processing helix chain 'J' and resid 632 through 646 Processing helix chain 'J' and resid 706 through 722 Processing helix chain 'J' and resid 727 through 738 Processing helix chain 'J' and resid 738 through 743 removed outlier: 4.167A pdb=" N PHE J 742 " --> pdb=" O LEU J 738 " (cutoff:3.500A) Processing helix chain 'J' and resid 745 through 759 Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.638A pdb=" N ASN K 59 " --> pdb=" O GLU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 89 Processing sheet with id=AA1, first strand: chain 'D' and resid 318 through 320 removed outlier: 7.160A pdb=" N THR B 367 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 382 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU C 315 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL A 417 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C 317 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU C 315 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR H 126 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE C 351 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ILE H 128 " --> pdb=" O ILE C 351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 137 through 138 Processing sheet with id=AA3, first strand: chain 'E' and resid 96 through 97 removed outlier: 6.817A pdb=" N GLY E 79 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TRP E 136 " --> pdb=" O GLY E 79 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET E 81 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN E 132 " --> pdb=" O GLY E 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 96 through 97 removed outlier: 6.758A pdb=" N TYR E 54 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE E 92 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LYS E 56 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N CYS E 55 " --> pdb=" O SER E 227 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE E 229 " --> pdb=" O CYS E 55 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE E 57 " --> pdb=" O PHE E 229 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 181 through 185 removed outlier: 9.733A pdb=" N LEU F 150 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU F 122 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU F 152 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP F 124 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LEU F 154 " --> pdb=" O TRP F 124 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR F 126 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU F 72 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TRP F 124 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY F 70 " --> pdb=" O TRP F 124 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA F 71 " --> pdb=" O SER F 86 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER F 86 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE F 73 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N SER F 40 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL F 83 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA F 42 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ASN F 85 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL F 41 " --> pdb=" O THR F 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AA7, first strand: chain 'G' and resid 110 through 112 removed outlier: 5.474A pdb=" N LEU G 152 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP G 146 " --> pdb=" O LEU G 152 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL G 154 " --> pdb=" O LYS G 144 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LYS G 144 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE G 156 " --> pdb=" O GLN G 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 12 through 15 removed outlier: 6.615A pdb=" N LYS I 4 " --> pdb=" O LEU I 67 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LEU I 69 " --> pdb=" O LYS I 4 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS I 6 " --> pdb=" O LEU I 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 534 through 538 removed outlier: 5.229A pdb=" N VAL K 24 " --> pdb=" O VAL J 591 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL J 591 " --> pdb=" O VAL K 24 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 577 through 579 Processing sheet with id=AB2, first strand: chain 'J' and resid 619 through 621 removed outlier: 3.985A pdb=" N LYS J 670 " --> pdb=" O VAL J 650 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL J 650 " --> pdb=" O LYS J 670 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 724 through 726 Processing sheet with id=AB4, first strand: chain 'K' and resid 79 through 80 removed outlier: 7.338A pdb=" N VAL K 70 " --> pdb=" O TYR K 106 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR K 106 " --> pdb=" O VAL K 70 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP K 72 " --> pdb=" O GLN K 104 " (cutoff:3.500A) 1316 hydrogen bonds defined for protein. 3822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.52 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4215 1.31 - 1.43: 6400 1.43 - 1.56: 14549 1.56 - 1.69: 0 1.69 - 1.82: 226 Bond restraints: 25390 Sorted by residual: bond pdb=" C ASP J 427 " pdb=" O ASP J 427 " ideal model delta sigma weight residual 1.236 1.175 0.061 1.15e-02 7.56e+03 2.80e+01 bond pdb=" C LYS J 431 " pdb=" O LYS J 431 " ideal model delta sigma weight residual 1.235 1.207 0.028 1.26e-02 6.30e+03 5.09e+00 bond pdb=" CA ASP J 427 " pdb=" C ASP J 427 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.24e-02 6.50e+03 5.09e+00 bond pdb=" CA CYS K 56 " pdb=" C CYS K 56 " ideal model delta sigma weight residual 1.523 1.551 -0.028 1.41e-02 5.03e+03 3.95e+00 bond pdb=" CA SER J 428 " pdb=" C SER J 428 " ideal model delta sigma weight residual 1.524 1.501 0.023 1.28e-02 6.10e+03 3.30e+00 ... (remaining 25385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 33862 2.33 - 4.67: 343 4.67 - 7.00: 52 7.00 - 9.33: 12 9.33 - 11.66: 1 Bond angle restraints: 34270 Sorted by residual: angle pdb=" N SER K 65 " pdb=" CA SER K 65 " pdb=" C SER K 65 " ideal model delta sigma weight residual 110.97 105.10 5.87 1.09e+00 8.42e-01 2.90e+01 angle pdb=" N GLU K 66 " pdb=" CA GLU K 66 " pdb=" C GLU K 66 " ideal model delta sigma weight residual 111.33 105.06 6.27 1.21e+00 6.83e-01 2.69e+01 angle pdb=" N VAL H 102 " pdb=" CA VAL H 102 " pdb=" C VAL H 102 " ideal model delta sigma weight residual 113.47 108.30 5.17 1.01e+00 9.80e-01 2.62e+01 angle pdb=" N TYR J 425 " pdb=" CA TYR J 425 " pdb=" C TYR J 425 " ideal model delta sigma weight residual 111.07 105.87 5.20 1.07e+00 8.73e-01 2.36e+01 angle pdb=" N ILE D 61 " pdb=" CA ILE D 61 " pdb=" C ILE D 61 " ideal model delta sigma weight residual 113.42 108.45 4.97 1.17e+00 7.31e-01 1.80e+01 ... (remaining 34265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 12976 17.90 - 35.81: 1900 35.81 - 53.71: 514 53.71 - 71.62: 105 71.62 - 89.52: 54 Dihedral angle restraints: 15549 sinusoidal: 6368 harmonic: 9181 Sorted by residual: dihedral pdb=" CA ILE D 330 " pdb=" C ILE D 330 " pdb=" N PRO D 331 " pdb=" CA PRO D 331 " ideal model delta harmonic sigma weight residual 180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLY F 293 " pdb=" C GLY F 293 " pdb=" N THR F 294 " pdb=" CA THR F 294 " ideal model delta harmonic sigma weight residual 180.00 158.82 21.18 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA LEU K 52 " pdb=" C LEU K 52 " pdb=" N CYS K 53 " pdb=" CA CYS K 53 " ideal model delta harmonic sigma weight residual 180.00 159.84 20.16 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 15546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2421 0.029 - 0.058: 989 0.058 - 0.087: 304 0.087 - 0.116: 134 0.116 - 0.146: 22 Chirality restraints: 3870 Sorted by residual: chirality pdb=" CA PRO D 331 " pdb=" N PRO D 331 " pdb=" C PRO D 331 " pdb=" CB PRO D 331 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CB ILE F 174 " pdb=" CA ILE F 174 " pdb=" CG1 ILE F 174 " pdb=" CG2 ILE F 174 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CG LEU B 96 " pdb=" CB LEU B 96 " pdb=" CD1 LEU B 96 " pdb=" CD2 LEU B 96 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 3867 not shown) Planarity restraints: 4380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 71 " 0.055 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO C 72 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO C 72 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 72 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 118 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" C GLU D 118 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU D 118 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP D 119 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 118 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.94e+00 pdb=" CD GLU D 118 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU D 118 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU D 118 " 0.012 2.00e-02 2.50e+03 ... (remaining 4377 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 22 2.57 - 3.15: 19676 3.15 - 3.73: 37671 3.73 - 4.32: 50712 4.32 - 4.90: 84329 Nonbonded interactions: 192410 Sorted by model distance: nonbonded pdb=" OD2 ASP K 97 " pdb="ZN ZN K 203 " model vdw 1.985 2.230 nonbonded pdb=" OD1 ASP K 97 " pdb="ZN ZN K 203 " model vdw 2.001 2.230 nonbonded pdb=" CG ASP K 97 " pdb="ZN ZN K 203 " model vdw 2.135 2.460 nonbonded pdb=" O GLU D 118 " pdb=" OE1 GLU D 118 " model vdw 2.394 3.040 nonbonded pdb=" O SER K 62 " pdb=" N THR K 64 " model vdw 2.438 3.120 ... (remaining 192405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.270 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 25402 Z= 0.152 Angle : 0.614 11.664 34276 Z= 0.348 Chirality : 0.038 0.146 3870 Planarity : 0.004 0.084 4380 Dihedral : 18.735 89.522 9587 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.34 % Favored : 94.50 % Rotamer: Outliers : 1.06 % Allowed : 28.90 % Favored : 70.04 % 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: -0.48 (0.15), residues: 3074 helix: 0.61 (0.13), residues: 1728 sheet: -0.60 (0.40), residues: 170 loop : -1.66 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 123 TYR 0.017 0.001 TYR D 187 PHE 0.020 0.001 PHE B 80 TRP 0.009 0.001 TRP K 33 HIS 0.004 0.001 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00265 (25390) covalent geometry : angle 0.61183 (34270) hydrogen bonds : bond 0.24070 ( 1314) hydrogen bonds : angle 6.29279 ( 3822) metal coordination : bond 0.01818 ( 11) metal coordination : angle 4.08904 ( 6) Misc. bond : bond 0.09770 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 37 VAL cc_start: -0.1203 (OUTLIER) cc_final: -0.1501 (t) REVERT: A 201 MET cc_start: 0.5212 (ppp) cc_final: 0.4691 (ppp) REVERT: B 89 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.6574 (ppp) REVERT: B 426 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8225 (mmtm) REVERT: C 38 ASN cc_start: 0.7227 (OUTLIER) cc_final: 0.6829 (t0) REVERT: C 68 MET cc_start: 0.6688 (tpp) cc_final: 0.6289 (tmm) REVERT: C 114 ARG cc_start: 0.6755 (mpt-90) cc_final: 0.6506 (mtt90) REVERT: C 322 MET cc_start: 0.8677 (ttp) cc_final: 0.8364 (ttt) REVERT: C 357 MET cc_start: 0.8097 (mmt) cc_final: 0.7727 (mmt) REVERT: D 1 MET cc_start: 0.5568 (tmm) cc_final: 0.5012 (tpt) REVERT: E 25 ILE cc_start: 0.8527 (mm) cc_final: 0.8277 (tt) REVERT: G 87 GLU cc_start: 0.8142 (pm20) cc_final: 0.7910 (pm20) REVERT: J 425 TYR cc_start: 0.5185 (m-80) cc_final: 0.4943 (t80) REVERT: J 454 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7571 (mmmt) REVERT: J 688 MET cc_start: 0.3262 (mmm) cc_final: 0.2111 (mtp) outliers start: 29 outliers final: 11 residues processed: 251 average time/residue: 0.1645 time to fit residues: 66.2968 Evaluate side-chains 228 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain J residue 426 CYS Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 711 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN H 47 HIS ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.125012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.083649 restraints weight = 51430.558| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.85 r_work: 0.3150 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25402 Z= 0.156 Angle : 0.557 10.406 34276 Z= 0.290 Chirality : 0.040 0.149 3870 Planarity : 0.004 0.077 4380 Dihedral : 4.960 52.347 3389 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.34 % Favored : 94.50 % Rotamer: Outliers : 2.96 % Allowed : 26.44 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.15), residues: 3074 helix: 1.04 (0.12), residues: 1828 sheet: -0.53 (0.41), residues: 158 loop : -1.64 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 123 TYR 0.016 0.001 TYR E 143 PHE 0.021 0.001 PHE F 112 TRP 0.008 0.001 TRP E 246 HIS 0.006 0.001 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00355 (25390) covalent geometry : angle 0.55493 (34270) hydrogen bonds : bond 0.05041 ( 1314) hydrogen bonds : angle 4.38010 ( 3822) metal coordination : bond 0.01401 ( 11) metal coordination : angle 3.66799 ( 6) Misc. bond : bond 0.00147 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 241 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.4690 (ppp) cc_final: 0.2236 (mtm) REVERT: A 201 MET cc_start: 0.6081 (ppp) cc_final: 0.5390 (ppp) REVERT: A 284 LEU cc_start: 0.0272 (OUTLIER) cc_final: -0.0284 (mp) REVERT: B 89 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7705 (ppp) REVERT: B 435 ASN cc_start: 0.8565 (t0) cc_final: 0.8355 (t0) REVERT: C 322 MET cc_start: 0.8814 (ttp) cc_final: 0.8441 (ttp) REVERT: C 357 MET cc_start: 0.8396 (mmt) cc_final: 0.7809 (mmt) REVERT: D 1 MET cc_start: 0.5930 (tmm) cc_final: 0.5623 (tpt) REVERT: D 271 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8180 (ttm170) REVERT: G 77 ASP cc_start: 0.8208 (m-30) cc_final: 0.7903 (m-30) REVERT: H 49 ASP cc_start: 0.8286 (t0) cc_final: 0.7903 (t0) REVERT: H 82 TRP cc_start: 0.7782 (OUTLIER) cc_final: 0.7435 (t-100) REVERT: J 425 TYR cc_start: 0.4753 (m-80) cc_final: 0.4269 (t80) REVERT: J 454 LYS cc_start: 0.8326 (mtmm) cc_final: 0.7808 (mmmt) REVERT: J 672 TYR cc_start: 0.6737 (t80) cc_final: 0.6500 (t80) REVERT: J 688 MET cc_start: 0.3546 (mmm) cc_final: 0.2585 (mtp) REVERT: K 105 LYS cc_start: 0.8691 (tttm) cc_final: 0.8311 (mtpt) outliers start: 81 outliers final: 42 residues processed: 309 average time/residue: 0.1532 time to fit residues: 76.6485 Evaluate side-chains 273 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 227 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 271 ARG Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 82 TRP Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain I residue 4 LYS Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain J residue 426 CYS Chi-restraints excluded: chain J residue 531 LEU Chi-restraints excluded: chain J residue 551 CYS Chi-restraints excluded: chain J residue 601 LEU Chi-restraints excluded: chain J residue 754 ASP Chi-restraints excluded: chain K residue 38 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 244 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 291 optimal weight: 5.9990 chunk 252 optimal weight: 0.0050 chunk 126 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 299 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 305 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 266 optimal weight: 1.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 HIS ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 GLN F 282 GLN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 ASN ** 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 = 0.4015 r_free = 0.4015 target = 0.135321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.094123 restraints weight = 51394.948| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.84 r_work: 0.3136 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25402 Z= 0.126 Angle : 0.501 13.438 34276 Z= 0.261 Chirality : 0.039 0.146 3870 Planarity : 0.004 0.075 4380 Dihedral : 4.491 53.363 3370 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.40 % Favored : 94.47 % Rotamer: Outliers : 2.96 % Allowed : 26.23 % Favored : 70.81 % 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: 0.39 (0.16), residues: 3074 helix: 1.39 (0.13), residues: 1843 sheet: -0.32 (0.40), residues: 170 loop : -1.71 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 123 TYR 0.014 0.001 TYR E 143 PHE 0.018 0.001 PHE A 301 TRP 0.011 0.001 TRP K 72 HIS 0.005 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00279 (25390) covalent geometry : angle 0.49944 (34270) hydrogen bonds : bond 0.04247 ( 1314) hydrogen bonds : angle 3.99279 ( 3822) metal coordination : bond 0.01255 ( 11) metal coordination : angle 3.02508 ( 6) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 244 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.5083 (ppp) cc_final: 0.2793 (mtm) REVERT: A 284 LEU cc_start: 0.0488 (OUTLIER) cc_final: -0.0025 (mp) REVERT: A 419 SER cc_start: 0.9088 (OUTLIER) cc_final: 0.8789 (m) REVERT: A 454 MET cc_start: 0.7700 (tpp) cc_final: 0.7355 (mtt) REVERT: B 82 LEU cc_start: 0.8600 (pt) cc_final: 0.8324 (pt) REVERT: B 84 ASN cc_start: 0.8578 (t0) cc_final: 0.8071 (p0) REVERT: B 89 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7648 (ppp) REVERT: B 223 HIS cc_start: 0.8584 (m-70) cc_final: 0.8326 (m90) REVERT: B 323 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8548 (mm) REVERT: B 334 HIS cc_start: 0.7802 (m90) cc_final: 0.7561 (m90) REVERT: B 435 ASN cc_start: 0.8691 (t0) cc_final: 0.8469 (t0) REVERT: C 68 MET cc_start: 0.7659 (tpp) cc_final: 0.7143 (tmm) REVERT: C 322 MET cc_start: 0.8674 (ttp) cc_final: 0.8315 (ttp) REVERT: C 357 MET cc_start: 0.8205 (mmt) cc_final: 0.7602 (mmt) REVERT: C 396 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7987 (pp20) REVERT: E 25 ILE cc_start: 0.8157 (mm) cc_final: 0.7857 (tt) REVERT: E 313 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: F 160 HIS cc_start: 0.8125 (p90) cc_final: 0.7803 (p90) REVERT: G 87 GLU cc_start: 0.8575 (pm20) cc_final: 0.8248 (pm20) REVERT: H 49 ASP cc_start: 0.8365 (t0) cc_final: 0.7838 (t0) REVERT: H 82 TRP cc_start: 0.7869 (OUTLIER) cc_final: 0.7528 (t-100) REVERT: I 34 GLU cc_start: 0.2585 (OUTLIER) cc_final: 0.2279 (mp0) REVERT: J 425 TYR cc_start: 0.4787 (m-80) cc_final: 0.4298 (t80) REVERT: J 454 LYS cc_start: 0.8361 (mtmm) cc_final: 0.7818 (tptp) REVERT: J 476 HIS cc_start: 0.9028 (m-70) cc_final: 0.8707 (m170) REVERT: J 672 TYR cc_start: 0.6876 (t80) cc_final: 0.6670 (t80) REVERT: J 676 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6384 (pttt) REVERT: J 688 MET cc_start: 0.3247 (mmm) cc_final: 0.2568 (mtp) outliers start: 81 outliers final: 41 residues processed: 313 average time/residue: 0.1554 time to fit residues: 79.5343 Evaluate side-chains 272 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 82 TRP Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain I residue 4 LYS Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain J residue 433 SER Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 551 CYS Chi-restraints excluded: chain J residue 601 LEU Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 676 LYS Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 754 ASP Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 90 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 126 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 270 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN F 282 GLN H 103 GLN ** H 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.132631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.092059 restraints weight = 49769.665| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.17 r_work: 0.3121 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25402 Z= 0.129 Angle : 0.490 7.878 34276 Z= 0.256 Chirality : 0.039 0.140 3870 Planarity : 0.004 0.074 4380 Dihedral : 4.457 55.090 3369 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.11 % Favored : 94.76 % Rotamer: Outliers : 3.37 % Allowed : 26.15 % Favored : 70.48 % 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: 0.57 (0.16), residues: 3074 helix: 1.52 (0.13), residues: 1850 sheet: -0.27 (0.41), residues: 171 loop : -1.62 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 344 TYR 0.014 0.001 TYR E 143 PHE 0.019 0.001 PHE E 96 TRP 0.010 0.001 TRP H 82 HIS 0.005 0.001 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00298 (25390) covalent geometry : angle 0.48784 (34270) hydrogen bonds : bond 0.03801 ( 1314) hydrogen bonds : angle 3.86896 ( 3822) metal coordination : bond 0.01064 ( 11) metal coordination : angle 3.17329 ( 6) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 246 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 37 VAL cc_start: 0.0352 (OUTLIER) cc_final: 0.0009 (t) REVERT: A 77 MET cc_start: 0.5301 (ppp) cc_final: 0.3007 (mtm) REVERT: A 284 LEU cc_start: 0.0348 (OUTLIER) cc_final: -0.0017 (mp) REVERT: A 454 MET cc_start: 0.7969 (tpp) cc_final: 0.7739 (mtt) REVERT: B 88 MET cc_start: 0.7672 (mpp) cc_final: 0.7438 (mpp) REVERT: B 89 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7630 (ppp) REVERT: B 323 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8734 (mm) REVERT: B 435 ASN cc_start: 0.8646 (t0) cc_final: 0.8405 (t0) REVERT: C 190 MET cc_start: 0.8538 (mtp) cc_final: 0.8159 (mtp) REVERT: C 322 MET cc_start: 0.8806 (ttp) cc_final: 0.8517 (ttp) REVERT: C 357 MET cc_start: 0.8410 (mmt) cc_final: 0.7844 (mmt) REVERT: D 271 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8278 (ttm170) REVERT: E 313 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: F 160 HIS cc_start: 0.8124 (p90) cc_final: 0.7855 (p90) REVERT: G 87 GLU cc_start: 0.8537 (pm20) cc_final: 0.8276 (pm20) REVERT: H 49 ASP cc_start: 0.8440 (t0) cc_final: 0.7896 (t0) REVERT: H 82 TRP cc_start: 0.8246 (OUTLIER) cc_final: 0.7916 (t-100) REVERT: I 34 GLU cc_start: 0.2784 (OUTLIER) cc_final: 0.2338 (mp0) REVERT: J 425 TYR cc_start: 0.4923 (m-80) cc_final: 0.4302 (t80) REVERT: J 454 LYS cc_start: 0.8319 (mtmm) cc_final: 0.7795 (tptp) REVERT: J 476 HIS cc_start: 0.9016 (m-70) cc_final: 0.8702 (m170) REVERT: J 676 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6375 (pttt) REVERT: J 688 MET cc_start: 0.3294 (mmm) cc_final: 0.2621 (mtp) REVERT: K 20 LYS cc_start: 0.8445 (mmmm) cc_final: 0.8074 (mmtm) outliers start: 92 outliers final: 52 residues processed: 322 average time/residue: 0.1639 time to fit residues: 84.5855 Evaluate side-chains 293 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 232 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 271 ARG Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 139 ASP Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 82 TRP Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain I residue 4 LYS Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain J residue 433 SER Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 551 CYS Chi-restraints excluded: chain J residue 601 LEU Chi-restraints excluded: chain J residue 605 THR Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 676 LYS Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 754 ASP Chi-restraints excluded: chain K residue 38 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 81 optimal weight: 20.0000 chunk 291 optimal weight: 1.9990 chunk 293 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 286 optimal weight: 10.0000 chunk 235 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN D 218 HIS D 241 GLN ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 ASN ** H 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.133396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.098230 restraints weight = 49217.574| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.02 r_work: 0.3154 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25402 Z= 0.117 Angle : 0.494 12.269 34276 Z= 0.255 Chirality : 0.038 0.146 3870 Planarity : 0.003 0.074 4380 Dihedral : 4.307 48.691 3367 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.57 % Rotamer: Outliers : 3.55 % Allowed : 26.34 % Favored : 70.12 % 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: 0.66 (0.16), residues: 3074 helix: 1.61 (0.13), residues: 1855 sheet: -0.27 (0.40), residues: 171 loop : -1.63 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 204 TYR 0.014 0.001 TYR E 143 PHE 0.021 0.001 PHE A 301 TRP 0.010 0.001 TRP H 82 HIS 0.005 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00267 (25390) covalent geometry : angle 0.49258 (34270) hydrogen bonds : bond 0.03665 ( 1314) hydrogen bonds : angle 3.80626 ( 3822) metal coordination : bond 0.01049 ( 11) metal coordination : angle 3.03224 ( 6) Misc. bond : bond 0.00046 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 243 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 37 VAL cc_start: 0.0310 (OUTLIER) cc_final: -0.0034 (t) REVERT: A 77 MET cc_start: 0.5321 (ppp) cc_final: 0.3014 (mtm) REVERT: A 201 MET cc_start: 0.7073 (tmm) cc_final: 0.6870 (ppp) REVERT: A 419 SER cc_start: 0.9187 (OUTLIER) cc_final: 0.8947 (m) REVERT: A 454 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7811 (mtt) REVERT: B 89 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7533 (ppp) REVERT: B 123 LYS cc_start: 0.8330 (mmtt) cc_final: 0.7974 (mtmm) REVERT: B 323 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8738 (mm) REVERT: B 435 ASN cc_start: 0.8642 (t0) cc_final: 0.8396 (t0) REVERT: C 68 MET cc_start: 0.7564 (tpp) cc_final: 0.7103 (tmm) REVERT: C 190 MET cc_start: 0.8490 (mtp) cc_final: 0.8093 (mtp) REVERT: C 322 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8519 (ttp) REVERT: C 357 MET cc_start: 0.8415 (mmt) cc_final: 0.7852 (mmt) REVERT: E 165 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8879 (t80) REVERT: E 313 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: F 160 HIS cc_start: 0.8072 (p90) cc_final: 0.7856 (p90) REVERT: G 87 GLU cc_start: 0.8499 (pm20) cc_final: 0.8280 (pm20) REVERT: H 49 ASP cc_start: 0.8460 (t0) cc_final: 0.7947 (t0) REVERT: H 82 TRP cc_start: 0.8305 (OUTLIER) cc_final: 0.7948 (t-100) REVERT: H 195 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7354 (pt0) REVERT: I 34 GLU cc_start: 0.2969 (OUTLIER) cc_final: 0.2487 (mp0) REVERT: J 425 TYR cc_start: 0.5007 (m-80) cc_final: 0.4359 (t80) REVERT: J 454 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7800 (tptp) REVERT: J 476 HIS cc_start: 0.8992 (m-70) cc_final: 0.8675 (m170) REVERT: J 676 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6350 (pttt) REVERT: J 688 MET cc_start: 0.3237 (mmm) cc_final: 0.2584 (mtp) REVERT: K 20 LYS cc_start: 0.8483 (mmmm) cc_final: 0.8099 (mmtm) outliers start: 97 outliers final: 62 residues processed: 324 average time/residue: 0.1560 time to fit residues: 82.9074 Evaluate side-chains 302 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 228 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 139 ASP Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 82 TRP Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain I residue 4 LYS Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain J residue 433 SER Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 551 CYS Chi-restraints excluded: chain J residue 601 LEU Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 650 VAL Chi-restraints excluded: chain J residue 676 LYS Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 754 ASP Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 56 CYS Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 118 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 256 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 chunk 197 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 255 optimal weight: 0.2980 chunk 95 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 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 = 0.4014 r_free = 0.4014 target = 0.133354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.098322 restraints weight = 49439.110| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.02 r_work: 0.3165 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25402 Z= 0.105 Angle : 0.489 10.922 34276 Z= 0.251 Chirality : 0.038 0.143 3870 Planarity : 0.003 0.071 4380 Dihedral : 4.238 47.047 3367 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.04 % Favored : 94.86 % Rotamer: Outliers : 3.40 % Allowed : 26.15 % Favored : 70.45 % 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: 0.74 (0.16), residues: 3074 helix: 1.70 (0.13), residues: 1852 sheet: -0.30 (0.40), residues: 171 loop : -1.65 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 561 TYR 0.013 0.001 TYR D 167 PHE 0.019 0.001 PHE A 301 TRP 0.009 0.001 TRP H 82 HIS 0.004 0.001 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00233 (25390) covalent geometry : angle 0.48744 (34270) hydrogen bonds : bond 0.03436 ( 1314) hydrogen bonds : angle 3.72651 ( 3822) metal coordination : bond 0.01051 ( 11) metal coordination : angle 2.75731 ( 6) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 249 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 37 VAL cc_start: 0.0405 (OUTLIER) cc_final: 0.0085 (t) REVERT: A 77 MET cc_start: 0.5289 (ppp) cc_final: 0.4083 (tmm) REVERT: A 201 MET cc_start: 0.7079 (tmm) cc_final: 0.6858 (ppp) REVERT: A 419 SER cc_start: 0.9164 (OUTLIER) cc_final: 0.8948 (m) REVERT: B 89 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7410 (ppp) REVERT: B 435 ASN cc_start: 0.8641 (t0) cc_final: 0.8395 (t0) REVERT: C 68 MET cc_start: 0.7481 (tpp) cc_final: 0.7117 (tmm) REVERT: C 119 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7563 (mtp180) REVERT: C 190 MET cc_start: 0.8472 (mtp) cc_final: 0.8057 (mtp) REVERT: C 322 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8495 (ttp) REVERT: C 357 MET cc_start: 0.8389 (mmt) cc_final: 0.7832 (mmt) REVERT: C 396 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: E 165 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8865 (t80) REVERT: E 313 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: H 49 ASP cc_start: 0.8457 (t0) cc_final: 0.7977 (t0) REVERT: H 82 TRP cc_start: 0.8337 (OUTLIER) cc_final: 0.7994 (t-100) REVERT: I 34 GLU cc_start: 0.3037 (OUTLIER) cc_final: 0.2597 (mp0) REVERT: J 425 TYR cc_start: 0.5026 (m-80) cc_final: 0.4197 (t80) REVERT: J 454 LYS cc_start: 0.8247 (mtmm) cc_final: 0.7792 (tptp) REVERT: J 476 HIS cc_start: 0.8986 (m-70) cc_final: 0.8669 (m170) REVERT: J 676 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6389 (pttt) REVERT: J 688 MET cc_start: 0.3217 (mmm) cc_final: 0.2579 (mtp) REVERT: K 20 LYS cc_start: 0.8486 (mmmm) cc_final: 0.8104 (mmtm) REVERT: K 92 GLN cc_start: 0.8114 (pm20) cc_final: 0.7858 (pm20) outliers start: 93 outliers final: 55 residues processed: 324 average time/residue: 0.1566 time to fit residues: 83.2689 Evaluate side-chains 296 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 230 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 82 TRP Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain I residue 4 LYS Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 551 CYS Chi-restraints excluded: chain J residue 601 LEU Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 650 VAL Chi-restraints excluded: chain J residue 676 LYS Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 754 ASP Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 56 CYS Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 37 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 281 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 262 optimal weight: 9.9990 chunk 120 optimal weight: 0.0170 chunk 5 optimal weight: 6.9990 chunk 229 optimal weight: 4.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN D 241 GLN ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN ** H 209 ASN ** 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 = 0.3975 r_free = 0.3975 target = 0.133287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.092776 restraints weight = 51302.397| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.12 r_work: 0.3073 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25402 Z= 0.180 Angle : 0.557 11.398 34276 Z= 0.286 Chirality : 0.041 0.157 3870 Planarity : 0.004 0.071 4380 Dihedral : 4.500 52.226 3367 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.66 % Favored : 94.24 % Rotamer: Outliers : 3.15 % Allowed : 26.63 % Favored : 70.23 % 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: 0.61 (0.16), residues: 3074 helix: 1.55 (0.13), residues: 1867 sheet: -0.41 (0.39), residues: 172 loop : -1.63 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 123 TYR 0.019 0.001 TYR E 143 PHE 0.024 0.002 PHE E 96 TRP 0.012 0.001 TRP H 82 HIS 0.011 0.001 HIS F 160 Details of bonding type rmsd covalent geometry : bond 0.00431 (25390) covalent geometry : angle 0.55454 (34270) hydrogen bonds : bond 0.04166 ( 1314) hydrogen bonds : angle 3.90052 ( 3822) metal coordination : bond 0.01455 ( 11) metal coordination : angle 3.95236 ( 6) Misc. bond : bond 0.00065 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 238 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 37 VAL cc_start: 0.0486 (OUTLIER) cc_final: 0.0169 (t) REVERT: A 77 MET cc_start: 0.5424 (ppp) cc_final: 0.3183 (mtm) REVERT: A 201 MET cc_start: 0.7155 (tmm) cc_final: 0.6898 (ppp) REVERT: A 284 LEU cc_start: 0.0186 (OUTLIER) cc_final: -0.0103 (mp) REVERT: B 89 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7584 (ppp) REVERT: B 323 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8725 (mm) REVERT: C 119 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7625 (mtp180) REVERT: C 153 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7647 (mmtm) REVERT: C 190 MET cc_start: 0.8597 (mtp) cc_final: 0.8236 (mtp) REVERT: C 357 MET cc_start: 0.8509 (mmt) cc_final: 0.7911 (mmt) REVERT: C 396 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: D 271 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8281 (ttm170) REVERT: E 313 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: F 64 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8414 (ptt-90) REVERT: G 220 LEU cc_start: 0.5736 (OUTLIER) cc_final: 0.5466 (mt) REVERT: H 49 ASP cc_start: 0.8497 (t0) cc_final: 0.7989 (t0) REVERT: H 82 TRP cc_start: 0.8377 (OUTLIER) cc_final: 0.8008 (t-100) REVERT: I 34 GLU cc_start: 0.3416 (OUTLIER) cc_final: 0.2841 (mp0) REVERT: J 425 TYR cc_start: 0.5040 (m-80) cc_final: 0.4293 (t80) REVERT: J 454 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7852 (tptp) REVERT: J 531 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7207 (mt) REVERT: J 676 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6389 (pttt) REVERT: J 688 MET cc_start: 0.3244 (mmm) cc_final: 0.2723 (mtp) REVERT: K 20 LYS cc_start: 0.8459 (mmmm) cc_final: 0.8072 (mmtm) REVERT: K 51 ASP cc_start: 0.7519 (m-30) cc_final: 0.7229 (m-30) REVERT: K 92 GLN cc_start: 0.8059 (pm20) cc_final: 0.7767 (pm20) outliers start: 86 outliers final: 54 residues processed: 307 average time/residue: 0.1553 time to fit residues: 77.4762 Evaluate side-chains 299 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 230 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 271 ARG Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 139 ASP Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 82 TRP Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain I residue 4 LYS Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain J residue 451 VAL Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 531 LEU Chi-restraints excluded: chain J residue 551 CYS Chi-restraints excluded: chain J residue 601 LEU Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 650 VAL Chi-restraints excluded: chain J residue 671 LEU Chi-restraints excluded: chain J residue 676 LYS Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 738 LEU Chi-restraints excluded: chain J residue 754 ASP Chi-restraints excluded: chain K residue 38 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 159 optimal weight: 2.9990 chunk 304 optimal weight: 10.0000 chunk 249 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 120 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 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 = 0.3993 r_free = 0.3993 target = 0.131317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.096477 restraints weight = 49670.261| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.98 r_work: 0.3128 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25402 Z= 0.116 Angle : 0.511 11.987 34276 Z= 0.262 Chirality : 0.039 0.151 3870 Planarity : 0.003 0.070 4380 Dihedral : 4.372 49.873 3367 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.27 % Favored : 94.63 % Rotamer: Outliers : 2.49 % Allowed : 27.62 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.15 % 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: 0.77 (0.16), residues: 3074 helix: 1.71 (0.13), residues: 1854 sheet: -0.34 (0.40), residues: 172 loop : -1.57 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 121 TYR 0.014 0.001 TYR F 105 PHE 0.018 0.001 PHE A 301 TRP 0.010 0.001 TRP B 67 HIS 0.004 0.001 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00263 (25390) covalent geometry : angle 0.50922 (34270) hydrogen bonds : bond 0.03545 ( 1314) hydrogen bonds : angle 3.76010 ( 3822) metal coordination : bond 0.01086 ( 11) metal coordination : angle 3.05356 ( 6) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 241 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 VAL cc_start: 0.0344 (OUTLIER) cc_final: 0.0021 (t) REVERT: A 77 MET cc_start: 0.5441 (ppp) cc_final: 0.4202 (tmm) REVERT: A 201 MET cc_start: 0.7153 (tmm) cc_final: 0.6910 (ppp) REVERT: A 284 LEU cc_start: 0.0163 (OUTLIER) cc_final: -0.0118 (mp) REVERT: A 356 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.7173 (mmt) REVERT: B 323 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8704 (mm) REVERT: C 68 MET cc_start: 0.7421 (tpp) cc_final: 0.6558 (tmm) REVERT: C 119 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7593 (mtp180) REVERT: C 190 MET cc_start: 0.8487 (mtp) cc_final: 0.8071 (mtp) REVERT: C 357 MET cc_start: 0.8422 (mmt) cc_final: 0.7833 (mmt) REVERT: C 372 MET cc_start: 0.8302 (tpp) cc_final: 0.8094 (tpp) REVERT: C 396 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: D 121 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.7263 (ttm-80) REVERT: E 313 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: H 49 ASP cc_start: 0.8475 (t0) cc_final: 0.7975 (t0) REVERT: H 82 TRP cc_start: 0.8407 (OUTLIER) cc_final: 0.8077 (t-100) REVERT: I 34 GLU cc_start: 0.3394 (OUTLIER) cc_final: 0.2936 (mp0) REVERT: J 425 TYR cc_start: 0.5040 (m-80) cc_final: 0.4285 (t80) REVERT: J 454 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7811 (tptp) REVERT: J 676 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6409 (pttt) REVERT: J 688 MET cc_start: 0.3211 (mmm) cc_final: 0.2758 (mtp) REVERT: K 20 LYS cc_start: 0.8481 (mmmm) cc_final: 0.8099 (mmtm) REVERT: K 92 GLN cc_start: 0.8047 (pm20) cc_final: 0.7780 (pm20) outliers start: 68 outliers final: 51 residues processed: 295 average time/residue: 0.1626 time to fit residues: 78.5349 Evaluate side-chains 291 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 230 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 139 ASP Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 82 TRP Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain I residue 4 LYS Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 551 CYS Chi-restraints excluded: chain J residue 601 LEU Chi-restraints excluded: chain J residue 605 THR Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 650 VAL Chi-restraints excluded: chain J residue 676 LYS Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 738 LEU Chi-restraints excluded: chain J residue 754 ASP Chi-restraints excluded: chain K residue 38 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 136 optimal weight: 0.5980 chunk 230 optimal weight: 0.0770 chunk 71 optimal weight: 0.0980 chunk 92 optimal weight: 0.9990 chunk 176 optimal weight: 0.5980 chunk 212 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 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 = 0.4013 r_free = 0.4013 target = 0.133444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.098799 restraints weight = 49972.662| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.09 r_work: 0.3150 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25402 Z= 0.096 Angle : 0.494 12.416 34276 Z= 0.253 Chirality : 0.038 0.176 3870 Planarity : 0.003 0.071 4380 Dihedral : 4.140 46.457 3364 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.43 % Favored : 94.47 % Rotamer: Outliers : 2.30 % Allowed : 27.62 % Favored : 70.08 % 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: 0.91 (0.16), residues: 3074 helix: 1.84 (0.13), residues: 1845 sheet: -0.23 (0.40), residues: 172 loop : -1.55 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 121 TYR 0.018 0.001 TYR A 185 PHE 0.015 0.001 PHE A 301 TRP 0.009 0.001 TRP E 246 HIS 0.005 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00206 (25390) covalent geometry : angle 0.49317 (34270) hydrogen bonds : bond 0.03197 ( 1314) hydrogen bonds : angle 3.66171 ( 3822) metal coordination : bond 0.00988 ( 11) metal coordination : angle 2.43431 ( 6) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 241 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 37 VAL cc_start: 0.0440 (OUTLIER) cc_final: 0.0118 (t) REVERT: A 77 MET cc_start: 0.5554 (ppp) cc_final: 0.4506 (tmm) REVERT: A 356 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7187 (mmt) REVERT: B 323 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8680 (mm) REVERT: C 68 MET cc_start: 0.7637 (tpp) cc_final: 0.7157 (tmm) REVERT: C 119 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7487 (mtp180) REVERT: C 190 MET cc_start: 0.8443 (mtp) cc_final: 0.8118 (mtt) REVERT: C 357 MET cc_start: 0.8389 (mmt) cc_final: 0.7794 (mmt) REVERT: C 396 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: D 121 ARG cc_start: 0.7593 (ttm-80) cc_final: 0.7150 (ttm-80) REVERT: E 313 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: G 77 ASP cc_start: 0.8256 (m-30) cc_final: 0.7950 (m-30) REVERT: H 49 ASP cc_start: 0.8328 (t0) cc_final: 0.7800 (t0) REVERT: H 82 TRP cc_start: 0.8199 (OUTLIER) cc_final: 0.7901 (t-100) REVERT: I 34 GLU cc_start: 0.3505 (OUTLIER) cc_final: 0.2983 (mp0) REVERT: J 425 TYR cc_start: 0.4998 (m-80) cc_final: 0.4186 (t80) REVERT: J 454 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7825 (tptp) REVERT: J 676 LYS cc_start: 0.6843 (OUTLIER) cc_final: 0.6371 (pttt) REVERT: J 688 MET cc_start: 0.3373 (mmm) cc_final: 0.2904 (mtp) REVERT: K 20 LYS cc_start: 0.8485 (mmmm) cc_final: 0.8099 (mmtm) REVERT: K 92 GLN cc_start: 0.8143 (pm20) cc_final: 0.7909 (pm20) outliers start: 63 outliers final: 44 residues processed: 290 average time/residue: 0.1618 time to fit residues: 76.7742 Evaluate side-chains 285 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 232 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 82 TRP Chi-restraints excluded: chain I residue 4 LYS Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 551 CYS Chi-restraints excluded: chain J residue 601 LEU Chi-restraints excluded: chain J residue 605 THR Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 650 VAL Chi-restraints excluded: chain J residue 676 LYS Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 738 LEU Chi-restraints excluded: chain J residue 754 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 279 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 203 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN F 253 ASN ** H 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.132437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.092070 restraints weight = 51207.448| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.98 r_work: 0.3063 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 25402 Z= 0.212 Angle : 0.582 12.255 34276 Z= 0.298 Chirality : 0.042 0.180 3870 Planarity : 0.004 0.068 4380 Dihedral : 4.485 53.802 3364 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.95 % Favored : 93.95 % Rotamer: Outliers : 2.27 % Allowed : 27.58 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.15 % 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: 0.68 (0.16), residues: 3074 helix: 1.60 (0.13), residues: 1851 sheet: -0.24 (0.40), residues: 170 loop : -1.56 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 121 TYR 0.022 0.002 TYR A 185 PHE 0.025 0.002 PHE E 96 TRP 0.013 0.001 TRP H 82 HIS 0.006 0.001 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00515 (25390) covalent geometry : angle 0.57945 (34270) hydrogen bonds : bond 0.04213 ( 1314) hydrogen bonds : angle 3.92255 ( 3822) metal coordination : bond 0.01520 ( 11) metal coordination : angle 4.13977 ( 6) Misc. bond : bond 0.00064 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6148 Ramachandran restraints generated. 3074 Oldfield, 0 Emsley, 3074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 230 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 37 VAL cc_start: 0.0316 (OUTLIER) cc_final: 0.0030 (t) REVERT: A 77 MET cc_start: 0.5598 (ppp) cc_final: 0.4381 (tmm) REVERT: A 356 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7281 (mmt) REVERT: C 68 MET cc_start: 0.7472 (tpp) cc_final: 0.6982 (tmm) REVERT: C 119 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7619 (mtp180) REVERT: C 190 MET cc_start: 0.8592 (mtp) cc_final: 0.8238 (mtp) REVERT: C 357 MET cc_start: 0.8517 (mmt) cc_final: 0.7936 (mmt) REVERT: D 121 ARG cc_start: 0.7535 (ttm-80) cc_final: 0.7108 (ttm-80) REVERT: E 313 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: F 64 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8454 (ptt-90) REVERT: H 49 ASP cc_start: 0.8518 (t0) cc_final: 0.8000 (t0) REVERT: H 82 TRP cc_start: 0.8469 (OUTLIER) cc_final: 0.8119 (t-100) REVERT: I 34 GLU cc_start: 0.3887 (OUTLIER) cc_final: 0.3318 (mp0) REVERT: J 425 TYR cc_start: 0.5011 (m-80) cc_final: 0.4229 (t80) REVERT: J 454 LYS cc_start: 0.8180 (mtmm) cc_final: 0.7883 (tptp) REVERT: J 676 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6409 (pttt) REVERT: J 688 MET cc_start: 0.3351 (mmm) cc_final: 0.2877 (mtp) REVERT: K 20 LYS cc_start: 0.8504 (mmmm) cc_final: 0.8088 (mmtm) REVERT: K 92 GLN cc_start: 0.8044 (pm20) cc_final: 0.7787 (pm20) outliers start: 62 outliers final: 44 residues processed: 280 average time/residue: 0.1676 time to fit residues: 76.4131 Evaluate side-chains 277 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 225 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 82 TRP Chi-restraints excluded: chain I residue 4 LYS Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain J residue 451 VAL Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 551 CYS Chi-restraints excluded: chain J residue 601 LEU Chi-restraints excluded: chain J residue 605 THR Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 650 VAL Chi-restraints excluded: chain J residue 676 LYS Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 738 LEU Chi-restraints excluded: chain J residue 754 ASP Chi-restraints excluded: chain K residue 38 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 248 optimal weight: 4.9990 chunk 9 optimal weight: 0.0370 chunk 233 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 232 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 ASN ** H 209 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 = 0.3986 r_free = 0.3986 target = 0.132224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.097317 restraints weight = 49373.138| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.08 r_work: 0.3109 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25402 Z= 0.126 Angle : 0.527 12.480 34276 Z= 0.270 Chirality : 0.039 0.158 3870 Planarity : 0.004 0.070 4380 Dihedral : 4.338 51.557 3364 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.56 % Favored : 94.34 % Rotamer: Outliers : 2.23 % Allowed : 27.62 % Favored : 70.15 % 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: 0.80 (0.16), residues: 3074 helix: 1.72 (0.13), residues: 1848 sheet: -0.28 (0.40), residues: 172 loop : -1.55 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 121 TYR 0.021 0.001 TYR A 185 PHE 0.017 0.001 PHE A 301 TRP 0.014 0.001 TRP B 67 HIS 0.004 0.001 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00293 (25390) covalent geometry : angle 0.52521 (34270) hydrogen bonds : bond 0.03604 ( 1314) hydrogen bonds : angle 3.79665 ( 3822) metal coordination : bond 0.01049 ( 11) metal coordination : angle 3.31953 ( 6) Misc. bond : bond 0.00040 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7280.43 seconds wall clock time: 125 minutes 19.50 seconds (7519.50 seconds total)