Starting phenix.real_space_refine on Fri Mar 6 10:01:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qo0_53252/03_2026/9qo0_53252.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qo0_53252/03_2026/9qo0_53252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qo0_53252/03_2026/9qo0_53252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qo0_53252/03_2026/9qo0_53252.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qo0_53252/03_2026/9qo0_53252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qo0_53252/03_2026/9qo0_53252.map" } resolution = 3.26 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= 0.002 sd= 0.028 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 6 5.49 5 S 165 5.16 5 C 18678 2.51 5 N 5005 2.21 5 O 5516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29373 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3168 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1694 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 4, 'TRANS': 209} Chain: "K" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 526 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "N" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 581 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "P" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 179 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "A" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3099 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 11, 'TRANS': 394} Chain breaks: 3 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 6, 'ARG:plan': 5, 'HIS:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 91 Chain: "B" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3301 Classifications: {'peptide': 404} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 393} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2843 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 12, 'TRANS': 341} Chain breaks: 1 Chain: "E" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2276 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 278} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2238 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 10, 'TRANS': 271} Chain breaks: 1 Chain: "H" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1384 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain breaks: 1 Chain: "I" Number of atoms: 4699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 4699 Classifications: {'peptide': 644} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 147} Link IDs: {'PTRANS': 10, 'TRANS': 633} Chain breaks: 12 Unresolved non-hydrogen bonds: 615 Unresolved non-hydrogen angles: 745 Unresolved non-hydrogen dihedrals: 527 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'HIS:plan': 3, 'TYR:plan': 10, 'GLU:plan': 29, 'ASN:plan1': 5, 'ASP:plan': 15, 'PHE:plan': 3, 'GLN:plan1': 6, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 373 Chain: "J" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 665 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS%COO:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 830 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 4 Chain: "M" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1851 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 7, 'TRANS': 229} Chain breaks: 7 Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "J" 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 26361 SG CYS J 75 122.017 74.201 109.201 1.00 53.76 S ATOM 26528 SG CYS J 94 121.094 73.444 104.857 1.00 41.68 S ATOM 26165 SG CYS J 42 125.483 80.299 96.637 1.00 71.60 S ATOM 26184 SG CYS J 45 124.777 81.771 93.013 1.00 87.13 S ATOM 26432 SG CYS J 83 122.648 82.671 95.517 1.00 62.97 S ATOM 26251 SG CYS J 53 123.436 87.120 94.134 1.00 86.58 S ATOM 26274 SG CYS J 56 124.024 90.433 92.707 1.00115.83 S ATOM 26311 SG CYS J 68 124.760 89.855 96.380 1.00 75.19 S Time building chain proxies: 5.97, per 1000 atoms: 0.20 Number of scatterers: 29373 At special positions: 0 Unit cell: (196.56, 160.92, 182.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 165 16.00 P 6 15.00 O 5516 8.00 N 5005 7.00 C 18678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 154 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" ND1 HIS J 77 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 94 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 75 " pdb=" ZN J 202 " pdb="ZN ZN J 202 " - pdb=" ND1 HIS J 80 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 83 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 42 " pdb=" ZN J 203 " pdb="ZN ZN J 203 " - pdb=" ND1 HIS J 82 " pdb="ZN ZN J 203 " - pdb=" SG CYS J 53 " pdb="ZN ZN J 203 " - pdb=" SG CYS J 68 " pdb="ZN ZN J 203 " - pdb=" SG CYS J 56 " Number of angles added : 6 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7186 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 18 sheets defined 64.6% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'D' and resid 4 through 15 removed outlier: 3.508A pdb=" N ASP D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 36 removed outlier: 4.024A pdb=" N LYS D 25 " --> pdb=" O ASP D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 53 Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.832A pdb=" N THR D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP D 68 " --> pdb=" O GLN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 removed outlier: 3.900A pdb=" N LYS D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLU D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE D 84 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N HIS D 86 " --> pdb=" O LYS D 82 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 96 Processing helix chain 'D' and resid 100 through 105 removed outlier: 3.740A pdb=" N ALA D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 117 removed outlier: 3.681A pdb=" N GLU D 117 " --> pdb=" O ILE D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 157 Processing helix chain 'D' and resid 160 through 175 removed outlier: 3.602A pdb=" N ALA D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 198 removed outlier: 3.654A pdb=" N GLN D 184 " --> pdb=" O ASN D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 212 removed outlier: 3.977A pdb=" N ALA D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 235 removed outlier: 3.505A pdb=" N ARG D 222 " --> pdb=" O HIS D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 252 Processing helix chain 'D' and resid 253 through 257 removed outlier: 3.755A pdb=" N GLN D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 274 through 277 Processing helix chain 'D' and resid 278 through 285 removed outlier: 3.539A pdb=" N ALA D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU D 285 " --> pdb=" O PHE D 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 278 through 285' Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.598A pdb=" N ALA D 291 " --> pdb=" O HIS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 313 Processing helix chain 'D' and resid 321 through 328 Processing helix chain 'D' and resid 331 through 346 removed outlier: 3.868A pdb=" N GLU D 336 " --> pdb=" O ALA D 332 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 392 Processing helix chain 'D' and resid 392 through 403 Processing helix chain 'G' and resid 11 through 17 removed outlier: 3.691A pdb=" N PHE G 15 " --> pdb=" O LEU G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 35 removed outlier: 3.509A pdb=" N LEU G 35 " --> pdb=" O ILE G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 49 removed outlier: 3.739A pdb=" N LEU G 49 " --> pdb=" O GLU G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 54 Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 60 through 73 removed outlier: 3.809A pdb=" N LEU G 64 " --> pdb=" O ASN G 60 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN G 65 " --> pdb=" O ALA G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 81 Processing helix chain 'G' and resid 89 through 108 removed outlier: 4.133A pdb=" N ARG G 107 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET G 108 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 121 removed outlier: 3.560A pdb=" N ASP G 119 " --> pdb=" O VAL G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 138 removed outlier: 3.559A pdb=" N LEU G 128 " --> pdb=" O ASN G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 223 removed outlier: 4.341A pdb=" N ASN G 168 " --> pdb=" O LYS G 164 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN G 169 " --> pdb=" O LYS G 165 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU G 176 " --> pdb=" O LYS G 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR G 205 " --> pdb=" O ASN G 201 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE G 216 " --> pdb=" O GLU G 212 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR G 219 " --> pdb=" O ASN G 215 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU G 220 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS G 221 " --> pdb=" O LYS G 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 55 through 60 removed outlier: 4.052A pdb=" N TYR K 59 " --> pdb=" O THR K 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 46 Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.670A pdb=" N TYR A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 67 removed outlier: 4.073A pdb=" N GLU A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.663A pdb=" N ALA A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 106 removed outlier: 3.508A pdb=" N TYR A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 155 removed outlier: 3.661A pdb=" N ASN A 155 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 175 Processing helix chain 'A' and resid 180 through 187 removed outlier: 3.947A pdb=" N ARG A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 213 removed outlier: 4.033A pdb=" N VAL A 208 " --> pdb=" O ASN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.578A pdb=" N GLU A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 260 removed outlier: 3.666A pdb=" N ALA A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.808A pdb=" N VAL A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 301 removed outlier: 3.870A pdb=" N ALA A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 313 through 321 removed outlier: 3.536A pdb=" N LYS A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.704A pdb=" N ARG A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 355 removed outlier: 3.849A pdb=" N CYS A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 379 Processing helix chain 'A' and resid 386 through 393 Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.875A pdb=" N GLN A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 462 removed outlier: 3.616A pdb=" N ASN A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 43 Processing helix chain 'B' and resid 51 through 61 removed outlier: 3.513A pdb=" N GLN B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 82 removed outlier: 3.564A pdb=" N PHE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 removed outlier: 3.834A pdb=" N MET B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 100 removed outlier: 4.300A pdb=" N THR B 97 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR B 98 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG B 100 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 118 Processing helix chain 'B' and resid 127 through 140 removed outlier: 3.564A pdb=" N THR B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 162 removed outlier: 3.682A pdb=" N TRP B 148 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 172 Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 193 through 209 removed outlier: 3.935A pdb=" N ILE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA B 207 " --> pdb=" O GLN B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 removed outlier: 4.014A pdb=" N LEU B 214 " --> pdb=" O ASN B 210 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B 215 " --> pdb=" O ASN B 211 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 249 removed outlier: 3.637A pdb=" N MET B 234 " --> pdb=" O HIS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 269 removed outlier: 3.827A pdb=" N THR B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.741A pdb=" N CYS B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.612A pdb=" N SER B 296 " --> pdb=" O PRO B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 322 through 333 removed outlier: 4.017A pdb=" N PHE B 326 " --> pdb=" O ASP B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 364 removed outlier: 3.860A pdb=" N LYS B 364 " --> pdb=" O ILE B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 381 through 395 removed outlier: 3.795A pdb=" N GLU B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 440 removed outlier: 3.558A pdb=" N THR B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN B 436 " --> pdb=" O ASN B 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 65 Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 90 through 96 removed outlier: 3.583A pdb=" N ILE C 93 " --> pdb=" O GLY C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 114 removed outlier: 3.607A pdb=" N GLY C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'C' and resid 139 through 153 removed outlier: 4.539A pdb=" N ALA C 143 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 177 through 195 removed outlier: 4.038A pdb=" N PHE C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR C 185 " --> pdb=" O PHE C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 removed outlier: 3.613A pdb=" N TYR C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 235 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 257 through 269 removed outlier: 3.606A pdb=" N HIS C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 282 removed outlier: 3.945A pdb=" N LEU C 275 " --> pdb=" O ASN C 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 276 " --> pdb=" O PRO C 272 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 289 removed outlier: 3.522A pdb=" N PHE C 286 " --> pdb=" O HIS C 282 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 312 removed outlier: 3.529A pdb=" N THR C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 312 " --> pdb=" O GLN C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 Processing helix chain 'C' and resid 330 through 344 removed outlier: 3.543A pdb=" N ALA C 334 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 399 removed outlier: 3.907A pdb=" N ASN C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 399 " --> pdb=" O GLN C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 408 Processing helix chain 'E' and resid 32 through 43 removed outlier: 3.709A pdb=" N GLN E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS E 43 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 72 Processing helix chain 'E' and resid 110 through 127 Processing helix chain 'E' and resid 148 through 161 removed outlier: 3.825A pdb=" N LEU E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN E 158 " --> pdb=" O THR E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 179 removed outlier: 3.546A pdb=" N THR E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 217 removed outlier: 3.516A pdb=" N HIS E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 242 Processing helix chain 'E' and resid 245 through 250 Processing helix chain 'E' and resid 258 through 280 removed outlier: 3.599A pdb=" N GLY E 264 " --> pdb=" O ASP E 260 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN E 265 " --> pdb=" O TYR E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 329 Processing helix chain 'F' and resid 44 through 62 removed outlier: 3.935A pdb=" N ILE F 48 " --> pdb=" O HIS F 44 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU F 62 " --> pdb=" O MET F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 114 removed outlier: 4.253A pdb=" N GLN F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 144 removed outlier: 4.325A pdb=" N VAL F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 207 removed outlier: 3.596A pdb=" N ILE F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR F 207 " --> pdb=" O VAL F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 248 removed outlier: 3.646A pdb=" N GLU F 219 " --> pdb=" O SER F 215 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG F 234 " --> pdb=" O MET F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 Processing helix chain 'F' and resid 272 through 313 Processing helix chain 'H' and resid 12 through 27 removed outlier: 3.549A pdb=" N LEU H 16 " --> pdb=" O SER H 12 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU H 25 " --> pdb=" O GLU H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 33 through 48 Processing helix chain 'H' and resid 49 through 60 removed outlier: 3.773A pdb=" N ALA H 53 " --> pdb=" O ASP H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 68 Processing helix chain 'H' and resid 69 through 84 removed outlier: 3.860A pdb=" N VAL H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 94 removed outlier: 4.099A pdb=" N ASN H 94 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 124 removed outlier: 3.908A pdb=" N ARG H 110 " --> pdb=" O MET H 106 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 137 Processing helix chain 'H' and resid 140 through 147 Processing helix chain 'H' and resid 148 through 152 removed outlier: 3.703A pdb=" N GLY H 152 " --> pdb=" O LEU H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 209 Processing helix chain 'I' and resid 20 through 33 removed outlier: 3.910A pdb=" N THR I 33 " --> pdb=" O GLN I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 55 Processing helix chain 'I' and resid 88 through 106 removed outlier: 3.624A pdb=" N ASP I 106 " --> pdb=" O ASN I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 137 removed outlier: 3.891A pdb=" N VAL I 132 " --> pdb=" O PHE I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 143 removed outlier: 4.062A pdb=" N HIS I 143 " --> pdb=" O TYR I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 149 removed outlier: 3.781A pdb=" N CYS I 149 " --> pdb=" O VAL I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 171 removed outlier: 3.645A pdb=" N TRP I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 189 removed outlier: 4.722A pdb=" N LYS I 177 " --> pdb=" O ARG I 173 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN I 178 " --> pdb=" O PRO I 174 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS I 185 " --> pdb=" O ASN I 181 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU I 186 " --> pdb=" O ALA I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 211 removed outlier: 4.099A pdb=" N GLU I 210 " --> pdb=" O GLN I 206 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU I 211 " --> pdb=" O SER I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 250 removed outlier: 4.064A pdb=" N PHE I 232 " --> pdb=" O TYR I 228 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU I 250 " --> pdb=" O ARG I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 279 removed outlier: 4.145A pdb=" N VAL I 275 " --> pdb=" O GLU I 271 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU I 279 " --> pdb=" O VAL I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 313 removed outlier: 3.520A pdb=" N GLU I 292 " --> pdb=" O ALA I 288 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU I 301 " --> pdb=" O GLU I 297 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ILE I 302 " --> pdb=" O LYS I 298 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS I 304 " --> pdb=" O LEU I 300 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN I 308 " --> pdb=" O HIS I 304 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN I 309 " --> pdb=" O THR I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 316 through 327 Processing helix chain 'I' and resid 330 through 356 removed outlier: 3.562A pdb=" N HIS I 345 " --> pdb=" O GLU I 341 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY I 356 " --> pdb=" O ILE I 352 " (cutoff:3.500A) Processing helix chain 'I' and resid 363 through 384 Processing helix chain 'I' and resid 388 through 405 removed outlier: 3.665A pdb=" N LYS I 397 " --> pdb=" O ALA I 393 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA I 398 " --> pdb=" O ALA I 394 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE I 403 " --> pdb=" O CYS I 399 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN I 405 " --> pdb=" O ARG I 401 " (cutoff:3.500A) Processing helix chain 'I' and resid 406 through 412 Processing helix chain 'I' and resid 417 through 430 removed outlier: 3.877A pdb=" N LEU I 421 " --> pdb=" O LYS I 417 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU I 422 " --> pdb=" O SER I 418 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 455 removed outlier: 4.342A pdb=" N TYR I 455 " --> pdb=" O VAL I 451 " (cutoff:3.500A) Processing helix chain 'I' and resid 458 through 477 removed outlier: 3.841A pdb=" N PHE I 462 " --> pdb=" O ASP I 458 " (cutoff:3.500A) Processing helix chain 'I' and resid 481 through 496 Processing helix chain 'I' and resid 497 through 502 removed outlier: 3.904A pdb=" N THR I 501 " --> pdb=" O GLY I 497 " (cutoff:3.500A) Processing helix chain 'I' and resid 504 through 528 removed outlier: 3.650A pdb=" N PHE I 508 " --> pdb=" O LEU I 504 " (cutoff:3.500A) Processing helix chain 'I' and resid 556 through 574 removed outlier: 3.571A pdb=" N GLU I 560 " --> pdb=" O PRO I 556 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG I 561 " --> pdb=" O SER I 557 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N SER I 562 " --> pdb=" O GLU I 558 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 615 Processing helix chain 'I' and resid 622 through 629 Processing helix chain 'I' and resid 632 through 646 removed outlier: 4.197A pdb=" N GLN I 638 " --> pdb=" O ASP I 634 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU I 643 " --> pdb=" O VAL I 639 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 723 Processing helix chain 'I' and resid 727 through 738 Processing helix chain 'I' and resid 745 through 759 removed outlier: 4.060A pdb=" N ILE I 749 " --> pdb=" O ARG I 745 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS I 750 " --> pdb=" O VAL I 746 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS I 751 " --> pdb=" O PRO I 747 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 57 removed outlier: 3.651A pdb=" N GLN J 57 " --> pdb=" O ILE J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 89 Processing helix chain 'L' and resid 18 through 22 removed outlier: 3.631A pdb=" N LYS L 22 " --> pdb=" O GLU L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 34 Processing helix chain 'L' and resid 57 through 65 removed outlier: 3.658A pdb=" N HIS L 64 " --> pdb=" O GLN L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 93 Processing helix chain 'L' and resid 96 through 111 removed outlier: 4.235A pdb=" N GLU L 102 " --> pdb=" O GLY L 98 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE L 104 " --> pdb=" O LEU L 100 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU L 105 " --> pdb=" O PHE L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 125 removed outlier: 3.780A pdb=" N VAL L 123 " --> pdb=" O THR L 119 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA L 124 " --> pdb=" O CYS L 120 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN L 125 " --> pdb=" O LYS L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 160 removed outlier: 3.508A pdb=" N GLU L 156 " --> pdb=" O GLN L 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 109 removed outlier: 3.925A pdb=" N LEU M 105 " --> pdb=" O PRO M 101 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY M 107 " --> pdb=" O GLU M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 122 removed outlier: 4.023A pdb=" N GLY M 122 " --> pdb=" O LEU M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 133 Processing helix chain 'M' and resid 148 through 158 removed outlier: 3.585A pdb=" N GLN M 158 " --> pdb=" O ARG M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 201 removed outlier: 3.822A pdb=" N LEU M 198 " --> pdb=" O GLU M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 219 through 228 Processing helix chain 'M' and resid 250 through 255 removed outlier: 4.459A pdb=" N CYS M 255 " --> pdb=" O LEU M 251 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 318 through 320 removed outlier: 8.057A pdb=" N ILE D 352 " --> pdb=" O THR B 367 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE B 369 " --> pdb=" O ILE D 352 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR B 367 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL A 382 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU C 315 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL A 417 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU C 317 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU C 315 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE C 360 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR H 126 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE C 351 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE H 128 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN H 154 " --> pdb=" O LEU H 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 110 through 112 Processing sheet with id=AA3, first strand: chain 'K' and resid 12 through 16 removed outlier: 9.011A pdb=" N LEU K 67 " --> pdb=" O LEU K 2 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS K 4 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU K 69 " --> pdb=" O LYS K 4 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS K 6 " --> pdb=" O LEU K 69 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N LEU K 71 " --> pdb=" O LYS K 6 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 12 through 13 removed outlier: 3.602A pdb=" N TYR N 12 " --> pdb=" O TYR N 19 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ILE N 66 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE N 59 " --> pdb=" O ILE N 66 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N LEU N 68 " --> pdb=" O TYR N 57 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR N 57 " --> pdb=" O LEU N 68 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG N 70 " --> pdb=" O VAL N 55 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 181 through 182 Processing sheet with id=AA6, first strand: chain 'C' and resid 137 through 138 Processing sheet with id=AA7, first strand: chain 'E' and resid 89 through 92 removed outlier: 6.868A pdb=" N TYR E 54 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ILE E 92 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS E 56 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE E 229 " --> pdb=" O ILE E 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 95 through 97 removed outlier: 6.594A pdb=" N TRP E 136 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ILE E 170 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N HIS E 138 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 183 through 185 removed outlier: 4.000A pdb=" N PHE F 151 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N PHE F 121 " --> pdb=" O GLY F 74 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY F 74 " --> pdb=" O PHE F 121 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY F 123 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY F 70 " --> pdb=" O TYR F 125 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS F 75 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL F 83 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA F 42 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL F 83 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL F 41 " --> pdb=" O THR F 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 91 through 93 Processing sheet with id=AB2, first strand: chain 'I' and resid 536 through 541 removed outlier: 9.389A pdb=" N VAL J 24 " --> pdb=" O GLY I 588 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY I 588 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 11.727A pdb=" N LYS J 26 " --> pdb=" O SER I 586 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N SER I 586 " --> pdb=" O LYS J 26 " (cutoff:3.500A) removed outlier: 10.716A pdb=" N ASN J 28 " --> pdb=" O GLN I 584 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N GLN I 584 " --> pdb=" O ASN J 28 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL J 30 " --> pdb=" O LEU I 582 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N THR I 600 " --> pdb=" O LEU I 680 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 619 through 621 removed outlier: 4.229A pdb=" N LYS I 670 " --> pdb=" O VAL I 650 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL I 650 " --> pdb=" O LYS I 670 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 725 through 726 Processing sheet with id=AB5, first strand: chain 'J' and resid 78 through 80 removed outlier: 7.418A pdb=" N VAL J 70 " --> pdb=" O TYR J 106 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N TYR J 106 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TRP J 72 " --> pdb=" O GLN J 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'M' and resid 139 through 140 Processing sheet with id=AB8, first strand: chain 'M' and resid 185 through 187 removed outlier: 7.138A pdb=" N MET M 186 " --> pdb=" O SER M 212 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N GLU M 214 " --> pdb=" O MET M 186 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 314 through 316 removed outlier: 4.122A pdb=" N LEU M 315 " --> pdb=" O HIS M 339 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER M 341 " --> pdb=" O LEU M 315 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU M 340 " --> pdb=" O GLN M 366 " (cutoff:3.500A) 1652 hydrogen bonds defined for protein. 4863 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: 4.69 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9626 1.35 - 1.47: 6832 1.47 - 1.60: 13155 1.60 - 1.72: 6 1.72 - 1.85: 255 Bond restraints: 29874 Sorted by residual: bond pdb=" O12 IHP B 501 " pdb=" P2 IHP B 501 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" O14 IHP B 501 " pdb=" P4 IHP B 501 " ideal model delta sigma weight residual 1.671 1.603 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" CA TYR A 211 " pdb=" C TYR A 211 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.29e-02 6.01e+03 1.10e+01 bond pdb=" O15 IHP B 501 " pdb=" P5 IHP B 501 " ideal model delta sigma weight residual 1.675 1.611 0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" O16 IHP B 501 " pdb=" P6 IHP B 501 " ideal model delta sigma weight residual 1.672 1.608 0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 29869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 39292 1.52 - 3.05: 874 3.05 - 4.57: 211 4.57 - 6.10: 46 6.10 - 7.62: 9 Bond angle restraints: 40432 Sorted by residual: angle pdb=" N VAL D 103 " pdb=" CA VAL D 103 " pdb=" C VAL D 103 " ideal model delta sigma weight residual 112.96 107.70 5.26 1.00e+00 1.00e+00 2.77e+01 angle pdb=" N TYR A 211 " pdb=" CA TYR A 211 " pdb=" C TYR A 211 " ideal model delta sigma weight residual 111.36 107.03 4.33 1.09e+00 8.42e-01 1.58e+01 angle pdb=" N ILE P 56 " pdb=" CA ILE P 56 " pdb=" C ILE P 56 " ideal model delta sigma weight residual 111.89 106.38 5.51 1.44e+00 4.82e-01 1.46e+01 angle pdb=" C GLU E 76 " pdb=" CA GLU E 76 " pdb=" CB GLU E 76 " ideal model delta sigma weight residual 109.89 115.91 -6.02 1.60e+00 3.91e-01 1.42e+01 angle pdb=" N VAL A 210 " pdb=" CA VAL A 210 " pdb=" C VAL A 210 " ideal model delta sigma weight residual 110.72 107.00 3.72 1.01e+00 9.80e-01 1.36e+01 ... (remaining 40427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 15552 17.91 - 35.81: 1846 35.81 - 53.72: 545 53.72 - 71.62: 145 71.62 - 89.53: 38 Dihedral angle restraints: 18126 sinusoidal: 7100 harmonic: 11026 Sorted by residual: dihedral pdb=" CA MET E 81 " pdb=" C MET E 81 " pdb=" N LEU E 82 " pdb=" CA LEU E 82 " ideal model delta harmonic sigma weight residual -180.00 -152.49 -27.51 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ILE M 201 " pdb=" C ILE M 201 " pdb=" N LEU M 202 " pdb=" CA LEU M 202 " ideal model delta harmonic sigma weight residual 180.00 153.74 26.26 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ILE J 44 " pdb=" C ILE J 44 " pdb=" N CYS J 45 " pdb=" CA CYS J 45 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 18123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 4047 0.052 - 0.105: 527 0.105 - 0.157: 88 0.157 - 0.210: 4 0.210 - 0.262: 4 Chirality restraints: 4670 Sorted by residual: chirality pdb=" CA ILE P 56 " pdb=" N ILE P 56 " pdb=" C ILE P 56 " pdb=" CB ILE P 56 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C1 IHP B 501 " pdb=" C2 IHP B 501 " pdb=" C6 IHP B 501 " pdb=" O11 IHP B 501 " both_signs ideal model delta sigma weight residual False 2.32 2.55 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C3 IHP B 501 " pdb=" C2 IHP B 501 " pdb=" C4 IHP B 501 " pdb=" O13 IHP B 501 " both_signs ideal model delta sigma weight residual False -2.34 -2.56 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 4667 not shown) Planarity restraints: 5136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 369 " 0.045 5.00e-02 4.00e+02 6.90e-02 7.62e+00 pdb=" N PRO C 370 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 370 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 370 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 42 " -0.196 9.50e-02 1.11e+02 8.81e-02 5.17e+00 pdb=" NE ARG K 42 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG K 42 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG K 42 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG K 42 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 209 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C SER A 209 " 0.038 2.00e-02 2.50e+03 pdb=" O SER A 209 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A 210 " -0.013 2.00e-02 2.50e+03 ... (remaining 5133 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 2 1.93 - 2.68: 630 2.68 - 3.42: 43510 3.42 - 4.16: 63609 4.16 - 4.90: 118099 Nonbonded interactions: 225850 Sorted by model distance: nonbonded pdb=" O GLY K 76 " pdb=" NZ LYS I 720 " model vdw 1.194 3.120 nonbonded pdb=" C GLY K 76 " pdb=" NZ LYS I 720 " model vdw 1.301 3.350 nonbonded pdb=" O21 IHP B 501 " pdb=" O32 IHP B 501 " model vdw 2.149 3.040 nonbonded pdb=" O GLU K 14 " pdb=" NZ LYS K 33 " model vdw 2.197 3.120 nonbonded pdb=" OE2 GLU B 252 " pdb=" ND2 ASN J 98 " model vdw 2.218 3.120 ... (remaining 225845 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.770 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 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 0.069 29886 Z= 0.158 Angle : 0.606 17.028 40440 Z= 0.321 Chirality : 0.037 0.262 4670 Planarity : 0.004 0.088 5136 Dihedral : 17.889 89.526 10937 Min Nonbonded Distance : 1.194 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.23 % Allowed : 24.46 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3644 helix: 1.07 (0.11), residues: 2201 sheet: -0.93 (0.36), residues: 215 loop : -1.56 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 764 TYR 0.020 0.001 TYR F 280 PHE 0.011 0.001 PHE A 446 TRP 0.032 0.001 TRP A 130 HIS 0.008 0.001 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00330 (29874) covalent geometry : angle 0.59703 (40432) SS BOND : bond 0.01450 ( 1) SS BOND : angle 3.98654 ( 2) hydrogen bonds : bond 0.14745 ( 1652) hydrogen bonds : angle 5.89362 ( 4863) metal coordination : bond 0.01515 ( 11) metal coordination : angle 8.03117 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 750 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7657 (mm-40) REVERT: D 91 LYS cc_start: 0.7697 (mmtm) cc_final: 0.7271 (mmtm) REVERT: D 100 GLU cc_start: 0.8092 (tt0) cc_final: 0.7514 (tm-30) REVERT: D 117 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7316 (mp0) REVERT: D 146 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7091 (tm-30) REVERT: D 193 ARG cc_start: 0.7763 (mtp180) cc_final: 0.7562 (tpp80) REVERT: D 221 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: D 252 ASP cc_start: 0.8385 (t0) cc_final: 0.8151 (t0) REVERT: G 11 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7808 (mt) REVERT: G 127 GLU cc_start: 0.6916 (tp30) cc_final: 0.6309 (tp30) REVERT: G 172 LYS cc_start: 0.8500 (mtmm) cc_final: 0.8247 (mtmm) REVERT: G 215 ASN cc_start: 0.8153 (t0) cc_final: 0.7924 (t0) REVERT: N 58 MET cc_start: 0.4935 (tmm) cc_final: 0.4494 (tmm) REVERT: A 90 MET cc_start: 0.8091 (mmm) cc_final: 0.7622 (mmm) REVERT: A 248 LYS cc_start: 0.8191 (tttt) cc_final: 0.7746 (ttpp) REVERT: A 306 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7924 (mp) REVERT: B 73 LYS cc_start: 0.6124 (mmtt) cc_final: 0.5686 (mmtt) REVERT: B 101 SER cc_start: 0.8945 (p) cc_final: 0.8654 (t) REVERT: B 128 LEU cc_start: 0.7398 (mt) cc_final: 0.6994 (tp) REVERT: B 196 GLU cc_start: 0.7866 (tt0) cc_final: 0.7599 (mt-10) REVERT: B 260 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: B 379 ASN cc_start: 0.8514 (t0) cc_final: 0.8058 (t0) REVERT: C 312 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7733 (mttp) REVERT: C 396 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7603 (tm-30) REVERT: E 38 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8079 (mm-30) REVERT: E 56 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8281 (mtpp) REVERT: E 166 VAL cc_start: 0.8880 (p) cc_final: 0.8542 (m) REVERT: E 193 TYR cc_start: 0.8120 (t80) cc_final: 0.7820 (t80) REVERT: E 225 GLU cc_start: 0.7289 (mp0) cc_final: 0.6778 (mp0) REVERT: E 272 LYS cc_start: 0.8379 (mttp) cc_final: 0.8138 (mttt) REVERT: F 234 ARG cc_start: 0.8066 (mmt-90) cc_final: 0.7721 (mpt180) REVERT: F 249 GLU cc_start: 0.7771 (mp0) cc_final: 0.7289 (mp0) REVERT: F 285 ASP cc_start: 0.7447 (m-30) cc_final: 0.7136 (m-30) REVERT: H 22 ASN cc_start: 0.7722 (m110) cc_final: 0.7440 (m110) REVERT: H 127 SER cc_start: 0.7986 (p) cc_final: 0.7761 (m) REVERT: H 195 GLN cc_start: 0.7173 (pp30) cc_final: 0.6917 (pp30) REVERT: I 278 TYR cc_start: 0.6399 (OUTLIER) cc_final: 0.6139 (m-10) REVERT: I 417 LYS cc_start: 0.7943 (mmmm) cc_final: 0.7502 (mmmm) REVERT: I 427 ASP cc_start: 0.7484 (t0) cc_final: 0.6223 (t0) REVERT: I 469 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6072 (mtp) REVERT: I 503 LYS cc_start: 0.8533 (ttpt) cc_final: 0.8235 (ttmm) REVERT: I 581 TRP cc_start: 0.7408 (m100) cc_final: 0.7125 (m-10) REVERT: I 735 LEU cc_start: 0.8922 (mt) cc_final: 0.8708 (mt) REVERT: L 90 GLN cc_start: 0.7475 (mm110) cc_final: 0.7236 (mm-40) REVERT: L 103 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.6010 (pp) REVERT: M 398 ARG cc_start: 0.8360 (mtt-85) cc_final: 0.7895 (mmt90) REVERT: M 412 ILE cc_start: 0.7234 (mp) cc_final: 0.6985 (mp) outliers start: 101 outliers final: 76 residues processed: 815 average time/residue: 0.2017 time to fit residues: 257.3032 Evaluate side-chains 800 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 716 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 69 PHE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain K residue 27 LYS Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 132 ASN Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain I residue 278 TYR Chi-restraints excluded: chain I residue 293 GLN Chi-restraints excluded: chain I residue 324 ASN Chi-restraints excluded: chain I residue 469 MET Chi-restraints excluded: chain I residue 502 SER Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 587 LYS Chi-restraints excluded: chain I residue 597 ASN Chi-restraints excluded: chain I residue 666 ASP Chi-restraints excluded: chain J residue 68 CYS Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 103 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 403 GLN G 60 ASN N 56 HIS A 151 ASN A 394 ASN A 447 GLN C 368 ASN E 123 ASN E 243 ASN F 50 ASN H 94 ASN H 96 HIS I 192 ASN I 374 HIS I 494 GLN J 104 GLN L 64 HIS M 184 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.161548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.131950 restraints weight = 51294.933| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.36 r_work: 0.3605 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29886 Z= 0.143 Angle : 0.593 14.217 40440 Z= 0.307 Chirality : 0.040 0.233 4670 Planarity : 0.004 0.047 5136 Dihedral : 7.444 67.700 4203 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.19 % Allowed : 22.70 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3644 helix: 1.29 (0.11), residues: 2243 sheet: -0.89 (0.37), residues: 205 loop : -1.57 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 764 TYR 0.017 0.001 TYR F 280 PHE 0.028 0.001 PHE B 85 TRP 0.019 0.002 TRP H 82 HIS 0.006 0.001 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00302 (29874) covalent geometry : angle 0.58549 (40432) SS BOND : bond 0.06510 ( 1) SS BOND : angle 6.48141 ( 2) hydrogen bonds : bond 0.05392 ( 1652) hydrogen bonds : angle 4.53571 ( 4863) metal coordination : bond 0.01297 ( 11) metal coordination : angle 6.90610 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 743 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8049 (tp40) REVERT: D 100 GLU cc_start: 0.8180 (tt0) cc_final: 0.7513 (tm-30) REVERT: D 117 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7362 (mp0) REVERT: D 146 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7437 (tm-30) REVERT: D 221 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: D 256 GLN cc_start: 0.7652 (mp10) cc_final: 0.7432 (mp10) REVERT: G 47 LEU cc_start: 0.8251 (tp) cc_final: 0.7957 (tt) REVERT: G 172 LYS cc_start: 0.8489 (mtmm) cc_final: 0.8247 (mtmm) REVERT: G 191 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7979 (mm-40) REVERT: G 215 ASN cc_start: 0.8080 (t0) cc_final: 0.7845 (t0) REVERT: N 58 MET cc_start: 0.4960 (OUTLIER) cc_final: 0.4632 (tmm) REVERT: A 35 TYR cc_start: 0.7461 (p90) cc_final: 0.7194 (p90) REVERT: A 84 ARG cc_start: 0.8003 (mtm110) cc_final: 0.7751 (mtm110) REVERT: A 90 MET cc_start: 0.8067 (mmm) cc_final: 0.7573 (mmm) REVERT: A 92 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6760 (pt0) REVERT: A 132 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: A 211 TYR cc_start: 0.7319 (m-80) cc_final: 0.7000 (m-80) REVERT: A 214 ASN cc_start: 0.7881 (t0) cc_final: 0.7431 (t0) REVERT: A 248 LYS cc_start: 0.8283 (tttt) cc_final: 0.7838 (ttpp) REVERT: B 73 LYS cc_start: 0.6391 (mmtt) cc_final: 0.5968 (mmtt) REVERT: B 100 ARG cc_start: 0.8678 (ptm160) cc_final: 0.8378 (ttp80) REVERT: B 101 SER cc_start: 0.9068 (p) cc_final: 0.8786 (t) REVERT: B 128 LEU cc_start: 0.7548 (mt) cc_final: 0.7019 (tp) REVERT: B 196 GLU cc_start: 0.7931 (tt0) cc_final: 0.7718 (mt-10) REVERT: B 250 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7546 (mm-30) REVERT: B 272 ARG cc_start: 0.7996 (mtp180) cc_final: 0.7794 (mtp180) REVERT: B 307 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7200 (tm-30) REVERT: B 379 ASN cc_start: 0.8447 (t0) cc_final: 0.8109 (t0) REVERT: C 263 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8043 (mp) REVERT: C 309 ARG cc_start: 0.8427 (ttm-80) cc_final: 0.8036 (ttp-170) REVERT: C 396 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7572 (tm-30) REVERT: C 397 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7815 (tp) REVERT: E 45 TRP cc_start: 0.7949 (p90) cc_final: 0.7407 (p90) REVERT: E 77 VAL cc_start: 0.8032 (m) cc_final: 0.7818 (m) REVERT: E 123 ASN cc_start: 0.8528 (m-40) cc_final: 0.8165 (m-40) REVERT: E 166 VAL cc_start: 0.8921 (p) cc_final: 0.8592 (m) REVERT: E 193 TYR cc_start: 0.8066 (t80) cc_final: 0.7718 (t80) REVERT: E 225 GLU cc_start: 0.7497 (mp0) cc_final: 0.7090 (mp0) REVERT: E 272 LYS cc_start: 0.8434 (mttp) cc_final: 0.8209 (mttt) REVERT: F 166 SER cc_start: 0.8192 (OUTLIER) cc_final: 0.7805 (p) REVERT: F 185 GLU cc_start: 0.7754 (mp0) cc_final: 0.7193 (mt-10) REVERT: F 234 ARG cc_start: 0.8146 (mmt-90) cc_final: 0.7918 (mpt180) REVERT: F 249 GLU cc_start: 0.7765 (mp0) cc_final: 0.7520 (mp0) REVERT: F 277 THR cc_start: 0.7859 (m) cc_final: 0.7592 (p) REVERT: H 18 ASP cc_start: 0.8369 (m-30) cc_final: 0.7822 (m-30) REVERT: H 22 ASN cc_start: 0.7750 (m110) cc_final: 0.7430 (m110) REVERT: H 127 SER cc_start: 0.8047 (p) cc_final: 0.7809 (m) REVERT: H 195 GLN cc_start: 0.7085 (pp30) cc_final: 0.6804 (pp30) REVERT: I 157 TYR cc_start: 0.5656 (t80) cc_final: 0.5345 (t80) REVERT: I 273 ARG cc_start: 0.8167 (mtm110) cc_final: 0.7757 (mtm110) REVERT: I 275 VAL cc_start: 0.7868 (t) cc_final: 0.7139 (m) REVERT: I 417 LYS cc_start: 0.7941 (mmmm) cc_final: 0.7505 (mmmm) REVERT: I 428 SER cc_start: 0.8300 (p) cc_final: 0.8034 (p) REVERT: I 450 MET cc_start: 0.6956 (tmm) cc_final: 0.6688 (tmm) REVERT: I 503 LYS cc_start: 0.8284 (ttpt) cc_final: 0.8012 (ttmm) REVERT: I 511 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8074 (mp) REVERT: I 735 LEU cc_start: 0.8889 (mt) cc_final: 0.8636 (mt) REVERT: J 46 ARG cc_start: 0.8166 (mtt90) cc_final: 0.7945 (mpt180) REVERT: L 90 GLN cc_start: 0.7532 (mm110) cc_final: 0.7105 (mm-40) REVERT: L 103 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.6064 (pp) REVERT: M 398 ARG cc_start: 0.8388 (mtt-85) cc_final: 0.7878 (mtt-85) REVERT: M 412 ILE cc_start: 0.7181 (mp) cc_final: 0.6968 (mp) outliers start: 131 outliers final: 72 residues processed: 819 average time/residue: 0.2017 time to fit residues: 256.6592 Evaluate side-chains 790 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 709 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 69 PHE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain N residue 58 MET Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 376 LYS Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 278 TYR Chi-restraints excluded: chain I residue 324 ASN Chi-restraints excluded: chain I residue 434 SER Chi-restraints excluded: chain I residue 469 MET Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 552 THR Chi-restraints excluded: chain I residue 578 LYS Chi-restraints excluded: chain I residue 585 LEU Chi-restraints excluded: chain I residue 597 ASN Chi-restraints excluded: chain I residue 721 MET Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 61 TRP Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain M residue 184 GLN Chi-restraints excluded: chain M residue 207 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 321 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 345 optimal weight: 3.9990 chunk 333 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 403 GLN A 394 ASN A 447 GLN B 208 GLN B 211 ASN E 162 GLN E 243 ASN F 50 ASN F 300 ASN H 96 HIS I 192 ASN I 374 HIS I 564 GLN J 104 GLN L 64 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.159285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129563 restraints weight = 51351.368| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.36 r_work: 0.3580 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 29886 Z= 0.218 Angle : 0.630 15.696 40440 Z= 0.324 Chirality : 0.042 0.212 4670 Planarity : 0.004 0.050 5136 Dihedral : 6.395 59.713 4098 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.90 % Allowed : 23.79 % Favored : 71.31 % 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: 0.17 (0.14), residues: 3644 helix: 1.15 (0.11), residues: 2231 sheet: -0.89 (0.35), residues: 222 loop : -1.67 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 135 TYR 0.023 0.002 TYR F 280 PHE 0.020 0.002 PHE I 243 TRP 0.022 0.002 TRP A 130 HIS 0.007 0.001 HIS I 524 Details of bonding type rmsd covalent geometry : bond 0.00501 (29874) covalent geometry : angle 0.62241 (40432) SS BOND : bond 0.01441 ( 1) SS BOND : angle 2.37860 ( 2) hydrogen bonds : bond 0.05990 ( 1652) hydrogen bonds : angle 4.56582 ( 4863) metal coordination : bond 0.01241 ( 11) metal coordination : angle 7.84456 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 740 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 GLN cc_start: 0.8256 (mm-40) cc_final: 0.8007 (tp40) REVERT: D 70 CYS cc_start: 0.6006 (OUTLIER) cc_final: 0.5617 (m) REVERT: D 100 GLU cc_start: 0.8179 (tt0) cc_final: 0.7528 (tm-30) REVERT: D 256 GLN cc_start: 0.7676 (mp10) cc_final: 0.7416 (mp10) REVERT: G 45 GLU cc_start: 0.7541 (mp0) cc_final: 0.7221 (mp0) REVERT: G 172 LYS cc_start: 0.8492 (mtmm) cc_final: 0.8218 (mtmm) REVERT: G 191 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8074 (mm-40) REVERT: G 208 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7556 (tm-30) REVERT: G 215 ASN cc_start: 0.8089 (t0) cc_final: 0.7856 (t0) REVERT: N 58 MET cc_start: 0.4928 (OUTLIER) cc_final: 0.4568 (tmm) REVERT: A 90 MET cc_start: 0.8149 (mmm) cc_final: 0.7713 (mmm) REVERT: A 92 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6920 (pt0) REVERT: A 211 TYR cc_start: 0.7394 (m-80) cc_final: 0.7192 (m-80) REVERT: A 214 ASN cc_start: 0.8048 (t0) cc_final: 0.7548 (t0) REVERT: A 248 LYS cc_start: 0.8304 (tttt) cc_final: 0.7802 (ttpp) REVERT: A 306 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8020 (mp) REVERT: A 410 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8297 (mm-30) REVERT: A 418 ASP cc_start: 0.7989 (t0) cc_final: 0.7786 (t0) REVERT: B 73 LYS cc_start: 0.6332 (mmtt) cc_final: 0.5888 (mmtt) REVERT: B 100 ARG cc_start: 0.8714 (ptm160) cc_final: 0.8382 (ttp-110) REVERT: B 101 SER cc_start: 0.9090 (p) cc_final: 0.8797 (t) REVERT: B 111 SER cc_start: 0.8642 (m) cc_final: 0.8319 (p) REVERT: B 128 LEU cc_start: 0.7520 (mt) cc_final: 0.7120 (tp) REVERT: B 196 GLU cc_start: 0.8114 (tt0) cc_final: 0.7852 (mt-10) REVERT: B 250 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 260 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: B 307 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7212 (tm-30) REVERT: B 379 ASN cc_start: 0.8504 (t0) cc_final: 0.8137 (t0) REVERT: C 263 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8046 (mp) REVERT: C 396 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7619 (tm-30) REVERT: E 45 TRP cc_start: 0.8014 (p90) cc_final: 0.7584 (p90) REVERT: E 76 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6712 (mm-30) REVERT: E 77 VAL cc_start: 0.8097 (m) cc_final: 0.7882 (m) REVERT: E 78 MET cc_start: 0.7794 (mmm) cc_final: 0.7583 (tpp) REVERT: E 166 VAL cc_start: 0.8918 (p) cc_final: 0.8605 (m) REVERT: E 171 ASP cc_start: 0.8053 (p0) cc_final: 0.7797 (p0) REVERT: E 193 TYR cc_start: 0.8102 (t80) cc_final: 0.7760 (t80) REVERT: E 225 GLU cc_start: 0.7448 (mp0) cc_final: 0.7061 (mp0) REVERT: E 272 LYS cc_start: 0.8467 (mttp) cc_final: 0.8244 (mttt) REVERT: F 76 GLN cc_start: 0.5804 (OUTLIER) cc_final: 0.5335 (pp30) REVERT: F 166 SER cc_start: 0.8285 (OUTLIER) cc_final: 0.7861 (p) REVERT: F 185 GLU cc_start: 0.7746 (mp0) cc_final: 0.7434 (mt-10) REVERT: F 249 GLU cc_start: 0.7799 (mp0) cc_final: 0.7416 (mp0) REVERT: F 277 THR cc_start: 0.7948 (OUTLIER) cc_final: 0.7631 (p) REVERT: H 18 ASP cc_start: 0.8287 (m-30) cc_final: 0.7703 (m-30) REVERT: H 22 ASN cc_start: 0.7708 (m110) cc_final: 0.7375 (m110) REVERT: H 116 ARG cc_start: 0.6422 (OUTLIER) cc_final: 0.5327 (ptt180) REVERT: H 127 SER cc_start: 0.8064 (p) cc_final: 0.7783 (m) REVERT: H 195 GLN cc_start: 0.7076 (pp30) cc_final: 0.6783 (pp30) REVERT: I 157 TYR cc_start: 0.5260 (OUTLIER) cc_final: 0.4961 (t80) REVERT: I 273 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7764 (mtm110) REVERT: I 287 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7527 (pt) REVERT: I 380 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7972 (tp) REVERT: I 417 LYS cc_start: 0.8038 (mmmm) cc_final: 0.7474 (mmmm) REVERT: I 428 SER cc_start: 0.8361 (p) cc_final: 0.8122 (p) REVERT: I 450 MET cc_start: 0.7004 (tmm) cc_final: 0.6701 (tmm) REVERT: I 503 LYS cc_start: 0.8377 (ttpt) cc_final: 0.8090 (ttmm) REVERT: I 510 ASP cc_start: 0.7933 (m-30) cc_final: 0.7652 (m-30) REVERT: I 511 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8121 (mp) REVERT: I 735 LEU cc_start: 0.8921 (mt) cc_final: 0.8676 (mt) REVERT: J 46 ARG cc_start: 0.8295 (mtt90) cc_final: 0.8060 (mpt180) REVERT: L 90 GLN cc_start: 0.7165 (mm110) cc_final: 0.6848 (mm-40) REVERT: L 103 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.6117 (pp) REVERT: M 398 ARG cc_start: 0.8488 (mtt-85) cc_final: 0.7956 (mtt-85) REVERT: M 412 ILE cc_start: 0.7158 (mp) cc_final: 0.6920 (mp) outliers start: 153 outliers final: 102 residues processed: 830 average time/residue: 0.2015 time to fit residues: 261.8140 Evaluate side-chains 844 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 726 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 69 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 58 MET Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 376 LYS Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 76 GLN Chi-restraints excluded: chain F residue 80 ASN Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 157 TYR Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 167 TRP Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 278 TYR Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 324 ASN Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 469 MET Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 501 THR Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 525 LEU Chi-restraints excluded: chain I residue 552 THR Chi-restraints excluded: chain I residue 572 SER Chi-restraints excluded: chain I residue 578 LYS Chi-restraints excluded: chain I residue 585 LEU Chi-restraints excluded: chain I residue 597 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain I residue 622 VAL Chi-restraints excluded: chain I residue 721 MET Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain M residue 220 ASP Chi-restraints excluded: chain M residue 282 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 367 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 chunk 340 optimal weight: 8.9990 chunk 264 optimal weight: 0.7980 chunk 95 optimal weight: 0.1980 chunk 258 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 232 optimal weight: 0.1980 chunk 311 optimal weight: 1.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN G 150 GLN A 394 ASN A 447 GLN B 176 HIS B 177 GLN E 159 GLN E 243 ASN F 300 ASN H 96 HIS I 51 ASN I 192 ASN ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS J 104 GLN L 49 ASN L 64 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.161751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.133573 restraints weight = 51130.051| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.52 r_work: 0.3615 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29886 Z= 0.125 Angle : 0.566 13.774 40440 Z= 0.290 Chirality : 0.039 0.204 4670 Planarity : 0.004 0.047 5136 Dihedral : 6.200 59.610 4094 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.51 % Allowed : 23.18 % Favored : 71.31 % 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 (0.14), residues: 3644 helix: 1.31 (0.11), residues: 2259 sheet: -0.83 (0.36), residues: 216 loop : -1.61 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 110 TYR 0.019 0.001 TYR F 280 PHE 0.013 0.001 PHE I 566 TRP 0.022 0.002 TRP A 130 HIS 0.006 0.001 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00264 (29874) covalent geometry : angle 0.56045 (40432) SS BOND : bond 0.00712 ( 1) SS BOND : angle 1.09578 ( 2) hydrogen bonds : bond 0.04813 ( 1652) hydrogen bonds : angle 4.29421 ( 4863) metal coordination : bond 0.01579 ( 11) metal coordination : angle 6.54158 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 734 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7490 (tm-30) REVERT: D 70 CYS cc_start: 0.6040 (OUTLIER) cc_final: 0.5692 (m) REVERT: D 96 VAL cc_start: 0.7257 (OUTLIER) cc_final: 0.7041 (t) REVERT: D 193 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7616 (ttt-90) REVERT: D 256 GLN cc_start: 0.7596 (mp10) cc_final: 0.7369 (mp10) REVERT: G 47 LEU cc_start: 0.8204 (tp) cc_final: 0.7868 (tt) REVERT: G 92 GLN cc_start: 0.7739 (mt0) cc_final: 0.7488 (mt0) REVERT: G 127 GLU cc_start: 0.6928 (tp30) cc_final: 0.6650 (mp0) REVERT: G 172 LYS cc_start: 0.8413 (mtmm) cc_final: 0.8162 (mtmm) REVERT: G 191 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8144 (mm-40) REVERT: G 207 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7324 (mp10) REVERT: G 208 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7545 (tm-30) REVERT: G 212 GLU cc_start: 0.8154 (tp30) cc_final: 0.7894 (tp30) REVERT: G 215 ASN cc_start: 0.8012 (t0) cc_final: 0.7785 (t0) REVERT: N 58 MET cc_start: 0.5133 (OUTLIER) cc_final: 0.4799 (tmm) REVERT: A 90 MET cc_start: 0.7994 (mmm) cc_final: 0.7544 (mmm) REVERT: A 211 TYR cc_start: 0.7302 (m-80) cc_final: 0.6948 (m-80) REVERT: A 214 ASN cc_start: 0.8083 (t0) cc_final: 0.7581 (t0) REVERT: A 248 LYS cc_start: 0.8269 (tttt) cc_final: 0.7880 (tttt) REVERT: A 262 LYS cc_start: 0.8671 (ttpt) cc_final: 0.8199 (ttpt) REVERT: A 307 GLN cc_start: 0.8256 (tm-30) cc_final: 0.8047 (tm-30) REVERT: A 418 ASP cc_start: 0.7927 (t0) cc_final: 0.7712 (t0) REVERT: B 73 LYS cc_start: 0.6335 (mmtt) cc_final: 0.5996 (mmtt) REVERT: B 100 ARG cc_start: 0.8680 (ptm160) cc_final: 0.8359 (ttp-110) REVERT: B 101 SER cc_start: 0.9047 (p) cc_final: 0.8768 (t) REVERT: B 111 SER cc_start: 0.8580 (m) cc_final: 0.8254 (p) REVERT: B 115 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7937 (tt) REVERT: B 128 LEU cc_start: 0.7416 (mt) cc_final: 0.6816 (tp) REVERT: B 133 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6849 (mt-10) REVERT: B 177 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7124 (mm-40) REVERT: B 225 LYS cc_start: 0.8213 (mppt) cc_final: 0.7970 (mppt) REVERT: B 238 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7558 (mmm160) REVERT: B 250 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7595 (mm-30) REVERT: B 260 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: B 307 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7093 (tm-30) REVERT: B 379 ASN cc_start: 0.8486 (t0) cc_final: 0.8105 (t0) REVERT: C 263 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8042 (mp) REVERT: C 381 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7908 (mp) REVERT: C 389 ARG cc_start: 0.8247 (tpp80) cc_final: 0.7928 (ttp-110) REVERT: C 396 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7594 (tm-30) REVERT: E 35 GLN cc_start: 0.8246 (tp40) cc_final: 0.8038 (tp40) REVERT: E 45 TRP cc_start: 0.7905 (p90) cc_final: 0.7470 (p90) REVERT: E 56 LYS cc_start: 0.8696 (mtpt) cc_final: 0.8375 (mtpp) REVERT: E 77 VAL cc_start: 0.8059 (m) cc_final: 0.7843 (m) REVERT: E 166 VAL cc_start: 0.8866 (p) cc_final: 0.8572 (m) REVERT: E 193 TYR cc_start: 0.8032 (t80) cc_final: 0.7662 (t80) REVERT: E 225 GLU cc_start: 0.7431 (mp0) cc_final: 0.7022 (mp0) REVERT: E 272 LYS cc_start: 0.8443 (mttp) cc_final: 0.8218 (mttt) REVERT: F 69 ILE cc_start: 0.8359 (mm) cc_final: 0.8142 (mm) REVERT: F 76 GLN cc_start: 0.5743 (OUTLIER) cc_final: 0.5284 (pp30) REVERT: F 106 TYR cc_start: 0.8133 (m-80) cc_final: 0.7614 (m-80) REVERT: F 124 TRP cc_start: 0.8582 (p-90) cc_final: 0.8119 (p-90) REVERT: F 165 VAL cc_start: 0.7792 (OUTLIER) cc_final: 0.7521 (p) REVERT: F 166 SER cc_start: 0.8259 (OUTLIER) cc_final: 0.7796 (p) REVERT: F 185 GLU cc_start: 0.7755 (mp0) cc_final: 0.7224 (mt-10) REVERT: F 249 GLU cc_start: 0.7742 (mp0) cc_final: 0.7532 (mp0) REVERT: F 277 THR cc_start: 0.7847 (m) cc_final: 0.7541 (p) REVERT: H 18 ASP cc_start: 0.8282 (m-30) cc_final: 0.7706 (m-30) REVERT: H 22 ASN cc_start: 0.7673 (m110) cc_final: 0.7321 (m110) REVERT: H 116 ARG cc_start: 0.6420 (OUTLIER) cc_final: 0.5338 (ptt180) REVERT: H 195 GLN cc_start: 0.7064 (pp30) cc_final: 0.6771 (pp30) REVERT: I 157 TYR cc_start: 0.5446 (OUTLIER) cc_final: 0.5088 (t80) REVERT: I 318 ASP cc_start: 0.6988 (p0) cc_final: 0.6167 (p0) REVERT: I 380 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7898 (tp) REVERT: I 417 LYS cc_start: 0.7984 (mmmm) cc_final: 0.7454 (mmmm) REVERT: I 428 SER cc_start: 0.8336 (p) cc_final: 0.8101 (p) REVERT: I 450 MET cc_start: 0.6973 (tmm) cc_final: 0.6643 (tmm) REVERT: I 503 LYS cc_start: 0.8258 (ttpt) cc_final: 0.7984 (ttmm) REVERT: I 511 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8049 (mp) REVERT: I 735 LEU cc_start: 0.8875 (mt) cc_final: 0.8628 (mt) REVERT: L 90 GLN cc_start: 0.6812 (mm110) cc_final: 0.6590 (mm-40) REVERT: L 103 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6211 (pp) REVERT: M 398 ARG cc_start: 0.8419 (mtt-85) cc_final: 0.7857 (mtt-85) REVERT: M 412 ILE cc_start: 0.7147 (OUTLIER) cc_final: 0.6925 (mp) outliers start: 172 outliers final: 98 residues processed: 845 average time/residue: 0.1914 time to fit residues: 252.8178 Evaluate side-chains 844 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 727 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 58 MET Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 177 GLN Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 376 LYS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 76 GLN Chi-restraints excluded: chain F residue 80 ASN Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 157 TYR Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 278 TYR Chi-restraints excluded: chain I residue 324 ASN Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 434 SER Chi-restraints excluded: chain I residue 469 MET Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 552 THR Chi-restraints excluded: chain I residue 578 LYS Chi-restraints excluded: chain I residue 585 LEU Chi-restraints excluded: chain I residue 597 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain I residue 721 MET Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain M residue 220 ASP Chi-restraints excluded: chain M residue 282 SER Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 412 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 318 optimal weight: 0.1980 chunk 331 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 342 optimal weight: 6.9990 chunk 251 optimal weight: 0.9980 chunk 191 optimal weight: 0.4980 chunk 209 optimal weight: 0.9990 chunk 315 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 247 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 176 ASN A 376 GLN A 394 ASN A 447 GLN B 169 GLN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN E 155 GLN E 243 ASN F 50 ASN H 96 HIS ** I 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS J 104 GLN L 64 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.161660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.132072 restraints weight = 51353.877| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.38 r_work: 0.3612 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29886 Z= 0.133 Angle : 0.569 13.366 40440 Z= 0.291 Chirality : 0.039 0.217 4670 Planarity : 0.004 0.049 5136 Dihedral : 6.054 58.554 4087 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.22 % Allowed : 24.34 % 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: 0.44 (0.14), residues: 3644 helix: 1.35 (0.11), residues: 2256 sheet: -0.62 (0.36), residues: 213 loop : -1.63 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 764 TYR 0.026 0.001 TYR E 114 PHE 0.028 0.001 PHE I 243 TRP 0.024 0.002 TRP A 130 HIS 0.005 0.001 HIS L 64 Details of bonding type rmsd covalent geometry : bond 0.00290 (29874) covalent geometry : angle 0.56400 (40432) SS BOND : bond 0.00701 ( 1) SS BOND : angle 0.89091 ( 2) hydrogen bonds : bond 0.04786 ( 1652) hydrogen bonds : angle 4.24567 ( 4863) metal coordination : bond 0.01242 ( 11) metal coordination : angle 6.42081 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 733 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7468 (tm-30) REVERT: D 70 CYS cc_start: 0.5850 (OUTLIER) cc_final: 0.5542 (m) REVERT: D 185 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7603 (mp) REVERT: D 193 ARG cc_start: 0.8060 (mmm-85) cc_final: 0.7584 (ttt-90) REVERT: D 256 GLN cc_start: 0.7580 (mp10) cc_final: 0.7335 (mp10) REVERT: D 286 MET cc_start: 0.7364 (mmp) cc_final: 0.7077 (mmp) REVERT: G 92 GLN cc_start: 0.7781 (mt0) cc_final: 0.7518 (mt0) REVERT: G 127 GLU cc_start: 0.6981 (tp30) cc_final: 0.6696 (mp0) REVERT: G 162 ILE cc_start: 0.7783 (tt) cc_final: 0.7574 (tp) REVERT: G 172 LYS cc_start: 0.8363 (mtmm) cc_final: 0.8109 (mtmm) REVERT: G 191 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8142 (mm-40) REVERT: G 208 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7587 (tm-30) REVERT: G 212 GLU cc_start: 0.8177 (tp30) cc_final: 0.7921 (tp30) REVERT: G 215 ASN cc_start: 0.8007 (t0) cc_final: 0.7779 (t0) REVERT: N 58 MET cc_start: 0.5147 (OUTLIER) cc_final: 0.4808 (tmm) REVERT: A 84 ARG cc_start: 0.8310 (ptp90) cc_final: 0.8007 (ptp90) REVERT: A 211 TYR cc_start: 0.7342 (m-80) cc_final: 0.6981 (m-80) REVERT: A 214 ASN cc_start: 0.8074 (t0) cc_final: 0.7545 (t0) REVERT: A 257 GLU cc_start: 0.7982 (tt0) cc_final: 0.7605 (tt0) REVERT: A 262 LYS cc_start: 0.8662 (ttpt) cc_final: 0.8232 (tttt) REVERT: A 279 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7838 (m-30) REVERT: A 307 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7997 (tm-30) REVERT: A 418 ASP cc_start: 0.7957 (t0) cc_final: 0.7740 (t0) REVERT: B 73 LYS cc_start: 0.6268 (mmtt) cc_final: 0.6036 (mmtt) REVERT: B 100 ARG cc_start: 0.8687 (ptm160) cc_final: 0.8386 (ttp-110) REVERT: B 101 SER cc_start: 0.9045 (p) cc_final: 0.8787 (t) REVERT: B 111 SER cc_start: 0.8605 (m) cc_final: 0.8290 (p) REVERT: B 128 LEU cc_start: 0.7396 (mt) cc_final: 0.6821 (tp) REVERT: B 133 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6850 (mt-10) REVERT: B 176 HIS cc_start: 0.7604 (m-70) cc_final: 0.7237 (m170) REVERT: B 238 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7626 (mmm160) REVERT: B 250 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7649 (mm-30) REVERT: B 260 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: B 379 ASN cc_start: 0.8487 (t0) cc_final: 0.8092 (t0) REVERT: C 119 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7924 (ptt180) REVERT: C 263 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8034 (mp) REVERT: C 381 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7918 (mp) REVERT: C 396 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7602 (tm-30) REVERT: E 35 GLN cc_start: 0.8237 (tp40) cc_final: 0.8007 (tp40) REVERT: E 45 TRP cc_start: 0.7930 (p90) cc_final: 0.7457 (p90) REVERT: E 52 PHE cc_start: 0.7923 (m-10) cc_final: 0.7647 (m-10) REVERT: E 166 VAL cc_start: 0.8876 (p) cc_final: 0.8573 (m) REVERT: E 193 TYR cc_start: 0.8060 (t80) cc_final: 0.7723 (t80) REVERT: E 225 GLU cc_start: 0.7420 (mp0) cc_final: 0.7006 (mp0) REVERT: F 76 GLN cc_start: 0.5730 (OUTLIER) cc_final: 0.5204 (pp30) REVERT: F 106 TYR cc_start: 0.8127 (m-80) cc_final: 0.7504 (m-80) REVERT: F 166 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.7905 (p) REVERT: F 185 GLU cc_start: 0.7668 (mp0) cc_final: 0.7169 (mt-10) REVERT: F 249 GLU cc_start: 0.7765 (mp0) cc_final: 0.7531 (mp0) REVERT: F 277 THR cc_start: 0.7818 (m) cc_final: 0.7530 (p) REVERT: H 18 ASP cc_start: 0.8287 (m-30) cc_final: 0.7692 (m-30) REVERT: H 22 ASN cc_start: 0.7678 (m110) cc_final: 0.7307 (m110) REVERT: H 116 ARG cc_start: 0.6402 (OUTLIER) cc_final: 0.5322 (ptt180) REVERT: H 195 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6697 (pp30) REVERT: I 157 TYR cc_start: 0.5400 (OUTLIER) cc_final: 0.5121 (t80) REVERT: I 318 ASP cc_start: 0.7034 (p0) cc_final: 0.6333 (p0) REVERT: I 380 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7939 (tp) REVERT: I 417 LYS cc_start: 0.7983 (mmmm) cc_final: 0.7474 (mmmm) REVERT: I 428 SER cc_start: 0.8395 (p) cc_final: 0.8163 (p) REVERT: I 450 MET cc_start: 0.6966 (tmm) cc_final: 0.6634 (tmm) REVERT: I 503 LYS cc_start: 0.8271 (ttpt) cc_final: 0.7992 (ttmm) REVERT: I 511 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8069 (mp) REVERT: I 722 ARG cc_start: 0.8601 (tpp80) cc_final: 0.8123 (tpp80) REVERT: I 735 LEU cc_start: 0.8920 (mt) cc_final: 0.8663 (mt) REVERT: L 103 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6171 (pp) REVERT: M 398 ARG cc_start: 0.8486 (mtt-85) cc_final: 0.7924 (mtt-85) REVERT: M 412 ILE cc_start: 0.7198 (OUTLIER) cc_final: 0.6969 (mp) outliers start: 163 outliers final: 101 residues processed: 832 average time/residue: 0.1924 time to fit residues: 250.2164 Evaluate side-chains 843 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 724 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 58 MET Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 376 LYS Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 76 GLN Chi-restraints excluded: chain F residue 80 ASN Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 157 TYR Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 278 TYR Chi-restraints excluded: chain I residue 324 ASN Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 434 SER Chi-restraints excluded: chain I residue 469 MET Chi-restraints excluded: chain I residue 485 GLU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 552 THR Chi-restraints excluded: chain I residue 578 LYS Chi-restraints excluded: chain I residue 585 LEU Chi-restraints excluded: chain I residue 597 ASN Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain I residue 721 MET Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 ASP Chi-restraints excluded: chain M residue 282 SER Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 412 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 175 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 367 optimal weight: 0.5980 chunk 165 optimal weight: 2.9990 chunk 348 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 246 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN A 447 GLN B 169 GLN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 ASN F 50 ASN H 96 HIS ** I 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS L 64 HIS M 204 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.155609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126778 restraints weight = 49820.166| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.39 r_work: 0.3547 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29886 Z= 0.184 Angle : 0.619 16.447 40440 Z= 0.316 Chirality : 0.041 0.206 4670 Planarity : 0.004 0.063 5136 Dihedral : 6.031 59.068 4083 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.03 % Allowed : 25.04 % Favored : 69.93 % 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: 0.27 (0.14), residues: 3644 helix: 1.24 (0.11), residues: 2254 sheet: -0.81 (0.37), residues: 212 loop : -1.73 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 273 TYR 0.016 0.002 TYR C 185 PHE 0.021 0.002 PHE I 243 TRP 0.029 0.002 TRP A 130 HIS 0.007 0.001 HIS I 524 Details of bonding type rmsd covalent geometry : bond 0.00421 (29874) covalent geometry : angle 0.61354 (40432) SS BOND : bond 0.00921 ( 1) SS BOND : angle 1.14746 ( 2) hydrogen bonds : bond 0.05357 ( 1652) hydrogen bonds : angle 4.36563 ( 4863) metal coordination : bond 0.01094 ( 11) metal coordination : angle 7.00947 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 745 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 GLN cc_start: 0.8290 (mm-40) cc_final: 0.8063 (tp40) REVERT: D 70 CYS cc_start: 0.5949 (OUTLIER) cc_final: 0.5697 (m) REVERT: D 177 GLU cc_start: 0.7973 (tp30) cc_final: 0.7750 (tp30) REVERT: D 185 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7677 (mp) REVERT: D 256 GLN cc_start: 0.7631 (mp10) cc_final: 0.7378 (mp10) REVERT: D 286 MET cc_start: 0.7376 (mmp) cc_final: 0.7077 (mmp) REVERT: G 55 LEU cc_start: 0.8037 (mp) cc_final: 0.7771 (tp) REVERT: G 92 GLN cc_start: 0.7803 (mt0) cc_final: 0.7571 (mt0) REVERT: G 127 GLU cc_start: 0.7054 (tp30) cc_final: 0.6721 (mp0) REVERT: G 172 LYS cc_start: 0.8397 (mtmm) cc_final: 0.8144 (mtmm) REVERT: G 191 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8111 (mm-40) REVERT: G 208 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7697 (tm-30) REVERT: G 212 GLU cc_start: 0.8169 (tp30) cc_final: 0.7955 (tp30) REVERT: G 215 ASN cc_start: 0.8061 (t0) cc_final: 0.7839 (t0) REVERT: K 1 MET cc_start: 0.7594 (ptm) cc_final: 0.7325 (ptm) REVERT: K 44 ILE cc_start: 0.7732 (tp) cc_final: 0.7520 (tp) REVERT: K 45 TYR cc_start: 0.8107 (t80) cc_final: 0.7897 (t80) REVERT: N 58 MET cc_start: 0.5205 (OUTLIER) cc_final: 0.4869 (tmm) REVERT: A 84 ARG cc_start: 0.8334 (ptp90) cc_final: 0.8082 (ptp90) REVERT: A 90 MET cc_start: 0.8106 (mmm) cc_final: 0.7613 (mmm) REVERT: A 211 TYR cc_start: 0.7410 (m-80) cc_final: 0.7065 (m-80) REVERT: A 214 ASN cc_start: 0.8083 (t0) cc_final: 0.7539 (t0) REVERT: A 248 LYS cc_start: 0.8280 (tttt) cc_final: 0.8043 (tttp) REVERT: A 257 GLU cc_start: 0.8002 (tt0) cc_final: 0.7738 (tt0) REVERT: A 279 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7785 (m-30) REVERT: A 307 GLN cc_start: 0.8332 (tm-30) cc_final: 0.8031 (tm-30) REVERT: B 72 LEU cc_start: 0.8067 (mt) cc_final: 0.7763 (mm) REVERT: B 73 LYS cc_start: 0.6359 (mmtt) cc_final: 0.5965 (mmtt) REVERT: B 101 SER cc_start: 0.9048 (p) cc_final: 0.8786 (t) REVERT: B 111 SER cc_start: 0.8619 (m) cc_final: 0.8312 (p) REVERT: B 120 SER cc_start: 0.7423 (t) cc_final: 0.7217 (m) REVERT: B 128 LEU cc_start: 0.7561 (mt) cc_final: 0.7065 (mt) REVERT: B 133 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6977 (mt-10) REVERT: B 238 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7519 (mmm160) REVERT: B 250 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7669 (mm-30) REVERT: B 260 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: B 379 ASN cc_start: 0.8510 (t0) cc_final: 0.8117 (t0) REVERT: C 167 MET cc_start: 0.7914 (mmm) cc_final: 0.7370 (mmt) REVERT: C 263 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8102 (mp) REVERT: C 396 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7659 (tm-30) REVERT: E 35 GLN cc_start: 0.8365 (tp40) cc_final: 0.8120 (tp40) REVERT: E 45 TRP cc_start: 0.8004 (p90) cc_final: 0.7533 (p90) REVERT: E 166 VAL cc_start: 0.8950 (p) cc_final: 0.8610 (m) REVERT: E 193 TYR cc_start: 0.8222 (t80) cc_final: 0.7816 (t80) REVERT: F 76 GLN cc_start: 0.5836 (OUTLIER) cc_final: 0.5336 (pp30) REVERT: F 185 GLU cc_start: 0.7763 (mp0) cc_final: 0.7217 (mt-10) REVERT: F 249 GLU cc_start: 0.7835 (mp0) cc_final: 0.7568 (mp0) REVERT: F 277 THR cc_start: 0.7954 (m) cc_final: 0.7706 (p) REVERT: F 280 TYR cc_start: 0.8198 (m-10) cc_final: 0.7953 (m-10) REVERT: H 18 ASP cc_start: 0.8260 (m-30) cc_final: 0.7729 (m-30) REVERT: H 22 ASN cc_start: 0.7678 (m110) cc_final: 0.7326 (m110) REVERT: H 116 ARG cc_start: 0.6474 (OUTLIER) cc_final: 0.5386 (ptt180) REVERT: H 163 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8606 (mt) REVERT: H 195 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6673 (pp30) REVERT: I 157 TYR cc_start: 0.5620 (OUTLIER) cc_final: 0.5360 (t80) REVERT: I 318 ASP cc_start: 0.7069 (p0) cc_final: 0.6237 (p0) REVERT: I 380 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7996 (tp) REVERT: I 417 LYS cc_start: 0.8074 (mmmm) cc_final: 0.7544 (mmmm) REVERT: I 428 SER cc_start: 0.8405 (p) cc_final: 0.8173 (p) REVERT: I 450 MET cc_start: 0.7054 (tmm) cc_final: 0.6662 (tmm) REVERT: I 503 LYS cc_start: 0.8370 (ttpt) cc_final: 0.8087 (ttmm) REVERT: I 511 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8114 (mp) REVERT: I 735 LEU cc_start: 0.8983 (mt) cc_final: 0.8720 (mt) REVERT: L 103 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.6134 (pp) REVERT: M 398 ARG cc_start: 0.8569 (mtt-85) cc_final: 0.8112 (mmt90) REVERT: M 412 ILE cc_start: 0.7221 (OUTLIER) cc_final: 0.6990 (mp) outliers start: 157 outliers final: 110 residues processed: 836 average time/residue: 0.1964 time to fit residues: 255.9151 Evaluate side-chains 850 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 724 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 69 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 58 MET Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 376 LYS Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 76 GLN Chi-restraints excluded: chain F residue 80 ASN Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 157 TYR Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 278 TYR Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 324 ASN Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 469 MET Chi-restraints excluded: chain I residue 485 GLU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 501 THR Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 525 LEU Chi-restraints excluded: chain I residue 552 THR Chi-restraints excluded: chain I residue 572 SER Chi-restraints excluded: chain I residue 578 LYS Chi-restraints excluded: chain I residue 585 LEU Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain I residue 706 ASP Chi-restraints excluded: chain I residue 721 MET Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 ASP Chi-restraints excluded: chain M residue 282 SER Chi-restraints excluded: chain M residue 412 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 105 optimal weight: 0.8980 chunk 336 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 158 optimal weight: 0.4980 chunk 203 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 237 optimal weight: 0.9980 chunk 191 optimal weight: 0.0770 chunk 147 optimal weight: 0.5980 chunk 290 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN A 447 GLN B 144 ASN B 169 GLN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 GLN E 243 ASN F 50 ASN F 300 ASN H 96 HIS ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS L 64 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.158137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.130223 restraints weight = 50072.974| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.60 r_work: 0.3569 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29886 Z= 0.123 Angle : 0.589 15.270 40440 Z= 0.298 Chirality : 0.039 0.226 4670 Planarity : 0.004 0.056 5136 Dihedral : 5.738 59.499 4076 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.42 % Allowed : 25.84 % Favored : 69.74 % 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: 0.49 (0.14), residues: 3644 helix: 1.42 (0.11), residues: 2250 sheet: -0.62 (0.37), residues: 216 loop : -1.66 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 764 TYR 0.023 0.001 TYR E 114 PHE 0.030 0.001 PHE I 243 TRP 0.031 0.002 TRP A 130 HIS 0.006 0.001 HIS L 64 Details of bonding type rmsd covalent geometry : bond 0.00264 (29874) covalent geometry : angle 0.58362 (40432) SS BOND : bond 0.00564 ( 1) SS BOND : angle 0.92254 ( 2) hydrogen bonds : bond 0.04525 ( 1652) hydrogen bonds : angle 4.18002 ( 4863) metal coordination : bond 0.01704 ( 11) metal coordination : angle 6.27363 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 724 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 ARG cc_start: 0.6667 (mtm-85) cc_final: 0.6318 (mtt-85) REVERT: D 64 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7466 (tm-30) REVERT: D 70 CYS cc_start: 0.5511 (OUTLIER) cc_final: 0.5263 (m) REVERT: D 177 GLU cc_start: 0.7793 (tp30) cc_final: 0.7580 (tp30) REVERT: D 185 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7466 (mp) REVERT: D 221 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: D 256 GLN cc_start: 0.7448 (mp10) cc_final: 0.7201 (mp10) REVERT: D 286 MET cc_start: 0.7165 (mmp) cc_final: 0.6858 (mmp) REVERT: G 92 GLN cc_start: 0.7527 (mt0) cc_final: 0.7321 (mt0) REVERT: G 127 GLU cc_start: 0.6554 (tp30) cc_final: 0.6324 (mp0) REVERT: G 172 LYS cc_start: 0.8097 (mtmm) cc_final: 0.7865 (mtmm) REVERT: G 208 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7514 (tm-30) REVERT: G 215 ASN cc_start: 0.7878 (t0) cc_final: 0.7661 (t0) REVERT: K 1 MET cc_start: 0.7496 (ptm) cc_final: 0.7240 (ptm) REVERT: K 45 TYR cc_start: 0.7976 (t80) cc_final: 0.7763 (t80) REVERT: N 58 MET cc_start: 0.5053 (OUTLIER) cc_final: 0.4748 (tmm) REVERT: A 84 ARG cc_start: 0.8150 (ptp90) cc_final: 0.7934 (ptp90) REVERT: A 90 MET cc_start: 0.7794 (mmm) cc_final: 0.7290 (mmm) REVERT: A 211 TYR cc_start: 0.7191 (m-80) cc_final: 0.6877 (m-80) REVERT: A 214 ASN cc_start: 0.7833 (t0) cc_final: 0.6879 (t0) REVERT: A 257 GLU cc_start: 0.7714 (tt0) cc_final: 0.7398 (tt0) REVERT: A 262 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8193 (tttt) REVERT: A 307 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7787 (tm-30) REVERT: A 444 LYS cc_start: 0.8195 (mtmm) cc_final: 0.7877 (mtpp) REVERT: B 72 LEU cc_start: 0.7936 (mt) cc_final: 0.7653 (mm) REVERT: B 75 MET cc_start: 0.7291 (ttm) cc_final: 0.6595 (tmm) REVERT: B 100 ARG cc_start: 0.8429 (ptm160) cc_final: 0.8172 (ttp-110) REVERT: B 101 SER cc_start: 0.8973 (p) cc_final: 0.8755 (t) REVERT: B 111 SER cc_start: 0.8475 (m) cc_final: 0.8125 (p) REVERT: B 120 SER cc_start: 0.7202 (t) cc_final: 0.7001 (m) REVERT: B 128 LEU cc_start: 0.7463 (mt) cc_final: 0.6949 (mt) REVERT: B 133 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6617 (mt-10) REVERT: B 155 LEU cc_start: 0.7986 (mp) cc_final: 0.7771 (tp) REVERT: B 238 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7436 (mmm160) REVERT: B 247 ARG cc_start: 0.8084 (ttm-80) cc_final: 0.7818 (ttp-110) REVERT: B 260 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: B 379 ASN cc_start: 0.8360 (t0) cc_final: 0.7910 (t0) REVERT: C 119 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.8015 (ptt180) REVERT: C 167 MET cc_start: 0.7644 (mmm) cc_final: 0.7433 (mmt) REVERT: C 263 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7948 (mp) REVERT: C 312 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7806 (mttp) REVERT: C 381 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7753 (mp) REVERT: C 396 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7296 (tm-30) REVERT: E 35 GLN cc_start: 0.8150 (tp40) cc_final: 0.7896 (tp40) REVERT: E 52 PHE cc_start: 0.7842 (m-10) cc_final: 0.7569 (m-10) REVERT: E 56 LYS cc_start: 0.8570 (mtpt) cc_final: 0.8243 (mtpp) REVERT: E 166 VAL cc_start: 0.8771 (p) cc_final: 0.8476 (m) REVERT: E 193 TYR cc_start: 0.8075 (t80) cc_final: 0.7662 (t80) REVERT: E 272 LYS cc_start: 0.8457 (mttp) cc_final: 0.8208 (mttt) REVERT: F 76 GLN cc_start: 0.5643 (OUTLIER) cc_final: 0.5174 (pp30) REVERT: F 166 SER cc_start: 0.8118 (OUTLIER) cc_final: 0.7673 (p) REVERT: F 185 GLU cc_start: 0.7577 (mp0) cc_final: 0.7122 (mt-10) REVERT: F 249 GLU cc_start: 0.7594 (mp0) cc_final: 0.7146 (mp0) REVERT: F 277 THR cc_start: 0.7706 (m) cc_final: 0.7451 (p) REVERT: F 280 TYR cc_start: 0.7895 (m-10) cc_final: 0.7645 (m-10) REVERT: H 18 ASP cc_start: 0.8094 (m-30) cc_final: 0.7533 (m-30) REVERT: H 22 ASN cc_start: 0.7605 (m110) cc_final: 0.7271 (m110) REVERT: H 116 ARG cc_start: 0.6101 (OUTLIER) cc_final: 0.5038 (ptt180) REVERT: H 163 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8551 (mt) REVERT: H 195 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.6438 (pp30) REVERT: I 157 TYR cc_start: 0.5393 (OUTLIER) cc_final: 0.5178 (t80) REVERT: I 318 ASP cc_start: 0.6951 (p0) cc_final: 0.6152 (p0) REVERT: I 417 LYS cc_start: 0.7948 (mmmm) cc_final: 0.7487 (mmmm) REVERT: I 428 SER cc_start: 0.8256 (p) cc_final: 0.8007 (p) REVERT: I 450 MET cc_start: 0.6599 (tmm) cc_final: 0.6382 (tmm) REVERT: I 469 MET cc_start: 0.6579 (OUTLIER) cc_final: 0.6340 (mtp) REVERT: I 503 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7802 (ttmm) REVERT: I 510 ASP cc_start: 0.7346 (m-30) cc_final: 0.7118 (m-30) REVERT: I 511 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7968 (mp) REVERT: I 735 LEU cc_start: 0.8865 (mt) cc_final: 0.8558 (mt) REVERT: L 103 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6124 (pp) REVERT: M 398 ARG cc_start: 0.8460 (mtt-85) cc_final: 0.7870 (mtt-85) REVERT: M 412 ILE cc_start: 0.7074 (OUTLIER) cc_final: 0.6846 (mp) outliers start: 138 outliers final: 94 residues processed: 810 average time/residue: 0.1955 time to fit residues: 248.7866 Evaluate side-chains 825 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 711 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 69 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 58 MET Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 76 GLN Chi-restraints excluded: chain F residue 80 ASN Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 157 TYR Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 278 TYR Chi-restraints excluded: chain I residue 324 ASN Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 434 SER Chi-restraints excluded: chain I residue 469 MET Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 552 THR Chi-restraints excluded: chain I residue 578 LYS Chi-restraints excluded: chain I residue 585 LEU Chi-restraints excluded: chain I residue 590 LEU Chi-restraints excluded: chain I residue 597 ASN Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 ASP Chi-restraints excluded: chain M residue 282 SER Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 412 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 174 optimal weight: 0.0980 chunk 300 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN B 169 GLN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 243 ASN F 50 ASN H 96 HIS ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS L 64 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.161676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132226 restraints weight = 50974.856| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.35 r_work: 0.3623 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29886 Z= 0.136 Angle : 0.600 14.060 40440 Z= 0.303 Chirality : 0.040 0.233 4670 Planarity : 0.004 0.058 5136 Dihedral : 5.664 59.184 4073 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.29 % Allowed : 26.29 % Favored : 69.42 % 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: 0.49 (0.14), residues: 3644 helix: 1.42 (0.11), residues: 2258 sheet: -0.64 (0.37), residues: 216 loop : -1.67 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 764 TYR 0.017 0.001 TYR E 114 PHE 0.018 0.001 PHE I 243 TRP 0.035 0.002 TRP A 130 HIS 0.006 0.001 HIS J 48 Details of bonding type rmsd covalent geometry : bond 0.00302 (29874) covalent geometry : angle 0.59511 (40432) SS BOND : bond 0.00627 ( 1) SS BOND : angle 0.97327 ( 2) hydrogen bonds : bond 0.04650 ( 1652) hydrogen bonds : angle 4.17911 ( 4863) metal coordination : bond 0.01325 ( 11) metal coordination : angle 6.22050 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 711 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 GLN cc_start: 0.8382 (mm-40) cc_final: 0.7646 (tm-30) REVERT: D 221 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: D 256 GLN cc_start: 0.7541 (mp10) cc_final: 0.7266 (mp10) REVERT: D 286 MET cc_start: 0.7369 (mmp) cc_final: 0.7089 (mmp) REVERT: G 92 GLN cc_start: 0.7754 (mt0) cc_final: 0.7518 (mt0) REVERT: G 127 GLU cc_start: 0.6954 (tp30) cc_final: 0.6640 (mp0) REVERT: G 172 LYS cc_start: 0.8323 (mtmm) cc_final: 0.8073 (mtmm) REVERT: G 208 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7649 (tm-30) REVERT: G 215 ASN cc_start: 0.7992 (t0) cc_final: 0.7770 (t0) REVERT: N 58 MET cc_start: 0.5091 (OUTLIER) cc_final: 0.4766 (tmm) REVERT: A 84 ARG cc_start: 0.8381 (ptp90) cc_final: 0.8141 (ptp90) REVERT: A 90 MET cc_start: 0.8062 (mmm) cc_final: 0.7549 (mmm) REVERT: A 211 TYR cc_start: 0.7294 (m-80) cc_final: 0.6887 (m-80) REVERT: A 214 ASN cc_start: 0.7969 (t0) cc_final: 0.6983 (t0) REVERT: A 257 GLU cc_start: 0.7968 (tt0) cc_final: 0.7650 (tt0) REVERT: A 262 LYS cc_start: 0.8649 (ttpt) cc_final: 0.8235 (tttt) REVERT: A 307 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7989 (tm-30) REVERT: A 444 LYS cc_start: 0.8384 (mtmm) cc_final: 0.8071 (mtpp) REVERT: B 72 LEU cc_start: 0.8030 (mt) cc_final: 0.7757 (mm) REVERT: B 75 MET cc_start: 0.7502 (ttm) cc_final: 0.6739 (tmm) REVERT: B 100 ARG cc_start: 0.8635 (ptm160) cc_final: 0.8344 (ttp-110) REVERT: B 101 SER cc_start: 0.8992 (p) cc_final: 0.8780 (t) REVERT: B 111 SER cc_start: 0.8567 (m) cc_final: 0.8249 (p) REVERT: B 128 LEU cc_start: 0.7555 (mt) cc_final: 0.7071 (mt) REVERT: B 133 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6776 (mt-10) REVERT: B 238 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7548 (mmm160) REVERT: B 247 ARG cc_start: 0.8291 (ttm-80) cc_final: 0.7958 (ttp-110) REVERT: B 260 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: B 379 ASN cc_start: 0.8466 (t0) cc_final: 0.8063 (t0) REVERT: C 119 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8164 (ptt180) REVERT: C 263 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8064 (mp) REVERT: C 312 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7877 (mttp) REVERT: C 381 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7900 (mp) REVERT: C 396 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7481 (tm-30) REVERT: E 35 GLN cc_start: 0.8230 (tp40) cc_final: 0.7970 (tp40) REVERT: E 52 PHE cc_start: 0.7917 (m-10) cc_final: 0.7677 (m-10) REVERT: E 56 LYS cc_start: 0.8677 (mtpt) cc_final: 0.8418 (mtpp) REVERT: E 166 VAL cc_start: 0.8854 (p) cc_final: 0.8545 (m) REVERT: E 193 TYR cc_start: 0.8105 (t80) cc_final: 0.7735 (t80) REVERT: E 272 LYS cc_start: 0.8401 (mttp) cc_final: 0.8168 (mttt) REVERT: F 76 GLN cc_start: 0.5694 (OUTLIER) cc_final: 0.5180 (pp30) REVERT: F 106 TYR cc_start: 0.8133 (m-80) cc_final: 0.7579 (m-80) REVERT: F 166 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.7857 (p) REVERT: F 185 GLU cc_start: 0.7678 (mp0) cc_final: 0.7209 (mt-10) REVERT: F 249 GLU cc_start: 0.7790 (mp0) cc_final: 0.7282 (mp0) REVERT: F 277 THR cc_start: 0.7752 (m) cc_final: 0.7458 (p) REVERT: F 280 TYR cc_start: 0.8119 (m-10) cc_final: 0.7840 (m-10) REVERT: H 18 ASP cc_start: 0.8235 (m-30) cc_final: 0.7661 (m-30) REVERT: H 22 ASN cc_start: 0.7694 (m110) cc_final: 0.7327 (m110) REVERT: H 116 ARG cc_start: 0.6380 (OUTLIER) cc_final: 0.5281 (ptt180) REVERT: H 163 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8561 (mt) REVERT: H 195 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6649 (pp30) REVERT: I 157 TYR cc_start: 0.5418 (OUTLIER) cc_final: 0.5160 (t80) REVERT: I 273 ARG cc_start: 0.8062 (mtm180) cc_final: 0.7725 (mtm110) REVERT: I 318 ASP cc_start: 0.7111 (p0) cc_final: 0.6333 (p0) REVERT: I 417 LYS cc_start: 0.7992 (mmmm) cc_final: 0.7477 (mmmm) REVERT: I 428 SER cc_start: 0.8392 (p) cc_final: 0.8145 (p) REVERT: I 450 MET cc_start: 0.6966 (tmm) cc_final: 0.6670 (tmm) REVERT: I 469 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6537 (mtp) REVERT: I 503 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7956 (ttmm) REVERT: I 511 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8063 (mp) REVERT: I 722 ARG cc_start: 0.8582 (tpp80) cc_final: 0.8356 (tpp80) REVERT: I 735 LEU cc_start: 0.8925 (mt) cc_final: 0.8647 (mt) REVERT: L 28 LYS cc_start: 0.6098 (mtmt) cc_final: 0.5893 (mtmt) REVERT: L 103 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6113 (pp) REVERT: M 398 ARG cc_start: 0.8473 (mtt-85) cc_final: 0.7913 (mtt-85) REVERT: M 408 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6196 (pm20) REVERT: M 412 ILE cc_start: 0.7150 (OUTLIER) cc_final: 0.6915 (mp) outliers start: 134 outliers final: 94 residues processed: 794 average time/residue: 0.1979 time to fit residues: 246.3610 Evaluate side-chains 816 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 703 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain K residue 27 LYS Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain N residue 58 MET Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 76 GLN Chi-restraints excluded: chain F residue 80 ASN Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 157 TYR Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 278 TYR Chi-restraints excluded: chain I residue 324 ASN Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 469 MET Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 501 THR Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 552 THR Chi-restraints excluded: chain I residue 578 LYS Chi-restraints excluded: chain I residue 585 LEU Chi-restraints excluded: chain I residue 590 LEU Chi-restraints excluded: chain I residue 597 ASN Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain M residue 185 HIS Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 ASP Chi-restraints excluded: chain M residue 282 SER Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 408 GLU Chi-restraints excluded: chain M residue 412 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 252 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 318 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 360 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 349 optimal weight: 0.0270 chunk 118 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 271 optimal weight: 0.9990 chunk 204 optimal weight: 0.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN B 169 GLN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 243 ASN F 50 ASN H 96 HIS ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.157815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.129764 restraints weight = 49697.316| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.63 r_work: 0.3569 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29886 Z= 0.134 Angle : 0.605 13.891 40440 Z= 0.305 Chirality : 0.040 0.289 4670 Planarity : 0.004 0.062 5136 Dihedral : 5.475 59.680 4068 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.19 % Allowed : 26.64 % Favored : 69.16 % 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: 0.50 (0.14), residues: 3644 helix: 1.43 (0.11), residues: 2255 sheet: -0.63 (0.37), residues: 211 loop : -1.68 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 764 TYR 0.033 0.001 TYR K 45 PHE 0.029 0.001 PHE I 243 TRP 0.038 0.002 TRP A 130 HIS 0.006 0.001 HIS J 48 Details of bonding type rmsd covalent geometry : bond 0.00299 (29874) covalent geometry : angle 0.59987 (40432) SS BOND : bond 0.00624 ( 1) SS BOND : angle 0.97361 ( 2) hydrogen bonds : bond 0.04574 ( 1652) hydrogen bonds : angle 4.15797 ( 4863) metal coordination : bond 0.01379 ( 11) metal coordination : angle 6.27990 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 714 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 ARG cc_start: 0.6613 (mtm-85) cc_final: 0.6221 (mtt-85) REVERT: D 64 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7533 (tm-30) REVERT: D 221 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: D 240 GLN cc_start: 0.7177 (mp10) cc_final: 0.6943 (mp10) REVERT: D 256 GLN cc_start: 0.7385 (mp10) cc_final: 0.7121 (mp10) REVERT: D 286 MET cc_start: 0.7170 (mmp) cc_final: 0.6854 (mmp) REVERT: G 92 GLN cc_start: 0.7535 (mt0) cc_final: 0.7322 (mt0) REVERT: G 127 GLU cc_start: 0.6617 (tp30) cc_final: 0.6351 (mp0) REVERT: G 172 LYS cc_start: 0.8110 (mtmm) cc_final: 0.7840 (mtmm) REVERT: G 208 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7554 (tm-30) REVERT: G 215 ASN cc_start: 0.7863 (t0) cc_final: 0.7642 (t0) REVERT: N 58 MET cc_start: 0.4908 (OUTLIER) cc_final: 0.4585 (tmm) REVERT: A 90 MET cc_start: 0.7789 (mmm) cc_final: 0.7292 (mmm) REVERT: A 211 TYR cc_start: 0.7197 (m-80) cc_final: 0.6817 (m-80) REVERT: A 214 ASN cc_start: 0.7875 (t0) cc_final: 0.6894 (t0) REVERT: A 257 GLU cc_start: 0.7724 (tt0) cc_final: 0.7109 (tt0) REVERT: A 262 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8238 (ttpt) REVERT: A 307 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 444 LYS cc_start: 0.8188 (mtmm) cc_final: 0.7872 (mtpp) REVERT: B 72 LEU cc_start: 0.7966 (mt) cc_final: 0.7714 (mm) REVERT: B 75 MET cc_start: 0.7239 (ttm) cc_final: 0.6582 (tmm) REVERT: B 100 ARG cc_start: 0.8405 (ptm160) cc_final: 0.8151 (ttp-110) REVERT: B 101 SER cc_start: 0.8956 (p) cc_final: 0.8743 (t) REVERT: B 111 SER cc_start: 0.8444 (m) cc_final: 0.8086 (p) REVERT: B 128 LEU cc_start: 0.7636 (mt) cc_final: 0.7042 (tp) REVERT: B 133 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6524 (mt-10) REVERT: B 155 LEU cc_start: 0.7983 (mp) cc_final: 0.7779 (tp) REVERT: B 238 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7304 (mmm160) REVERT: B 247 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7811 (ttp-110) REVERT: B 260 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: B 379 ASN cc_start: 0.8357 (t0) cc_final: 0.7915 (t0) REVERT: B 435 ASN cc_start: 0.7902 (p0) cc_final: 0.7634 (p0) REVERT: C 119 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.8025 (ptt180) REVERT: C 263 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7940 (mp) REVERT: C 309 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.8121 (ttp-170) REVERT: C 312 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7785 (mttp) REVERT: C 381 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7758 (mp) REVERT: C 396 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7271 (tm-30) REVERT: E 35 GLN cc_start: 0.8135 (tp40) cc_final: 0.7867 (tp40) REVERT: E 56 LYS cc_start: 0.8582 (mtpt) cc_final: 0.8278 (mtpp) REVERT: E 166 VAL cc_start: 0.8787 (p) cc_final: 0.8451 (m) REVERT: E 193 TYR cc_start: 0.8125 (t80) cc_final: 0.7697 (t80) REVERT: E 272 LYS cc_start: 0.8425 (mttp) cc_final: 0.8182 (mttt) REVERT: F 76 GLN cc_start: 0.5620 (OUTLIER) cc_final: 0.5097 (pp30) REVERT: F 138 VAL cc_start: 0.8567 (p) cc_final: 0.8325 (m) REVERT: F 166 SER cc_start: 0.8129 (OUTLIER) cc_final: 0.7691 (p) REVERT: F 185 GLU cc_start: 0.7613 (mp0) cc_final: 0.7153 (mt-10) REVERT: F 249 GLU cc_start: 0.7623 (mp0) cc_final: 0.7147 (mp0) REVERT: F 277 THR cc_start: 0.7706 (m) cc_final: 0.7450 (p) REVERT: F 280 TYR cc_start: 0.7927 (m-10) cc_final: 0.7642 (m-10) REVERT: H 18 ASP cc_start: 0.8081 (m-30) cc_final: 0.7523 (m-30) REVERT: H 22 ASN cc_start: 0.7524 (m110) cc_final: 0.7194 (m110) REVERT: H 116 ARG cc_start: 0.6119 (OUTLIER) cc_final: 0.5059 (ptt180) REVERT: H 163 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8554 (mt) REVERT: H 195 GLN cc_start: 0.6870 (OUTLIER) cc_final: 0.6452 (pp30) REVERT: I 318 ASP cc_start: 0.7016 (p0) cc_final: 0.6220 (p0) REVERT: I 324 ASN cc_start: 0.7609 (OUTLIER) cc_final: 0.6951 (t0) REVERT: I 417 LYS cc_start: 0.7971 (mmmm) cc_final: 0.7407 (mmmm) REVERT: I 450 MET cc_start: 0.6595 (tmm) cc_final: 0.6372 (tmm) REVERT: I 469 MET cc_start: 0.6629 (OUTLIER) cc_final: 0.6405 (mtp) REVERT: I 503 LYS cc_start: 0.8148 (ttpt) cc_final: 0.7846 (ttmm) REVERT: I 511 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7972 (mp) REVERT: I 712 GLN cc_start: 0.7771 (tt0) cc_final: 0.7543 (mt0) REVERT: I 735 LEU cc_start: 0.8884 (mt) cc_final: 0.8593 (mt) REVERT: L 28 LYS cc_start: 0.5966 (mtmt) cc_final: 0.5763 (mtmt) REVERT: L 103 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6144 (pp) REVERT: L 111 ASP cc_start: 0.6914 (m-30) cc_final: 0.6674 (m-30) REVERT: M 398 ARG cc_start: 0.8417 (mtt-85) cc_final: 0.7815 (mtt-85) REVERT: M 412 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6869 (mp) outliers start: 131 outliers final: 99 residues processed: 793 average time/residue: 0.2041 time to fit residues: 252.3905 Evaluate side-chains 823 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 706 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain K residue 27 LYS Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain N residue 58 MET Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 76 GLN Chi-restraints excluded: chain F residue 80 ASN Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 278 TYR Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 324 ASN Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 434 SER Chi-restraints excluded: chain I residue 469 MET Chi-restraints excluded: chain I residue 485 GLU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 501 THR Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 552 THR Chi-restraints excluded: chain I residue 578 LYS Chi-restraints excluded: chain I residue 585 LEU Chi-restraints excluded: chain I residue 597 ASN Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain I residue 715 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 ASP Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 412 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 44 optimal weight: 0.0060 chunk 174 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 306 optimal weight: 0.4980 chunk 54 optimal weight: 0.2980 chunk 93 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 311 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN B 55 GLN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 243 ASN F 50 ASN F 300 ASN H 96 HIS ** I 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS L 64 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.159292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.130980 restraints weight = 49950.378| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.72 r_work: 0.3569 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29886 Z= 0.122 Angle : 0.617 13.397 40440 Z= 0.310 Chirality : 0.040 0.270 4670 Planarity : 0.004 0.065 5136 Dihedral : 5.313 59.809 4066 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.78 % Allowed : 27.19 % Favored : 69.04 % 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: 0.56 (0.14), residues: 3644 helix: 1.47 (0.11), residues: 2262 sheet: -0.67 (0.37), residues: 205 loop : -1.64 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I 764 TYR 0.024 0.001 TYR K 45 PHE 0.021 0.001 PHE I 243 TRP 0.039 0.002 TRP A 130 HIS 0.010 0.001 HIS J 48 Details of bonding type rmsd covalent geometry : bond 0.00265 (29874) covalent geometry : angle 0.61291 (40432) SS BOND : bond 0.00522 ( 1) SS BOND : angle 0.87679 ( 2) hydrogen bonds : bond 0.04263 ( 1652) hydrogen bonds : angle 4.09497 ( 4863) metal coordination : bond 0.01559 ( 11) metal coordination : angle 5.77087 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 704 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 ARG cc_start: 0.6580 (mtm-85) cc_final: 0.6249 (mtt-85) REVERT: D 64 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7551 (tm-30) REVERT: D 221 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: D 224 GLU cc_start: 0.7438 (tp30) cc_final: 0.7183 (tp30) REVERT: D 240 GLN cc_start: 0.7186 (mp10) cc_final: 0.6961 (mp10) REVERT: D 256 GLN cc_start: 0.7377 (mp10) cc_final: 0.7043 (mp10) REVERT: D 286 MET cc_start: 0.7184 (mmp) cc_final: 0.6871 (mmp) REVERT: D 364 ARG cc_start: 0.7606 (mtm110) cc_final: 0.7152 (mtm110) REVERT: G 92 GLN cc_start: 0.7494 (mt0) cc_final: 0.7281 (mt0) REVERT: G 127 GLU cc_start: 0.6587 (tp30) cc_final: 0.6319 (mp0) REVERT: G 172 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7848 (mtmm) REVERT: G 208 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7552 (tm-30) REVERT: G 215 ASN cc_start: 0.7761 (t0) cc_final: 0.7504 (t0) REVERT: N 58 MET cc_start: 0.4934 (OUTLIER) cc_final: 0.4608 (tmm) REVERT: A 90 MET cc_start: 0.7888 (mmm) cc_final: 0.7366 (mmm) REVERT: A 211 TYR cc_start: 0.7228 (m-80) cc_final: 0.6807 (m-80) REVERT: A 214 ASN cc_start: 0.7867 (t0) cc_final: 0.6872 (t0) REVERT: A 248 LYS cc_start: 0.8110 (tttt) cc_final: 0.7874 (tttp) REVERT: A 257 GLU cc_start: 0.7721 (tt0) cc_final: 0.6964 (tt0) REVERT: A 262 LYS cc_start: 0.8545 (ttpt) cc_final: 0.8250 (ttpt) REVERT: A 307 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 444 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7891 (mtpp) REVERT: B 72 LEU cc_start: 0.7944 (mt) cc_final: 0.7680 (mm) REVERT: B 75 MET cc_start: 0.7217 (ttm) cc_final: 0.6550 (tmm) REVERT: B 100 ARG cc_start: 0.8377 (ptm160) cc_final: 0.8120 (ttp-110) REVERT: B 111 SER cc_start: 0.8437 (m) cc_final: 0.8097 (p) REVERT: B 128 LEU cc_start: 0.7600 (mt) cc_final: 0.6976 (tp) REVERT: B 133 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6551 (mt-10) REVERT: B 181 THR cc_start: 0.7296 (t) cc_final: 0.7064 (m) REVERT: B 238 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7366 (mmm160) REVERT: B 247 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7771 (ttp-110) REVERT: B 260 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: B 379 ASN cc_start: 0.8379 (t0) cc_final: 0.7943 (t0) REVERT: B 435 ASN cc_start: 0.7895 (p0) cc_final: 0.7598 (p0) REVERT: C 119 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.8047 (ptt180) REVERT: C 263 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7927 (mp) REVERT: C 309 ARG cc_start: 0.8417 (ttm-80) cc_final: 0.8079 (ttp-170) REVERT: C 312 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7744 (mttp) REVERT: C 381 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7760 (mp) REVERT: E 35 GLN cc_start: 0.8204 (tp40) cc_final: 0.7928 (tp40) REVERT: E 56 LYS cc_start: 0.8551 (mtpt) cc_final: 0.8270 (mtpp) REVERT: E 89 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.7696 (t) REVERT: E 166 VAL cc_start: 0.8729 (p) cc_final: 0.8410 (m) REVERT: E 193 TYR cc_start: 0.8101 (t80) cc_final: 0.7688 (t80) REVERT: E 272 LYS cc_start: 0.8425 (mttp) cc_final: 0.8179 (mttt) REVERT: F 76 GLN cc_start: 0.5602 (OUTLIER) cc_final: 0.5076 (pp30) REVERT: F 106 TYR cc_start: 0.8041 (m-80) cc_final: 0.7564 (m-80) REVERT: F 138 VAL cc_start: 0.8553 (p) cc_final: 0.8323 (m) REVERT: F 166 SER cc_start: 0.8103 (OUTLIER) cc_final: 0.7748 (p) REVERT: F 185 GLU cc_start: 0.7594 (mp0) cc_final: 0.7105 (mt-10) REVERT: F 249 GLU cc_start: 0.7614 (mp0) cc_final: 0.7380 (mp0) REVERT: F 277 THR cc_start: 0.7652 (m) cc_final: 0.7392 (p) REVERT: F 280 TYR cc_start: 0.7894 (m-10) cc_final: 0.7613 (m-10) REVERT: H 22 ASN cc_start: 0.7607 (m110) cc_final: 0.7247 (m110) REVERT: H 116 ARG cc_start: 0.6013 (OUTLIER) cc_final: 0.4958 (ptt180) REVERT: H 163 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8539 (mt) REVERT: H 195 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6403 (pp30) REVERT: I 318 ASP cc_start: 0.7048 (p0) cc_final: 0.6282 (p0) REVERT: I 324 ASN cc_start: 0.7575 (OUTLIER) cc_final: 0.6985 (t0) REVERT: I 417 LYS cc_start: 0.7918 (mmmm) cc_final: 0.7375 (mmmm) REVERT: I 450 MET cc_start: 0.6626 (tmm) cc_final: 0.6391 (tmm) REVERT: I 503 LYS cc_start: 0.8125 (ttpt) cc_final: 0.7851 (ttmm) REVERT: I 712 GLN cc_start: 0.7807 (tt0) cc_final: 0.7578 (mt0) REVERT: I 735 LEU cc_start: 0.8871 (mt) cc_final: 0.8558 (mt) REVERT: J 101 TRP cc_start: 0.8411 (t-100) cc_final: 0.8171 (t-100) REVERT: L 28 LYS cc_start: 0.5911 (mtmt) cc_final: 0.5649 (mtmt) REVERT: L 103 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.6089 (pp) REVERT: L 111 ASP cc_start: 0.6848 (m-30) cc_final: 0.6554 (m-30) REVERT: M 398 ARG cc_start: 0.8413 (mtt-85) cc_final: 0.7824 (mtt-85) REVERT: M 412 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6854 (mp) outliers start: 118 outliers final: 91 residues processed: 778 average time/residue: 0.2028 time to fit residues: 246.1473 Evaluate side-chains 807 residues out of total 3329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 699 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain K residue 27 LYS Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain N residue 58 MET Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 76 GLN Chi-restraints excluded: chain F residue 80 ASN Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 278 TYR Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 308 GLN Chi-restraints excluded: chain I residue 324 ASN Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 434 SER Chi-restraints excluded: chain I residue 485 GLU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 501 THR Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 552 THR Chi-restraints excluded: chain I residue 578 LYS Chi-restraints excluded: chain I residue 585 LEU Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain I residue 715 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 ASP Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 412 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 153 optimal weight: 1.9990 chunk 303 optimal weight: 0.6980 chunk 342 optimal weight: 0.7980 chunk 196 optimal weight: 0.0040 chunk 204 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 238 optimal weight: 0.9990 chunk 146 optimal weight: 0.1980 chunk 236 optimal weight: 2.9990 chunk 288 optimal weight: 0.9980 chunk 364 optimal weight: 0.0010 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN B 169 GLN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 243 ASN F 50 ASN H 96 HIS I 374 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.159785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.131916 restraints weight = 50329.321| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.63 r_work: 0.3600 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29886 Z= 0.117 Angle : 0.616 12.984 40440 Z= 0.308 Chirality : 0.039 0.258 4670 Planarity : 0.004 0.066 5136 Dihedral : 5.008 59.220 4060 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.52 % Allowed : 27.76 % Favored : 68.72 % 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: 0.62 (0.14), residues: 3644 helix: 1.50 (0.11), residues: 2273 sheet: -0.52 (0.37), residues: 205 loop : -1.62 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 764 TYR 0.025 0.001 TYR K 45 PHE 0.030 0.001 PHE I 243 TRP 0.037 0.002 TRP A 130 HIS 0.011 0.001 HIS J 48 Details of bonding type rmsd covalent geometry : bond 0.00249 (29874) covalent geometry : angle 0.61210 (40432) SS BOND : bond 0.00412 ( 1) SS BOND : angle 0.84320 ( 2) hydrogen bonds : bond 0.03957 ( 1652) hydrogen bonds : angle 4.03347 ( 4863) metal coordination : bond 0.01645 ( 11) metal coordination : angle 5.46389 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10239.72 seconds wall clock time: 175 minutes 13.14 seconds (10513.14 seconds total)