Starting phenix.real_space_refine on Tue May 5 18:02:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjc_60140/05_2026/8zjc_60140.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjc_60140/05_2026/8zjc_60140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zjc_60140/05_2026/8zjc_60140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjc_60140/05_2026/8zjc_60140.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjc_60140/05_2026/8zjc_60140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjc_60140/05_2026/8zjc_60140.cif" } resolution = 2.5 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= 0.003 sd= 0.231 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 Fe 10 7.16 5 P 12 5.49 5 S 114 5.16 5 C 20937 2.51 5 N 5315 2.21 5 O 5923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 236 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32311 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3344 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 12, 'TRANS': 418} Chain: "B" Number of atoms: 2735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2735 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 339} Chain: "C" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3090 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 365} Chain: "D" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1961 Classifications: {'peptide': 248} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 225} Chain: "E" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1411 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 173} Chain: "F" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 624 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "G" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1019 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "H" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 773 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "I" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 442 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "L" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3344 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 12, 'TRANS': 418} Chain: "M" Number of atoms: 2735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2735 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 339} Chain: "N" Number of atoms: 3083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3083 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 365} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1961 Classifications: {'peptide': 248} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 225} Chain: "P" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1411 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 173} Chain: "Q" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 633 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "R" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1019 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "S" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 773 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "T" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 443 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "V" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 406 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "C" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 352 Unusual residues: {'8PE': 1, '9PE': 2, 'CN3': 1, 'CN5': 1, 'HEM': 2, 'UQ6': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'6PH': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 231 Unusual residues: {'8PE': 1, 'CN3': 1, 'HEM': 2, 'UQ6': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'6PH': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 27649 SG CYS P 178 95.445 78.380 27.911 1.00 82.38 S Time building chain proxies: 7.08, per 1000 atoms: 0.22 Number of scatterers: 32311 At special positions: 0 Unit cell: (122.88, 137.28, 168, 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) Fe 10 26.01 S 114 16.00 P 12 15.00 O 5923 8.00 N 5315 7.00 C 20937 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.77 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.53 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" NE2 HIS E 161 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 178 " pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" NE2 HIS P 161 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 178 " Number of angles added : 2 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7464 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 22 sheets defined 55.2% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 63 through 67 removed outlier: 4.051A pdb=" N ASN A 67 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 78 removed outlier: 3.544A pdb=" N ASN A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 88 removed outlier: 3.682A pdb=" N VAL A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 112 through 122 removed outlier: 3.749A pdb=" N SER A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 155 removed outlier: 3.543A pdb=" N LYS A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 169 removed outlier: 3.521A pdb=" N HIS A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.602A pdb=" N LEU A 176 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 removed outlier: 3.815A pdb=" N GLU A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 201 removed outlier: 3.658A pdb=" N LEU A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 215 through 225 removed outlier: 3.506A pdb=" N VAL A 220 " --> pdb=" O HIS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.505A pdb=" N GLN A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.952A pdb=" N GLN A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 Processing helix chain 'A' and resid 339 through 357 removed outlier: 3.560A pdb=" N GLN A 350 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 354 " --> pdb=" O GLN A 350 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR A 355 " --> pdb=" O TRP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 379 Processing helix chain 'A' and resid 382 through 398 removed outlier: 3.545A pdb=" N ASP A 386 " --> pdb=" O ASN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 411 removed outlier: 3.662A pdb=" N LYS A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 426 removed outlier: 3.590A pdb=" N VAL A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.616A pdb=" N ILE A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'B' and resid 38 through 42 Processing helix chain 'B' and resid 46 through 53 removed outlier: 3.530A pdb=" N LEU B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 75 removed outlier: 3.606A pdb=" N LEU B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 111 removed outlier: 3.975A pdb=" N TYR B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN B 103 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.747A pdb=" N LEU B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 137 through 151 Processing helix chain 'B' and resid 168 through 180 removed outlier: 3.550A pdb=" N LYS B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 193 through 203 removed outlier: 3.552A pdb=" N ASP B 202 " --> pdb=" O LYS B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 249 through 262 removed outlier: 3.527A pdb=" N TYR B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 4.420A pdb=" N GLY B 269 " --> pdb=" O GLU B 266 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 271 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 311 removed outlier: 3.581A pdb=" N VAL B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 328 removed outlier: 3.567A pdb=" N LEU B 323 " --> pdb=" O ASN B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.954A pdb=" N VAL B 343 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 9 through 18 removed outlier: 3.758A pdb=" N VAL C 13 " --> pdb=" O TYR C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 30 Processing helix chain 'C' and resid 31 through 52 removed outlier: 3.613A pdb=" N LEU C 35 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 37 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET C 52 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 Processing helix chain 'C' and resid 74 through 103 removed outlier: 3.570A pdb=" N LEU C 78 " --> pdb=" O ASN C 74 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 135 removed outlier: 3.831A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 149 removed outlier: 3.659A pdb=" N TRP C 142 " --> pdb=" O GLN C 138 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 146 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 153 Processing helix chain 'C' and resid 157 through 167 removed outlier: 3.561A pdb=" N ILE C 161 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER C 163 " --> pdb=" O ASN C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 203 removed outlier: 3.654A pdb=" N ALA C 181 " --> pdb=" O GLN C 177 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) Proline residue: C 187 - end of helix removed outlier: 3.593A pdb=" N ALA C 192 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE C 203 " --> pdb=" O MET C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 247 removed outlier: 3.818A pdb=" N VAL C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.520A pdb=" N ASN C 256 " --> pdb=" O HIS C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 275 through 283 Processing helix chain 'C' and resid 287 through 301 removed outlier: 4.197A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.557A pdb=" N ASP C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 340 removed outlier: 3.717A pdb=" N PHE C 327 " --> pdb=" O LYS C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 356 Processing helix chain 'C' and resid 356 through 365 removed outlier: 3.688A pdb=" N PHE C 360 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 364 " --> pdb=" O PHE C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 383 removed outlier: 3.540A pdb=" N GLY C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG C 382 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'D' and resid 86 through 100 removed outlier: 3.594A pdb=" N GLN D 95 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 104 Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.605A pdb=" N ASN D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 168 removed outlier: 3.507A pdb=" N ALA D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 196 Processing helix chain 'D' and resid 243 through 260 Processing helix chain 'D' and resid 262 through 292 removed outlier: 3.585A pdb=" N LYS D 267 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D 271 " --> pdb=" O LYS D 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 285 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'E' and resid 48 through 52 removed outlier: 4.123A pdb=" N GLY E 52 " --> pdb=" O ALA E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 80 removed outlier: 3.997A pdb=" N MET E 59 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS E 72 " --> pdb=" O SER E 68 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 85 through 91 removed outlier: 3.931A pdb=" N MET E 91 " --> pdb=" O ASP E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'F' and resid 78 through 83 Processing helix chain 'F' and resid 84 through 88 removed outlier: 3.717A pdb=" N THR F 88 " --> pdb=" O PHE F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 109 removed outlier: 3.584A pdb=" N ALA F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR F 98 " --> pdb=" O LEU F 94 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU F 100 " --> pdb=" O HIS F 96 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N CYS F 101 " --> pdb=" O HIS F 97 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL F 105 " --> pdb=" O CYS F 101 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS F 106 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN F 108 " --> pdb=" O ARG F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 143 removed outlier: 3.550A pdb=" N ALA F 139 " --> pdb=" O ASP F 135 " (cutoff:3.500A) Proline residue: F 140 - end of helix removed outlier: 4.804A pdb=" N PHE F 143 " --> pdb=" O ALA F 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 17 removed outlier: 3.719A pdb=" N TYR G 14 " --> pdb=" O ARG G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 24 removed outlier: 3.898A pdb=" N LYS G 23 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU G 24 " --> pdb=" O LEU G 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 20 through 24' Processing helix chain 'G' and resid 25 through 35 Processing helix chain 'G' and resid 38 through 42 Processing helix chain 'G' and resid 44 through 48 Processing helix chain 'G' and resid 53 through 62 Processing helix chain 'G' and resid 64 through 84 removed outlier: 3.572A pdb=" N ALA G 70 " --> pdb=" O ASP G 66 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 122 removed outlier: 3.539A pdb=" N GLU G 109 " --> pdb=" O PRO G 105 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA G 110 " --> pdb=" O TYR G 106 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA G 113 " --> pdb=" O GLU G 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 56 removed outlier: 3.752A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 81 removed outlier: 3.784A pdb=" N ILE H 61 " --> pdb=" O LEU H 57 " (cutoff:3.500A) Proline residue: H 62 - end of helix removed outlier: 3.658A pdb=" N TYR H 81 " --> pdb=" O ASN H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 94 removed outlier: 3.726A pdb=" N ARG H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN H 93 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL H 94 " --> pdb=" O GLU H 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 11 removed outlier: 3.782A pdb=" N PHE I 11 " --> pdb=" O TYR I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 44 removed outlier: 3.676A pdb=" N VAL I 27 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR I 30 " --> pdb=" O PHE I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 53 Processing helix chain 'L' and resid 58 through 62 Processing helix chain 'L' and resid 63 through 67 removed outlier: 4.051A pdb=" N ASN L 67 " --> pdb=" O PRO L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 78 removed outlier: 3.544A pdb=" N ASN L 75 " --> pdb=" O ASN L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 88 removed outlier: 3.681A pdb=" N VAL L 85 " --> pdb=" O GLU L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 111 No H-bonds generated for 'chain 'L' and resid 109 through 111' Processing helix chain 'L' and resid 112 through 122 removed outlier: 3.749A pdb=" N SER L 116 " --> pdb=" O SER L 112 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU L 117 " --> pdb=" O THR L 113 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP L 118 " --> pdb=" O ASP L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 155 removed outlier: 3.544A pdb=" N LYS L 146 " --> pdb=" O LYS L 142 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU L 153 " --> pdb=" O GLN L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 155 through 169 removed outlier: 3.521A pdb=" N HIS L 165 " --> pdb=" O LEU L 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 176 removed outlier: 3.602A pdb=" N LEU L 176 " --> pdb=" O PRO L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 186 removed outlier: 3.815A pdb=" N GLU L 186 " --> pdb=" O LEU L 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 201 removed outlier: 3.659A pdb=" N LEU L 193 " --> pdb=" O VAL L 189 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN L 199 " --> pdb=" O SER L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 215 through 225 removed outlier: 3.506A pdb=" N VAL L 220 " --> pdb=" O HIS L 216 " (cutoff:3.500A) Processing helix chain 'L' and resid 274 through 283 removed outlier: 3.505A pdb=" N GLN L 283 " --> pdb=" O LYS L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 298 removed outlier: 3.952A pdb=" N GLN L 298 " --> pdb=" O SER L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 302 through 307 Processing helix chain 'L' and resid 339 through 357 removed outlier: 3.561A pdb=" N GLN L 350 " --> pdb=" O PHE L 346 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG L 353 " --> pdb=" O LYS L 349 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU L 354 " --> pdb=" O GLN L 350 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR L 355 " --> pdb=" O TRP L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 379 Processing helix chain 'L' and resid 382 through 398 removed outlier: 3.545A pdb=" N ASP L 386 " --> pdb=" O ASN L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 402 through 411 removed outlier: 3.662A pdb=" N LYS L 408 " --> pdb=" O GLY L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 426 removed outlier: 3.589A pdb=" N VAL L 418 " --> pdb=" O THR L 414 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS L 424 " --> pdb=" O ALA L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 444 through 450 removed outlier: 3.617A pdb=" N ILE L 448 " --> pdb=" O ASP L 444 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 453 No H-bonds generated for 'chain 'L' and resid 451 through 453' Processing helix chain 'M' and resid 38 through 42 Processing helix chain 'M' and resid 46 through 53 removed outlier: 3.530A pdb=" N LEU M 50 " --> pdb=" O GLY M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 75 removed outlier: 3.606A pdb=" N LEU M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU M 74 " --> pdb=" O GLU M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 111 removed outlier: 3.975A pdb=" N TYR M 101 " --> pdb=" O ASP M 97 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN M 103 " --> pdb=" O PRO M 99 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU M 105 " --> pdb=" O TYR M 101 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU M 109 " --> pdb=" O LEU M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 122 removed outlier: 3.747A pdb=" N LEU M 119 " --> pdb=" O LYS M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 135 Processing helix chain 'M' and resid 137 through 151 Processing helix chain 'M' and resid 168 through 180 removed outlier: 3.549A pdb=" N LYS M 178 " --> pdb=" O ASP M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 183 No H-bonds generated for 'chain 'M' and resid 181 through 183' Processing helix chain 'M' and resid 193 through 203 removed outlier: 3.552A pdb=" N ASP M 202 " --> pdb=" O LYS M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 204 through 209 Processing helix chain 'M' and resid 246 through 248 No H-bonds generated for 'chain 'M' and resid 246 through 248' Processing helix chain 'M' and resid 249 through 262 removed outlier: 3.527A pdb=" N TYR M 253 " --> pdb=" O SER M 249 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR M 261 " --> pdb=" O ALA M 257 " (cutoff:3.500A) Processing helix chain 'M' and resid 266 through 271 removed outlier: 4.420A pdb=" N GLY M 269 " --> pdb=" O GLU M 266 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE M 271 " --> pdb=" O SER M 268 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 311 removed outlier: 3.582A pdb=" N VAL M 297 " --> pdb=" O ASP M 293 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS M 303 " --> pdb=" O SER M 299 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS M 310 " --> pdb=" O ALA M 306 " (cutoff:3.500A) Processing helix chain 'M' and resid 317 through 328 removed outlier: 3.566A pdb=" N LEU M 323 " --> pdb=" O ASN M 319 " (cutoff:3.500A) Processing helix chain 'M' and resid 339 through 343 removed outlier: 3.954A pdb=" N VAL M 343 " --> pdb=" O PHE M 340 " (cutoff:3.500A) Processing helix chain 'M' and resid 364 through 368 Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 9 through 18 removed outlier: 3.782A pdb=" N VAL N 13 " --> pdb=" O TYR N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 30 Processing helix chain 'N' and resid 31 through 51 removed outlier: 3.617A pdb=" N LEU N 35 " --> pdb=" O ASN N 31 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY N 37 " --> pdb=" O GLY N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 71 Processing helix chain 'N' and resid 74 through 104 removed outlier: 3.543A pdb=" N LEU N 78 " --> pdb=" O ASN N 74 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 removed outlier: 3.504A pdb=" N ILE N 119 " --> pdb=" O ASN N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 149 removed outlier: 3.656A pdb=" N TRP N 142 " --> pdb=" O GLN N 138 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 153 Processing helix chain 'N' and resid 157 through 167 removed outlier: 3.510A pdb=" N VAL N 162 " --> pdb=" O GLY N 158 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER N 163 " --> pdb=" O ASN N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 200 removed outlier: 3.607A pdb=" N ALA N 181 " --> pdb=" O GLN N 177 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU N 185 " --> pdb=" O ALA N 181 " (cutoff:3.500A) Proline residue: N 187 - end of helix removed outlier: 3.565A pdb=" N ALA N 192 " --> pdb=" O PHE N 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 247 removed outlier: 3.819A pdb=" N VAL N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR N 232 " --> pdb=" O LYS N 228 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU N 235 " --> pdb=" O VAL N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 258 removed outlier: 3.512A pdb=" N ASN N 256 " --> pdb=" O HIS N 253 " (cutoff:3.500A) Processing helix chain 'N' and resid 272 through 274 No H-bonds generated for 'chain 'N' and resid 272 through 274' Processing helix chain 'N' and resid 275 through 283 removed outlier: 3.637A pdb=" N ARG N 283 " --> pdb=" O TYR N 279 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.506A pdb=" N VAL N 292 " --> pdb=" O LYS N 288 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 304 through 309 removed outlier: 3.536A pdb=" N ASP N 309 " --> pdb=" O LEU N 305 " (cutoff:3.500A) Processing helix chain 'N' and resid 319 through 340 removed outlier: 3.630A pdb=" N PHE N 327 " --> pdb=" O LYS N 323 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY N 337 " --> pdb=" O PHE N 333 " (cutoff:3.500A) Processing helix chain 'N' and resid 349 through 365 removed outlier: 3.686A pdb=" N PHE N 360 " --> pdb=" O THR N 356 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE N 363 " --> pdb=" O TYR N 359 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU N 364 " --> pdb=" O PHE N 360 " (cutoff:3.500A) Processing helix chain 'N' and resid 366 through 381 removed outlier: 3.557A pdb=" N GLY N 381 " --> pdb=" O LEU N 377 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 68 Processing helix chain 'O' and resid 86 through 100 removed outlier: 3.595A pdb=" N GLN O 95 " --> pdb=" O ARG O 91 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL O 96 " --> pdb=" O ARG O 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 104 Processing helix chain 'O' and resid 111 through 116 Processing helix chain 'O' and resid 121 through 130 removed outlier: 3.605A pdb=" N ASN O 127 " --> pdb=" O GLU O 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 161 through 168 removed outlier: 3.507A pdb=" N ALA O 168 " --> pdb=" O ALA O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 196 Processing helix chain 'O' and resid 243 through 260 Processing helix chain 'O' and resid 262 through 292 removed outlier: 3.586A pdb=" N LYS O 267 " --> pdb=" O HIS O 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG O 268 " --> pdb=" O ASP O 264 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU O 271 " --> pdb=" O LYS O 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS O 272 " --> pdb=" O ARG O 268 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE O 285 " --> pdb=" O TYR O 281 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP O 286 " --> pdb=" O LEU O 282 " (cutoff:3.500A) Processing helix chain 'O' and resid 292 through 297 Processing helix chain 'P' and resid 50 through 80 removed outlier: 4.122A pdb=" N TYR P 55 " --> pdb=" O LYS P 51 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA P 56 " --> pdb=" O GLY P 52 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR P 57 " --> pdb=" O ARG P 53 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET P 59 " --> pdb=" O TYR P 55 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY P 61 " --> pdb=" O TYR P 57 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS P 72 " --> pdb=" O SER P 68 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL P 75 " --> pdb=" O ALA P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 83 No H-bonds generated for 'chain 'P' and resid 81 through 83' Processing helix chain 'P' and resid 85 through 91 removed outlier: 3.886A pdb=" N MET P 91 " --> pdb=" O ASP P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 147 Processing helix chain 'Q' and resid 76 through 85 removed outlier: 3.962A pdb=" N ASP Q 80 " --> pdb=" O ASP Q 76 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU Q 81 " --> pdb=" O GLN Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 109 removed outlier: 3.758A pdb=" N ALA Q 93 " --> pdb=" O GLU Q 89 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU Q 94 " --> pdb=" O GLU Q 90 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL Q 95 " --> pdb=" O GLY Q 91 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS Q 96 " --> pdb=" O LYS Q 92 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N CYS Q 101 " --> pdb=" O HIS Q 97 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG Q 104 " --> pdb=" O GLU Q 100 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE Q 107 " --> pdb=" O GLU Q 103 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN Q 108 " --> pdb=" O ARG Q 104 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLN Q 109 " --> pdb=" O VAL Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 143 removed outlier: 3.595A pdb=" N THR Q 138 " --> pdb=" O LEU Q 134 " (cutoff:3.500A) Proline residue: Q 140 - end of helix removed outlier: 4.763A pdb=" N PHE Q 143 " --> pdb=" O ALA Q 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 17 removed outlier: 3.718A pdb=" N TYR R 14 " --> pdb=" O ARG R 10 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 24 removed outlier: 3.898A pdb=" N LYS R 23 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU R 24 " --> pdb=" O LEU R 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 20 through 24' Processing helix chain 'R' and resid 25 through 35 Processing helix chain 'R' and resid 38 through 42 Processing helix chain 'R' and resid 44 through 48 Processing helix chain 'R' and resid 53 through 62 Processing helix chain 'R' and resid 64 through 84 removed outlier: 3.571A pdb=" N ALA R 70 " --> pdb=" O ASP R 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR R 84 " --> pdb=" O GLN R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 122 removed outlier: 3.539A pdb=" N GLU R 109 " --> pdb=" O PRO R 105 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA R 110 " --> pdb=" O TYR R 106 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA R 113 " --> pdb=" O GLU R 109 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 56 removed outlier: 3.752A pdb=" N ARG S 50 " --> pdb=" O PHE S 46 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) Processing helix chain 'S' and resid 56 through 81 removed outlier: 3.784A pdb=" N ILE S 61 " --> pdb=" O LEU S 57 " (cutoff:3.500A) Proline residue: S 62 - end of helix removed outlier: 3.657A pdb=" N TYR S 81 " --> pdb=" O ASN S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 94 removed outlier: 3.726A pdb=" N ARG S 91 " --> pdb=" O GLU S 87 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN S 93 " --> pdb=" O LEU S 89 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL S 94 " --> pdb=" O GLU S 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 16 through 44 removed outlier: 3.775A pdb=" N PHE T 26 " --> pdb=" O PHE T 22 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL T 27 " --> pdb=" O ALA T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 54 Processing helix chain 'U' and resid 26 through 39 Processing helix chain 'V' and resid 20 through 25 Processing helix chain 'V' and resid 33 through 37 removed outlier: 3.935A pdb=" N SER V 37 " --> pdb=" O GLY V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 39 through 45 removed outlier: 4.130A pdb=" N VAL V 43 " --> pdb=" O LEU V 39 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR V 45 " --> pdb=" O LEU V 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 33 removed outlier: 4.763A pdb=" N VAL A 37 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY A 212 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 96 " --> pdb=" O SER A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 287 through 289 removed outlier: 3.589A pdb=" N ASN A 314 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 437 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 252 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE H 24 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 18 through 22 removed outlier: 6.076A pdb=" N THR B 18 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLY B 189 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER B 20 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 228 through 232 removed outlier: 6.567A pdb=" N ASN B 229 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N GLY B 357 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL B 231 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 282 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 273 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 312 through 313 Processing sheet with id=AA6, first strand: chain 'C' and resid 22 through 23 Processing sheet with id=AA7, first strand: chain 'D' and resid 133 through 136 removed outlier: 4.430A pdb=" N LYS D 145 " --> pdb=" O ASP D 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 213 through 214 Processing sheet with id=AA9, first strand: chain 'E' and resid 108 through 109 removed outlier: 3.695A pdb=" N VAL E 109 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL E 116 " --> pdb=" O VAL E 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 176 through 178 removed outlier: 3.537A pdb=" N SER E 183 " --> pdb=" O CYS E 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 206 through 207 removed outlier: 3.539A pdb=" N GLU E 206 " --> pdb=" O ILE E 213 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE E 213 " --> pdb=" O GLU E 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'L' and resid 29 through 33 removed outlier: 4.763A pdb=" N VAL L 37 " --> pdb=" O ALA L 206 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY L 212 " --> pdb=" O GLU L 41 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN L 96 " --> pdb=" O SER L 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 287 through 289 removed outlier: 3.590A pdb=" N ASN L 314 " --> pdb=" O ALA L 333 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY L 437 " --> pdb=" O LEU L 251 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG L 252 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE S 24 " --> pdb=" O ARG L 252 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 18 through 22 removed outlier: 6.077A pdb=" N THR M 18 " --> pdb=" O VAL M 187 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLY M 189 " --> pdb=" O THR M 18 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER M 20 " --> pdb=" O GLY M 189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 228 through 232 removed outlier: 6.501A pdb=" N ASN M 229 " --> pdb=" O ALA M 355 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLY M 357 " --> pdb=" O ASN M 229 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL M 231 " --> pdb=" O GLY M 357 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY M 282 " --> pdb=" O PHE M 279 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER M 273 " --> pdb=" O PHE M 288 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 312 through 313 Processing sheet with id=AB8, first strand: chain 'N' and resid 22 through 23 Processing sheet with id=AB9, first strand: chain 'O' and resid 133 through 136 removed outlier: 4.431A pdb=" N LYS O 145 " --> pdb=" O ASP O 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 213 through 214 Processing sheet with id=AC2, first strand: chain 'P' and resid 108 through 109 removed outlier: 3.696A pdb=" N VAL P 109 " --> pdb=" O VAL P 116 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL P 116 " --> pdb=" O VAL P 109 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 176 through 178 removed outlier: 3.537A pdb=" N SER P 183 " --> pdb=" O CYS P 178 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 206 through 207 removed outlier: 3.539A pdb=" N GLU P 206 " --> pdb=" O ILE P 213 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE P 213 " --> pdb=" O GLU P 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 1475 hydrogen bonds defined for protein. 4176 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: 5.84 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.36: 10525 1.36 - 1.58: 22351 1.58 - 1.80: 178 1.80 - 2.02: 50 2.02 - 2.24: 27 Bond restraints: 33131 Sorted by residual: bond pdb=" O11 6PH P 302 " pdb=" P 6PH P 302 " ideal model delta sigma weight residual 2.292 1.643 0.649 2.00e-02 2.50e+03 1.05e+03 bond pdb=" O11 6PH L 501 " pdb=" P 6PH L 501 " ideal model delta sigma weight residual 2.292 1.650 0.642 2.00e-02 2.50e+03 1.03e+03 bond pdb=" C TYR N 54 " pdb=" N SER N 55 " ideal model delta sigma weight residual 1.331 1.589 -0.258 1.38e-02 5.25e+03 3.50e+02 bond pdb=" C PRO S 36 " pdb=" N LEU S 37 " ideal model delta sigma weight residual 1.328 1.566 -0.238 1.30e-02 5.92e+03 3.35e+02 bond pdb=" C LEU P 137 " pdb=" N LYS P 138 " ideal model delta sigma weight residual 1.334 1.538 -0.204 1.20e-02 6.94e+03 2.89e+02 ... (remaining 33126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.43: 44855 9.43 - 18.85: 100 18.85 - 28.28: 6 28.28 - 37.71: 4 37.71 - 47.13: 2 Bond angle restraints: 44967 Sorted by residual: angle pdb=" O TYR E 57 " pdb=" C TYR E 57 " pdb=" N PHE E 58 " ideal model delta sigma weight residual 122.22 102.27 19.95 1.17e+00 7.31e-01 2.91e+02 angle pdb=" O11 6PH P 302 " pdb=" P 6PH P 302 " pdb=" O13 6PH P 302 " ideal model delta sigma weight residual 62.77 109.90 -47.13 3.00e+00 1.11e-01 2.47e+02 angle pdb=" O11 6PH L 501 " pdb=" P 6PH L 501 " pdb=" O13 6PH L 501 " ideal model delta sigma weight residual 62.77 109.85 -47.08 3.00e+00 1.11e-01 2.46e+02 angle pdb=" O ALA U 36 " pdb=" C ALA U 36 " pdb=" N SER U 37 " ideal model delta sigma weight residual 122.23 140.65 -18.42 1.30e+00 5.92e-01 2.01e+02 angle pdb=" CA ALA U 36 " pdb=" C ALA U 36 " pdb=" N SER U 37 " ideal model delta sigma weight residual 117.48 99.54 17.94 1.41e+00 5.03e-01 1.62e+02 ... (remaining 44962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.36: 18981 33.36 - 66.72: 568 66.72 - 100.08: 85 100.08 - 133.43: 13 133.43 - 166.79: 8 Dihedral angle restraints: 19655 sinusoidal: 8056 harmonic: 11599 Sorted by residual: dihedral pdb=" CA MET V 38 " pdb=" C MET V 38 " pdb=" N LEU V 39 " pdb=" CA LEU V 39 " ideal model delta harmonic sigma weight residual 180.00 128.31 51.69 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CD ARG E 53 " pdb=" NE ARG E 53 " pdb=" CZ ARG E 53 " pdb=" NH1 ARG E 53 " ideal model delta sinusoidal sigma weight residual 0.00 85.78 -85.78 1 1.00e+01 1.00e-02 8.89e+01 dihedral pdb=" CA LYS P 105 " pdb=" C LYS P 105 " pdb=" N ASN P 106 " pdb=" CA ASN P 106 " ideal model delta harmonic sigma weight residual 180.00 139.73 40.27 0 5.00e+00 4.00e-02 6.49e+01 ... (remaining 19652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 4831 0.160 - 0.321: 38 0.321 - 0.481: 2 0.481 - 0.641: 0 0.641 - 0.802: 6 Chirality restraints: 4877 Sorted by residual: chirality pdb=" CG LEU E 162 " pdb=" CB LEU E 162 " pdb=" CD1 LEU E 162 " pdb=" CD2 LEU E 162 " both_signs ideal model delta sigma weight residual False -2.59 -1.79 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CG LEU P 162 " pdb=" CB LEU P 162 " pdb=" CD1 LEU P 162 " pdb=" CD2 LEU P 162 " both_signs ideal model delta sigma weight residual False -2.59 -1.79 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" CB ILE E 154 " pdb=" CA ILE E 154 " pdb=" CG1 ILE E 154 " pdb=" CG2 ILE E 154 " both_signs ideal model delta sigma weight residual False 2.64 1.86 0.79 2.00e-01 2.50e+01 1.56e+01 ... (remaining 4874 not shown) Planarity restraints: 5688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 53 " 1.074 9.50e-02 1.11e+02 4.81e-01 1.40e+02 pdb=" NE ARG E 53 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG E 53 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG E 53 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG E 53 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 99 " 0.041 2.00e-02 2.50e+03 8.70e-02 7.56e+01 pdb=" C GLU F 99 " -0.150 2.00e-02 2.50e+03 pdb=" O GLU F 99 " 0.058 2.00e-02 2.50e+03 pdb=" N GLU F 100 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 57 " -0.047 2.00e-02 2.50e+03 7.73e-02 5.98e+01 pdb=" C TYR E 57 " 0.134 2.00e-02 2.50e+03 pdb=" O TYR E 57 " -0.042 2.00e-02 2.50e+03 pdb=" N PHE E 58 " -0.045 2.00e-02 2.50e+03 ... (remaining 5685 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 9484 2.83 - 3.35: 27255 3.35 - 3.86: 49616 3.86 - 4.38: 61843 4.38 - 4.90: 104861 Nonbonded interactions: 253059 Sorted by model distance: nonbonded pdb=" C THR E 122 " pdb=" N HIS E 124 " model vdw 2.309 3.350 nonbonded pdb=" O TYR N 132 " pdb=" OG SER N 140 " model vdw 2.393 3.040 nonbonded pdb=" N PRO E 123 " pdb=" N HIS E 124 " model vdw 2.400 2.560 nonbonded pdb=" O VAL B 108 " pdb=" OG1 THR B 112 " model vdw 2.408 3.040 nonbonded pdb=" O VAL M 108 " pdb=" OG1 THR M 112 " model vdw 2.409 3.040 ... (remaining 253054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'L' and resid 27 through 457) } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and (resid 1 through 155 or (resid 156 and (name N or name CA or name \ C or name O or name CB )) or resid 157 through 267 or (resid 268 and (name N or \ name CA or name C or name O or name CB )) or resid 269 through 385)) selection = (chain 'N' and resid 1 through 385) } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'E' selection = (chain 'P' and resid 31 through 301) } ncs_group { reference = chain 'F' selection = (chain 'Q' and resid 74 through 147) } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = (chain 'I' and resid 5 through 57) selection = (chain 'T' and resid 5 through 57) } ncs_group { reference = (chain 'U' and resid 11 through 53) selection = (chain 'V' and resid 11 through 53) } 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 31.880 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.017 1.106 33143 Z= 0.662 Angle : 1.330 47.134 44973 Z= 0.687 Chirality : 0.062 0.802 4877 Planarity : 0.010 0.481 5688 Dihedral : 17.130 166.792 12185 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.11 % Favored : 94.66 % Rotamer: Outliers : 2.11 % Allowed : 1.70 % Favored : 96.18 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.23 (0.10), residues: 3952 helix: -3.49 (0.07), residues: 1905 sheet: -0.99 (0.29), residues: 294 loop : -2.15 (0.13), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG E 146 TYR 0.023 0.002 TYR V 26 PHE 0.046 0.003 PHE V 15 TRP 0.025 0.002 TRP P 176 HIS 0.019 0.002 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.01202 (33131) covalent geometry : angle 1.31204 (44967) SS BOND : bond 0.62904 ( 2) SS BOND : angle 20.07962 ( 4) hydrogen bonds : bond 0.34387 ( 1475) hydrogen bonds : angle 8.98465 ( 4176) metal coordination : bond 0.74285 ( 4) metal coordination : angle 16.16571 ( 2) Misc. bond : bond 0.50394 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 482 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.8475 (mttm) cc_final: 0.7929 (mtpp) REVERT: B 347 LYS cc_start: 0.7355 (ptpt) cc_final: 0.6926 (pptt) REVERT: C 370 ILE cc_start: 0.7473 (pt) cc_final: 0.7257 (mm) REVERT: E 135 SER cc_start: 0.3153 (OUTLIER) cc_final: 0.2825 (p) REVERT: F 100 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6637 (mt-10) REVERT: G 10 ARG cc_start: 0.7894 (ttm170) cc_final: 0.7577 (mtm110) REVERT: G 111 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8082 (mt-10) REVERT: G 116 GLU cc_start: 0.8191 (tt0) cc_final: 0.7983 (tt0) REVERT: O 62 MET cc_start: 0.6386 (mtm) cc_final: 0.6107 (mtm) REVERT: P 40 ASP cc_start: 0.7075 (m-30) cc_final: 0.6827 (m-30) REVERT: P 110 LYS cc_start: 0.3860 (OUTLIER) cc_final: 0.3279 (mptm) REVERT: P 124 HIS cc_start: 0.3217 (OUTLIER) cc_final: 0.2841 (m-70) REVERT: P 146 ARG cc_start: 0.2086 (OUTLIER) cc_final: 0.1439 (ttp-170) REVERT: P 169 GLU cc_start: 0.1719 (OUTLIER) cc_final: -0.0172 (pm20) REVERT: R 10 ARG cc_start: 0.7906 (ttm170) cc_final: 0.7575 (mtm110) REVERT: R 57 GLN cc_start: 0.8379 (mm110) cc_final: 0.8171 (mm110) outliers start: 72 outliers final: 20 residues processed: 545 average time/residue: 0.7453 time to fit residues: 473.6047 Evaluate side-chains 411 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 385 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 146 ARG Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain P residue 110 LYS Chi-restraints excluded: chain P residue 124 HIS Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 134 MET Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 146 ARG Chi-restraints excluded: chain P residue 148 LYS Chi-restraints excluded: chain P residue 169 GLU Chi-restraints excluded: chain P residue 191 ILE Chi-restraints excluded: chain P residue 200 LEU Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain Q residue 101 CYS Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain V residue 33 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 310 GLN A 373 GLN B 191 ASN B 328 GLN B 339 ASN C 14 ASN C 57 ASN E 38 ASN E 112 GLN E 130 ASN E 181 HIS E 184 HIS F 131 GLN G 3 GLN G 91 ASN H 42 HIS ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 ASN L 310 GLN L 373 GLN M 191 ASN M 328 GLN M 339 ASN N 14 ASN N 22 GLN N 261 ASN P 38 ASN P 112 GLN P 120 HIS P 127 GLN P 130 ASN P 181 HIS P 184 HIS Q 131 GLN R 3 GLN R 91 ASN S 42 HIS V 14 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.189608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.147142 restraints weight = 29944.348| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.40 r_work: 0.3472 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 33143 Z= 0.153 Angle : 0.686 11.851 44973 Z= 0.347 Chirality : 0.045 0.204 4877 Planarity : 0.006 0.083 5688 Dihedral : 15.745 166.241 4863 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.28 % Favored : 95.67 % Rotamer: Outliers : 2.06 % Allowed : 7.05 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.12), residues: 3952 helix: -0.96 (0.10), residues: 1950 sheet: -0.04 (0.28), residues: 334 loop : -1.64 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 53 TYR 0.020 0.002 TYR S 68 PHE 0.022 0.002 PHE I 11 TRP 0.020 0.002 TRP V 33 HIS 0.007 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00328 (33131) covalent geometry : angle 0.68566 (44967) SS BOND : bond 0.02583 ( 2) SS BOND : angle 1.54924 ( 4) hydrogen bonds : bond 0.07123 ( 1475) hydrogen bonds : angle 4.63503 ( 4176) metal coordination : bond 0.02196 ( 4) metal coordination : angle 1.08228 ( 2) Misc. bond : bond 0.07025 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 393 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASP cc_start: 0.7599 (m-30) cc_final: 0.7354 (m-30) REVERT: A 122 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7629 (mt0) REVERT: A 142 LYS cc_start: 0.8327 (mttm) cc_final: 0.7615 (mtpp) REVERT: A 221 ASN cc_start: 0.7167 (m110) cc_final: 0.6684 (m-40) REVERT: A 239 LYS cc_start: 0.6700 (OUTLIER) cc_final: 0.6353 (tmtm) REVERT: A 360 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6887 (t70) REVERT: B 54 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.7199 (t80) REVERT: B 347 LYS cc_start: 0.7358 (ptpt) cc_final: 0.6391 (pptt) REVERT: C 356 THR cc_start: 0.8087 (t) cc_final: 0.7677 (m) REVERT: D 67 HIS cc_start: 0.7202 (t-170) cc_final: 0.6412 (m170) REVERT: D 235 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7110 (mm-30) REVERT: E 76 GLU cc_start: 0.7633 (pt0) cc_final: 0.7283 (mt-10) REVERT: E 155 MET cc_start: 0.3894 (tpp) cc_final: 0.3009 (tpt) REVERT: G 51 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8087 (pt0) REVERT: H 71 LYS cc_start: 0.7229 (mtpt) cc_final: 0.6986 (mtpp) REVERT: L 122 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7826 (mt0) REVERT: L 203 ASN cc_start: 0.7596 (t0) cc_final: 0.7384 (t0) REVERT: L 360 ASP cc_start: 0.6819 (OUTLIER) cc_final: 0.6558 (t70) REVERT: M 54 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7192 (t80) REVERT: M 347 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.6507 (pptt) REVERT: O 235 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7133 (mm-30) REVERT: P 146 ARG cc_start: 0.1384 (OUTLIER) cc_final: 0.1083 (ttp-170) REVERT: P 191 ILE cc_start: 0.2697 (OUTLIER) cc_final: 0.2143 (pt) REVERT: R 51 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8142 (pt0) REVERT: S 71 LYS cc_start: 0.7532 (mtpp) cc_final: 0.7327 (mtpt) outliers start: 70 outliers final: 21 residues processed: 442 average time/residue: 0.7160 time to fit residues: 371.8385 Evaluate side-chains 398 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 365 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain L residue 122 GLN Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 360 ASP Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 347 LYS Chi-restraints excluded: chain N residue 293 ILE Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 134 MET Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 146 ARG Chi-restraints excluded: chain P residue 155 MET Chi-restraints excluded: chain P residue 191 ILE Chi-restraints excluded: chain P residue 200 LEU Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain V residue 33 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 346 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 257 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 380 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 318 optimal weight: 0.0370 overall best weight: 1.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 376 GLN B 191 ASN B 339 ASN C 14 ASN E 38 ASN E 120 HIS F 131 GLN G 91 ASN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 ASN L 376 GLN M 191 ASN M 339 ASN N 14 ASN N 261 ASN N 338 GLN P 38 ASN Q 131 GLN R 91 ASN T 14 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.190350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148577 restraints weight = 30099.139| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.41 r_work: 0.3489 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.147 33143 Z= 0.130 Angle : 0.598 10.550 44973 Z= 0.299 Chirality : 0.042 0.166 4877 Planarity : 0.005 0.066 5688 Dihedral : 14.985 168.070 4821 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.97 % Favored : 96.00 % Rotamer: Outliers : 1.94 % Allowed : 8.58 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.13), residues: 3952 helix: 0.28 (0.12), residues: 1955 sheet: 0.16 (0.27), residues: 342 loop : -1.40 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 365 TYR 0.019 0.001 TYR S 68 PHE 0.018 0.001 PHE I 32 TRP 0.019 0.001 TRP V 33 HIS 0.005 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00274 (33131) covalent geometry : angle 0.59728 (44967) SS BOND : bond 0.00444 ( 2) SS BOND : angle 1.42462 ( 4) hydrogen bonds : bond 0.06180 ( 1475) hydrogen bonds : angle 4.25327 ( 4176) metal coordination : bond 0.02256 ( 4) metal coordination : angle 1.75971 ( 2) Misc. bond : bond 0.09944 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 398 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASP cc_start: 0.7375 (m-30) cc_final: 0.7162 (m-30) REVERT: A 122 GLN cc_start: 0.7851 (mp10) cc_final: 0.7592 (mt0) REVERT: A 142 LYS cc_start: 0.8301 (mttm) cc_final: 0.7575 (mtpp) REVERT: A 182 LEU cc_start: 0.8882 (mt) cc_final: 0.8581 (mp) REVERT: A 221 ASN cc_start: 0.7099 (m110) cc_final: 0.6552 (m-40) REVERT: B 54 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.7177 (t80) REVERT: B 292 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7254 (pt0) REVERT: C 356 THR cc_start: 0.8107 (t) cc_final: 0.7693 (m) REVERT: D 67 HIS cc_start: 0.7235 (t-170) cc_final: 0.6482 (m170) REVERT: D 235 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7091 (mm-30) REVERT: E 200 LEU cc_start: 0.3686 (OUTLIER) cc_final: 0.3379 (mm) REVERT: G 51 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8077 (pt0) REVERT: H 35 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6893 (ptpt) REVERT: H 71 LYS cc_start: 0.7239 (mtpt) cc_final: 0.7031 (mtpp) REVERT: L 182 LEU cc_start: 0.8890 (mt) cc_final: 0.8597 (mp) REVERT: L 221 ASN cc_start: 0.7214 (m-40) cc_final: 0.6665 (m-40) REVERT: L 360 ASP cc_start: 0.6816 (OUTLIER) cc_final: 0.6597 (t70) REVERT: M 54 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.7098 (t80) REVERT: M 347 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.6515 (pptt) REVERT: O 67 HIS cc_start: 0.7234 (t-170) cc_final: 0.6496 (m170) REVERT: O 235 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7207 (tp30) REVERT: P 40 ASP cc_start: 0.7167 (m-30) cc_final: 0.6775 (m-30) REVERT: Q 83 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6246 (tm-30) REVERT: Q 121 GLU cc_start: 0.7253 (tt0) cc_final: 0.6906 (tt0) REVERT: R 51 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8125 (pt0) outliers start: 66 outliers final: 18 residues processed: 442 average time/residue: 0.7074 time to fit residues: 367.3245 Evaluate side-chains 397 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 369 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 360 ASP Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain M residue 347 LYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 134 MET Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain V residue 33 TRP Chi-restraints excluded: chain V residue 46 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 91 optimal weight: 10.0000 chunk 245 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 326 optimal weight: 0.6980 chunk 367 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 chunk 343 optimal weight: 7.9990 chunk 299 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 ASN B 339 ASN C 73 HIS C 74 ASN E 38 ASN F 131 GLN G 91 ASN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 203 ASN L 310 GLN M 191 ASN M 252 GLN M 339 ASN N 73 HIS P 38 ASN P 199 ASN Q 131 GLN R 91 ASN S 42 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.182539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.140017 restraints weight = 29818.613| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.40 r_work: 0.3388 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.250 33143 Z= 0.277 Angle : 0.821 11.474 44973 Z= 0.414 Chirality : 0.052 0.247 4877 Planarity : 0.006 0.067 5688 Dihedral : 15.548 173.904 4808 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.78 % Favored : 95.19 % Rotamer: Outliers : 2.56 % Allowed : 9.66 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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: -0.84 (0.13), residues: 3952 helix: 0.08 (0.12), residues: 1963 sheet: 0.19 (0.27), residues: 338 loop : -1.45 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 110 TYR 0.022 0.003 TYR H 68 PHE 0.033 0.003 PHE R 45 TRP 0.021 0.003 TRP V 33 HIS 0.007 0.002 HIS H 15 Details of bonding type rmsd covalent geometry : bond 0.00664 (33131) covalent geometry : angle 0.82036 (44967) SS BOND : bond 0.00260 ( 2) SS BOND : angle 1.98346 ( 4) hydrogen bonds : bond 0.09607 ( 1475) hydrogen bonds : angle 4.66201 ( 4176) metal coordination : bond 0.01004 ( 4) metal coordination : angle 3.92151 ( 2) Misc. bond : bond 0.14906 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 363 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 ASP cc_start: 0.7590 (m-30) cc_final: 0.7367 (m-30) REVERT: A 122 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: A 142 LYS cc_start: 0.8336 (mttm) cc_final: 0.7569 (mtpp) REVERT: A 182 LEU cc_start: 0.8890 (mt) cc_final: 0.8530 (mp) REVERT: A 217 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6387 (pm20) REVERT: A 221 ASN cc_start: 0.7216 (m110) cc_final: 0.6743 (m-40) REVERT: A 224 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7205 (tt0) REVERT: A 341 ASP cc_start: 0.8147 (p0) cc_final: 0.7831 (p0) REVERT: B 54 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.7258 (t80) REVERT: C 5 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8712 (mtpp) REVERT: C 253 HIS cc_start: 0.8884 (t-90) cc_final: 0.8658 (t-90) REVERT: D 67 HIS cc_start: 0.7254 (t-170) cc_final: 0.6690 (m170) REVERT: D 235 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7089 (mm-30) REVERT: E 35 ARG cc_start: 0.7845 (mmm160) cc_final: 0.7640 (mmp80) REVERT: E 76 GLU cc_start: 0.7755 (pt0) cc_final: 0.7314 (mt-10) REVERT: E 200 LEU cc_start: 0.3115 (OUTLIER) cc_final: 0.2721 (mm) REVERT: G 51 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8424 (pt0) REVERT: H 71 LYS cc_start: 0.7344 (mtpt) cc_final: 0.7045 (mtpp) REVERT: L 118 ASP cc_start: 0.6900 (m-30) cc_final: 0.6679 (m-30) REVERT: L 182 LEU cc_start: 0.8903 (mt) cc_final: 0.8538 (mp) REVERT: L 221 ASN cc_start: 0.7213 (m-40) cc_final: 0.6722 (m-40) REVERT: L 224 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7182 (tt0) REVERT: L 341 ASP cc_start: 0.8167 (p0) cc_final: 0.7844 (p0) REVERT: M 54 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.7271 (t80) REVERT: M 135 GLU cc_start: 0.8261 (pt0) cc_final: 0.8046 (pt0) REVERT: M 347 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.6481 (pptt) REVERT: O 67 HIS cc_start: 0.7260 (t-170) cc_final: 0.6701 (m170) REVERT: O 235 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7065 (mm-30) REVERT: P 35 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7392 (mmp80) REVERT: P 40 ASP cc_start: 0.7224 (m-30) cc_final: 0.6827 (m-30) REVERT: P 155 MET cc_start: 0.3369 (OUTLIER) cc_final: 0.2927 (ttt) REVERT: Q 89 GLU cc_start: 0.5844 (OUTLIER) cc_final: 0.5304 (pp20) REVERT: R 51 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8426 (pt0) REVERT: V 33 TRP cc_start: -0.0639 (OUTLIER) cc_final: -0.1350 (p-90) outliers start: 87 outliers final: 38 residues processed: 420 average time/residue: 0.7272 time to fit residues: 357.7145 Evaluate side-chains 412 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 359 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 224 GLU Chi-restraints excluded: chain L residue 306 ILE Chi-restraints excluded: chain L residue 360 ASP Chi-restraints excluded: chain L residue 396 ILE Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 222 LYS Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain M residue 345 ASP Chi-restraints excluded: chain M residue 347 LYS Chi-restraints excluded: chain O residue 222 SER Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 134 MET Chi-restraints excluded: chain P residue 142 THR Chi-restraints excluded: chain P residue 155 MET Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 118 ASP Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain U residue 31 MET Chi-restraints excluded: chain V residue 33 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 374 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 258 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 378 optimal weight: 9.9990 chunk 236 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 ASN B 339 ASN C 73 HIS C 338 GLN D 122 ASN E 38 ASN F 131 GLN G 91 ASN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 191 ASN M 339 ASN O 122 ASN P 38 ASN Q 131 GLN R 91 ASN S 15 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.185119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.143027 restraints weight = 30001.293| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.41 r_work: 0.3422 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.216 33143 Z= 0.170 Angle : 0.667 10.932 44973 Z= 0.335 Chirality : 0.045 0.214 4877 Planarity : 0.005 0.062 5688 Dihedral : 14.976 177.196 4806 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Rotamer: Outliers : 2.41 % Allowed : 10.54 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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: -0.46 (0.13), residues: 3952 helix: 0.46 (0.12), residues: 1971 sheet: 0.28 (0.27), residues: 342 loop : -1.33 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 119 TYR 0.019 0.002 TYR S 68 PHE 0.020 0.002 PHE G 45 TRP 0.020 0.002 TRP V 33 HIS 0.014 0.001 HIS S 15 Details of bonding type rmsd covalent geometry : bond 0.00383 (33131) covalent geometry : angle 0.66653 (44967) SS BOND : bond 0.00211 ( 2) SS BOND : angle 1.39275 ( 4) hydrogen bonds : bond 0.07328 ( 1475) hydrogen bonds : angle 4.38765 ( 4176) metal coordination : bond 0.00915 ( 4) metal coordination : angle 4.35490 ( 2) Misc. bond : bond 0.12537 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 378 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASP cc_start: 0.7467 (m-30) cc_final: 0.7243 (m-30) REVERT: A 142 LYS cc_start: 0.8309 (mttm) cc_final: 0.7596 (mtpp) REVERT: A 182 LEU cc_start: 0.8927 (mt) cc_final: 0.8579 (mp) REVERT: A 221 ASN cc_start: 0.7077 (m110) cc_final: 0.6594 (m-40) REVERT: B 54 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.7264 (t80) REVERT: C 5 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8720 (mtpp) REVERT: C 253 HIS cc_start: 0.8877 (t-90) cc_final: 0.8591 (t-90) REVERT: D 67 HIS cc_start: 0.7283 (t-170) cc_final: 0.6666 (m170) REVERT: D 235 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7139 (mm-30) REVERT: E 200 LEU cc_start: 0.3145 (OUTLIER) cc_final: 0.2605 (mm) REVERT: F 117 LEU cc_start: 0.3669 (OUTLIER) cc_final: 0.3063 (tt) REVERT: G 51 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8472 (pt0) REVERT: H 71 LYS cc_start: 0.7284 (mtpt) cc_final: 0.6968 (mtpp) REVERT: L 114 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.7077 (m-30) REVERT: L 118 ASP cc_start: 0.6839 (m-30) cc_final: 0.6585 (m-30) REVERT: L 182 LEU cc_start: 0.8943 (mt) cc_final: 0.8597 (mp) REVERT: L 221 ASN cc_start: 0.7203 (m-40) cc_final: 0.6740 (m-40) REVERT: M 54 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.7252 (t80) REVERT: M 135 GLU cc_start: 0.8239 (pt0) cc_final: 0.8014 (pt0) REVERT: M 347 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.6517 (pptt) REVERT: N 253 HIS cc_start: 0.8885 (t-90) cc_final: 0.8574 (t-90) REVERT: O 67 HIS cc_start: 0.7280 (t-170) cc_final: 0.6674 (m170) REVERT: O 235 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7097 (mm-30) REVERT: P 40 ASP cc_start: 0.7250 (m-30) cc_final: 0.6873 (m-30) REVERT: P 55 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.7034 (t80) REVERT: P 155 MET cc_start: 0.2600 (OUTLIER) cc_final: 0.2314 (ttt) REVERT: P 165 VAL cc_start: 0.3714 (OUTLIER) cc_final: 0.3205 (t) REVERT: R 51 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8464 (pt0) REVERT: R 98 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: V 33 TRP cc_start: -0.0661 (OUTLIER) cc_final: -0.1464 (p-90) outliers start: 82 outliers final: 41 residues processed: 426 average time/residue: 0.7450 time to fit residues: 370.3754 Evaluate side-chains 425 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 370 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 360 ASP Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 396 ILE Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain M residue 344 LYS Chi-restraints excluded: chain M residue 345 ASP Chi-restraints excluded: chain M residue 347 LYS Chi-restraints excluded: chain N residue 263 LEU Chi-restraints excluded: chain N residue 293 ILE Chi-restraints excluded: chain O residue 222 SER Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 134 MET Chi-restraints excluded: chain P residue 142 THR Chi-restraints excluded: chain P residue 155 MET Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 98 GLU Chi-restraints excluded: chain R residue 118 ASP Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain U residue 31 MET Chi-restraints excluded: chain V residue 33 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 287 optimal weight: 1.9990 chunk 290 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 213 optimal weight: 6.9990 chunk 239 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN B 191 ASN B 339 ASN E 38 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN F 131 GLN G 91 ASN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 231 GLN M 191 ASN M 339 ASN P 38 ASN Q 108 GLN Q 131 GLN R 91 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.185474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.143557 restraints weight = 30022.780| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.39 r_work: 0.3429 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.220 33143 Z= 0.164 Angle : 0.653 10.724 44973 Z= 0.327 Chirality : 0.045 0.197 4877 Planarity : 0.005 0.061 5688 Dihedral : 14.665 177.659 4806 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.66 % Favored : 95.32 % Rotamer: Outliers : 2.70 % Allowed : 11.28 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.13), residues: 3952 helix: 0.65 (0.12), residues: 1979 sheet: 0.35 (0.27), residues: 342 loop : -1.24 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 21 TYR 0.021 0.002 TYR S 68 PHE 0.020 0.002 PHE G 45 TRP 0.019 0.002 TRP V 33 HIS 0.006 0.001 HIS N 197 Details of bonding type rmsd covalent geometry : bond 0.00367 (33131) covalent geometry : angle 0.65238 (44967) SS BOND : bond 0.00259 ( 2) SS BOND : angle 1.43114 ( 4) hydrogen bonds : bond 0.07119 ( 1475) hydrogen bonds : angle 4.30312 ( 4176) metal coordination : bond 0.00811 ( 4) metal coordination : angle 4.17681 ( 2) Misc. bond : bond 0.13043 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 391 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.8311 (mttm) cc_final: 0.7590 (mtpp) REVERT: A 182 LEU cc_start: 0.8943 (mt) cc_final: 0.8594 (mp) REVERT: A 217 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6380 (pm20) REVERT: A 221 ASN cc_start: 0.7083 (m110) cc_final: 0.6606 (m-40) REVERT: B 54 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7254 (t80) REVERT: B 220 GLU cc_start: 0.6673 (mt-10) cc_final: 0.6399 (mt-10) REVERT: C 5 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8711 (mtpp) REVERT: C 253 HIS cc_start: 0.8864 (t-90) cc_final: 0.8587 (t-90) REVERT: D 67 HIS cc_start: 0.7267 (t-170) cc_final: 0.6644 (m170) REVERT: D 235 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7149 (mm-30) REVERT: E 55 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.6883 (t80) REVERT: E 200 LEU cc_start: 0.3459 (OUTLIER) cc_final: 0.2919 (mm) REVERT: F 117 LEU cc_start: 0.3383 (OUTLIER) cc_final: 0.2819 (tt) REVERT: G 51 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8449 (pt0) REVERT: H 71 LYS cc_start: 0.7349 (mtpt) cc_final: 0.7021 (mtpp) REVERT: L 114 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7082 (m-30) REVERT: L 118 ASP cc_start: 0.6901 (m-30) cc_final: 0.6633 (m-30) REVERT: L 182 LEU cc_start: 0.8935 (mt) cc_final: 0.8596 (mp) REVERT: L 217 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6372 (pm20) REVERT: L 221 ASN cc_start: 0.7279 (m-40) cc_final: 0.6764 (m-40) REVERT: M 54 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7249 (t80) REVERT: M 347 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.6497 (pptt) REVERT: N 253 HIS cc_start: 0.8879 (t-90) cc_final: 0.8593 (t-90) REVERT: O 67 HIS cc_start: 0.7263 (t-170) cc_final: 0.6631 (m170) REVERT: P 40 ASP cc_start: 0.7285 (m-30) cc_final: 0.6993 (m-30) REVERT: P 55 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.7099 (t80) REVERT: P 165 VAL cc_start: 0.3867 (OUTLIER) cc_final: 0.3366 (t) REVERT: Q 88 THR cc_start: 0.5791 (OUTLIER) cc_final: 0.5511 (p) REVERT: R 51 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8432 (pt0) outliers start: 92 outliers final: 38 residues processed: 448 average time/residue: 0.7236 time to fit residues: 381.5544 Evaluate side-chains 434 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 381 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 217 GLU Chi-restraints excluded: chain L residue 306 ILE Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 222 LYS Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain M residue 344 LYS Chi-restraints excluded: chain M residue 347 LYS Chi-restraints excluded: chain N residue 263 LEU Chi-restraints excluded: chain O residue 222 SER Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 134 MET Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 88 THR Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 118 ASP Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain U residue 31 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 321 optimal weight: 9.9990 chunk 338 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 369 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 239 optimal weight: 8.9990 chunk 96 optimal weight: 0.6980 chunk 256 optimal weight: 5.9990 chunk 388 optimal weight: 20.0000 chunk 330 optimal weight: 1.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 ASN B 339 ASN E 38 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 GLN F 131 GLN G 91 ASN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 336 ASN M 191 ASN M 339 ASN N 73 HIS N 338 GLN P 38 ASN P 47 ASN Q 131 GLN R 91 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.184323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141331 restraints weight = 30102.964| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.52 r_work: 0.3408 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.254 33143 Z= 0.195 Angle : 0.705 10.914 44973 Z= 0.353 Chirality : 0.047 0.211 4877 Planarity : 0.005 0.061 5688 Dihedral : 14.759 170.344 4803 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.62 % Rotamer: Outliers : 2.56 % Allowed : 11.92 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 3952 helix: 0.55 (0.12), residues: 1977 sheet: 0.34 (0.27), residues: 342 loop : -1.25 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 110 TYR 0.021 0.002 TYR H 68 PHE 0.024 0.002 PHE G 45 TRP 0.014 0.002 TRP V 33 HIS 0.007 0.001 HIS N 197 Details of bonding type rmsd covalent geometry : bond 0.00448 (33131) covalent geometry : angle 0.70452 (44967) SS BOND : bond 0.00246 ( 2) SS BOND : angle 1.57177 ( 4) hydrogen bonds : bond 0.07974 ( 1475) hydrogen bonds : angle 4.38631 ( 4176) metal coordination : bond 0.00624 ( 4) metal coordination : angle 4.63504 ( 2) Misc. bond : bond 0.14911 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 378 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6725 (m-30) REVERT: A 142 LYS cc_start: 0.8290 (mttm) cc_final: 0.7568 (mtpp) REVERT: A 182 LEU cc_start: 0.8922 (mt) cc_final: 0.8542 (mp) REVERT: A 221 ASN cc_start: 0.7115 (m110) cc_final: 0.6650 (m-40) REVERT: B 54 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7251 (t80) REVERT: B 220 GLU cc_start: 0.6712 (mt-10) cc_final: 0.6445 (mt-10) REVERT: C 5 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8719 (mtpp) REVERT: D 67 HIS cc_start: 0.7213 (t-170) cc_final: 0.6598 (m170) REVERT: D 235 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7110 (mm-30) REVERT: E 55 TYR cc_start: 0.7615 (OUTLIER) cc_final: 0.6923 (t80) REVERT: F 117 LEU cc_start: 0.3379 (OUTLIER) cc_final: 0.2830 (tt) REVERT: G 51 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8484 (pt0) REVERT: G 82 GLU cc_start: 0.8094 (tp30) cc_final: 0.7760 (mm-30) REVERT: H 71 LYS cc_start: 0.7344 (mtpt) cc_final: 0.6993 (mtpp) REVERT: L 114 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.7095 (m-30) REVERT: L 118 ASP cc_start: 0.6868 (m-30) cc_final: 0.6613 (m-30) REVERT: L 182 LEU cc_start: 0.8927 (mt) cc_final: 0.8552 (mp) REVERT: L 221 ASN cc_start: 0.7356 (m-40) cc_final: 0.6857 (m-40) REVERT: L 341 ASP cc_start: 0.8235 (p0) cc_final: 0.7902 (p0) REVERT: M 54 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.7247 (t80) REVERT: M 347 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.6471 (pptt) REVERT: N 101 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7737 (tp) REVERT: O 67 HIS cc_start: 0.7221 (t-170) cc_final: 0.6603 (m170) REVERT: P 40 ASP cc_start: 0.7307 (m-30) cc_final: 0.7071 (m-30) REVERT: P 55 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.7167 (t80) REVERT: P 165 VAL cc_start: 0.3920 (OUTLIER) cc_final: 0.3428 (t) REVERT: Q 88 THR cc_start: 0.5906 (OUTLIER) cc_final: 0.5656 (p) REVERT: Q 89 GLU cc_start: 0.5674 (OUTLIER) cc_final: 0.5449 (pp20) REVERT: R 51 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8470 (pt0) REVERT: R 98 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7515 (mt-10) outliers start: 87 outliers final: 50 residues processed: 432 average time/residue: 0.7453 time to fit residues: 377.0680 Evaluate side-chains 434 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 368 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 306 ILE Chi-restraints excluded: chain L residue 360 ASP Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 396 ILE Chi-restraints excluded: chain L residue 454 MET Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 222 LYS Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain M residue 344 LYS Chi-restraints excluded: chain M residue 345 ASP Chi-restraints excluded: chain M residue 347 LYS Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 263 LEU Chi-restraints excluded: chain O residue 222 SER Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain P residue 47 ASN Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 142 THR Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 88 THR Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 98 GLU Chi-restraints excluded: chain R residue 118 ASP Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain U residue 31 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 151 optimal weight: 3.9990 chunk 304 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 319 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 359 optimal weight: 7.9990 chunk 218 optimal weight: 7.9990 chunk 212 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 ASN B 339 ASN C 338 GLN E 38 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN G 91 ASN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 336 ASN M 191 ASN M 339 ASN P 38 ASN P 47 ASN Q 131 GLN R 91 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.185829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.143536 restraints weight = 30113.726| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.47 r_work: 0.3428 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.233 33143 Z= 0.162 Angle : 0.653 10.940 44973 Z= 0.327 Chirality : 0.045 0.200 4877 Planarity : 0.005 0.061 5688 Dihedral : 14.508 161.751 4798 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.28 % Favored : 95.70 % Rotamer: Outliers : 2.41 % Allowed : 12.48 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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: -0.14 (0.13), residues: 3952 helix: 0.73 (0.12), residues: 1977 sheet: 0.38 (0.27), residues: 342 loop : -1.19 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 199 TYR 0.019 0.002 TYR S 68 PHE 0.019 0.002 PHE G 45 TRP 0.013 0.002 TRP E 176 HIS 0.006 0.001 HIS N 197 Details of bonding type rmsd covalent geometry : bond 0.00362 (33131) covalent geometry : angle 0.65213 (44967) SS BOND : bond 0.00229 ( 2) SS BOND : angle 1.38215 ( 4) hydrogen bonds : bond 0.07055 ( 1475) hydrogen bonds : angle 4.26733 ( 4176) metal coordination : bond 0.00608 ( 4) metal coordination : angle 4.24158 ( 2) Misc. bond : bond 0.13555 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 384 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6704 (m-30) REVERT: A 142 LYS cc_start: 0.8327 (mttm) cc_final: 0.7614 (mtpp) REVERT: A 182 LEU cc_start: 0.8934 (mt) cc_final: 0.8568 (mp) REVERT: A 217 GLU cc_start: 0.6583 (pm20) cc_final: 0.6379 (pm20) REVERT: A 221 ASN cc_start: 0.7078 (m110) cc_final: 0.6598 (m-40) REVERT: A 455 MET cc_start: 0.5438 (mmt) cc_final: 0.4829 (mmt) REVERT: B 54 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.7251 (t80) REVERT: B 220 GLU cc_start: 0.6740 (mt-10) cc_final: 0.6463 (mt-10) REVERT: C 5 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8727 (mtpp) REVERT: C 253 HIS cc_start: 0.8849 (t-90) cc_final: 0.8561 (t-90) REVERT: D 67 HIS cc_start: 0.7251 (t-170) cc_final: 0.6609 (m170) REVERT: E 200 LEU cc_start: 0.3565 (OUTLIER) cc_final: 0.3092 (mm) REVERT: F 117 LEU cc_start: 0.3429 (OUTLIER) cc_final: 0.2867 (tt) REVERT: G 51 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8485 (pt0) REVERT: H 71 LYS cc_start: 0.7365 (mtpt) cc_final: 0.7002 (mtpp) REVERT: L 114 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.7091 (m-30) REVERT: L 118 ASP cc_start: 0.6921 (m-30) cc_final: 0.6652 (m-30) REVERT: L 182 LEU cc_start: 0.8925 (mt) cc_final: 0.8575 (mp) REVERT: L 217 GLU cc_start: 0.6581 (pm20) cc_final: 0.6332 (pm20) REVERT: L 221 ASN cc_start: 0.7355 (m-40) cc_final: 0.6848 (m-40) REVERT: M 54 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7250 (t80) REVERT: M 347 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.6511 (pptt) REVERT: N 253 HIS cc_start: 0.8902 (t-90) cc_final: 0.8611 (t-90) REVERT: O 67 HIS cc_start: 0.7243 (t-170) cc_final: 0.6605 (m170) REVERT: P 40 ASP cc_start: 0.7332 (m-30) cc_final: 0.7048 (m-30) REVERT: P 55 TYR cc_start: 0.7679 (OUTLIER) cc_final: 0.7132 (t80) REVERT: Q 88 THR cc_start: 0.5881 (OUTLIER) cc_final: 0.5655 (p) REVERT: R 51 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8437 (pt0) REVERT: R 98 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7575 (mt-10) outliers start: 82 outliers final: 47 residues processed: 436 average time/residue: 0.7134 time to fit residues: 365.0590 Evaluate side-chains 437 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 377 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 306 ILE Chi-restraints excluded: chain L residue 360 ASP Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 222 LYS Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain M residue 344 LYS Chi-restraints excluded: chain M residue 345 ASP Chi-restraints excluded: chain M residue 347 LYS Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 263 LEU Chi-restraints excluded: chain O residue 222 SER Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain P residue 47 ASN Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 142 THR Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 88 THR Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 98 GLU Chi-restraints excluded: chain R residue 118 ASP Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain U residue 31 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 208 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 265 optimal weight: 0.7980 chunk 274 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 chunk 264 optimal weight: 0.9980 chunk 235 optimal weight: 7.9990 chunk 355 optimal weight: 0.3980 chunk 32 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 ASN B 339 ASN C 22 GLN E 38 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN G 91 ASN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 191 ASN M 339 ASN P 38 ASN Q 131 GLN R 91 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.188491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.147290 restraints weight = 30041.642| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.40 r_work: 0.3473 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.182 33143 Z= 0.126 Angle : 0.587 11.481 44973 Z= 0.293 Chirality : 0.042 0.183 4877 Planarity : 0.004 0.060 5688 Dihedral : 14.066 160.312 4798 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.74 % Favored : 96.23 % Rotamer: Outliers : 1.88 % Allowed : 13.33 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.13), residues: 3952 helix: 1.00 (0.12), residues: 1977 sheet: 0.49 (0.27), residues: 340 loop : -1.08 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 199 TYR 0.020 0.001 TYR H 68 PHE 0.016 0.001 PHE A 315 TRP 0.015 0.001 TRP E 176 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00273 (33131) covalent geometry : angle 0.58620 (44967) SS BOND : bond 0.00224 ( 2) SS BOND : angle 1.12429 ( 4) hydrogen bonds : bond 0.05733 ( 1475) hydrogen bonds : angle 4.09147 ( 4176) metal coordination : bond 0.00641 ( 4) metal coordination : angle 3.58766 ( 2) Misc. bond : bond 0.11083 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 382 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASP cc_start: 0.6874 (OUTLIER) cc_final: 0.6615 (m-30) REVERT: A 142 LYS cc_start: 0.8296 (mttm) cc_final: 0.7581 (mtpp) REVERT: A 182 LEU cc_start: 0.8907 (mt) cc_final: 0.8557 (mp) REVERT: A 217 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6415 (pm20) REVERT: A 221 ASN cc_start: 0.7174 (m110) cc_final: 0.6694 (m-40) REVERT: A 241 LYS cc_start: 0.8278 (ttmm) cc_final: 0.7939 (mtpt) REVERT: A 455 MET cc_start: 0.5179 (mmt) cc_final: 0.4577 (mmt) REVERT: B 54 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.7199 (t80) REVERT: B 220 GLU cc_start: 0.6709 (mt-10) cc_final: 0.6497 (mt-10) REVERT: D 67 HIS cc_start: 0.7156 (t-170) cc_final: 0.6494 (m170) REVERT: E 200 LEU cc_start: 0.3609 (OUTLIER) cc_final: 0.3104 (mm) REVERT: F 117 LEU cc_start: 0.3490 (OUTLIER) cc_final: 0.2866 (tt) REVERT: G 51 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8199 (pt0) REVERT: H 71 LYS cc_start: 0.7328 (mtpt) cc_final: 0.6981 (mtpp) REVERT: L 118 ASP cc_start: 0.6851 (m-30) cc_final: 0.6601 (m-30) REVERT: L 182 LEU cc_start: 0.8929 (mt) cc_final: 0.8584 (mp) REVERT: L 217 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6398 (pm20) REVERT: L 221 ASN cc_start: 0.7437 (m-40) cc_final: 0.6911 (m-40) REVERT: M 54 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.7196 (t80) REVERT: M 347 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.6493 (pptt) REVERT: N 253 HIS cc_start: 0.8865 (t-90) cc_final: 0.8589 (t-90) REVERT: O 67 HIS cc_start: 0.7152 (t-170) cc_final: 0.6497 (m170) REVERT: P 40 ASP cc_start: 0.7280 (m-30) cc_final: 0.7071 (m-30) REVERT: Q 88 THR cc_start: 0.5875 (OUTLIER) cc_final: 0.5657 (p) REVERT: R 51 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8215 (pt0) REVERT: R 98 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7580 (mt-10) outliers start: 64 outliers final: 35 residues processed: 423 average time/residue: 0.7054 time to fit residues: 351.9136 Evaluate side-chains 424 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 377 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain L residue 146 LYS Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 217 GLU Chi-restraints excluded: chain L residue 306 ILE Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 207 SER Chi-restraints excluded: chain M residue 222 LYS Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain M residue 344 LYS Chi-restraints excluded: chain M residue 347 LYS Chi-restraints excluded: chain N residue 263 LEU Chi-restraints excluded: chain O residue 222 SER Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 142 THR Chi-restraints excluded: chain Q residue 88 THR Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 98 GLU Chi-restraints excluded: chain R residue 118 ASP Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 71 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 92 optimal weight: 9.9990 chunk 355 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 386 optimal weight: 0.0570 chunk 126 optimal weight: 9.9990 chunk 310 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 192 optimal weight: 20.0000 chunk 290 optimal weight: 10.0000 overall best weight: 4.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 ASN B 339 ASN C 73 HIS C 338 GLN E 38 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN G 91 ASN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 191 ASN M 339 ASN N 73 HIS N 261 ASN N 338 GLN P 38 ASN Q 131 GLN R 91 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.183501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140474 restraints weight = 30062.252| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.58 r_work: 0.3394 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.290 33143 Z= 0.229 Angle : 0.748 10.763 44973 Z= 0.373 Chirality : 0.049 0.232 4877 Planarity : 0.005 0.058 5688 Dihedral : 14.616 157.603 4798 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 1.73 % Allowed : 13.63 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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: -0.21 (0.13), residues: 3952 helix: 0.63 (0.12), residues: 1973 sheet: 0.46 (0.27), residues: 338 loop : -1.18 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 110 TYR 0.023 0.003 TYR Q 133 PHE 0.028 0.002 PHE R 45 TRP 0.015 0.002 TRP O 257 HIS 0.007 0.001 HIS N 197 Details of bonding type rmsd covalent geometry : bond 0.00538 (33131) covalent geometry : angle 0.74696 (44967) SS BOND : bond 0.00218 ( 2) SS BOND : angle 1.65048 ( 4) hydrogen bonds : bond 0.08569 ( 1475) hydrogen bonds : angle 4.40525 ( 4176) metal coordination : bond 0.00783 ( 4) metal coordination : angle 5.09147 ( 2) Misc. bond : bond 0.17031 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 367 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6739 (m-30) REVERT: A 142 LYS cc_start: 0.8375 (mttm) cc_final: 0.7661 (mtpp) REVERT: A 182 LEU cc_start: 0.8944 (mt) cc_final: 0.8559 (mp) REVERT: A 221 ASN cc_start: 0.7185 (m110) cc_final: 0.6708 (m-40) REVERT: A 241 LYS cc_start: 0.8260 (ttmm) cc_final: 0.7947 (mtpt) REVERT: A 341 ASP cc_start: 0.8206 (p0) cc_final: 0.7862 (p0) REVERT: A 455 MET cc_start: 0.5483 (mmt) cc_final: 0.4875 (mmt) REVERT: B 54 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.7291 (t80) REVERT: B 220 GLU cc_start: 0.6740 (mt-10) cc_final: 0.6449 (mt-10) REVERT: C 253 HIS cc_start: 0.8896 (t-90) cc_final: 0.8600 (t-90) REVERT: D 67 HIS cc_start: 0.7240 (t-170) cc_final: 0.6659 (m170) REVERT: E 55 TYR cc_start: 0.7664 (OUTLIER) cc_final: 0.7027 (t80) REVERT: F 117 LEU cc_start: 0.3231 (OUTLIER) cc_final: 0.2679 (tt) REVERT: G 51 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8469 (pt0) REVERT: H 71 LYS cc_start: 0.7448 (mtpt) cc_final: 0.7062 (mtpp) REVERT: L 118 ASP cc_start: 0.6997 (m-30) cc_final: 0.6745 (m-30) REVERT: L 182 LEU cc_start: 0.8945 (mt) cc_final: 0.8559 (mp) REVERT: L 221 ASN cc_start: 0.7510 (m-40) cc_final: 0.7036 (m-40) REVERT: L 341 ASP cc_start: 0.8252 (p0) cc_final: 0.7913 (p0) REVERT: M 54 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.7287 (t80) REVERT: M 347 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.6545 (pptt) REVERT: N 253 HIS cc_start: 0.8896 (t-90) cc_final: 0.8619 (t-90) REVERT: O 67 HIS cc_start: 0.7238 (t-170) cc_final: 0.6664 (m170) REVERT: P 165 VAL cc_start: 0.3884 (OUTLIER) cc_final: 0.3366 (t) REVERT: Q 88 THR cc_start: 0.6189 (OUTLIER) cc_final: 0.5918 (p) REVERT: R 51 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8447 (pt0) REVERT: R 98 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7544 (mt-10) outliers start: 59 outliers final: 37 residues processed: 405 average time/residue: 0.7192 time to fit residues: 341.5457 Evaluate side-chains 410 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 362 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain L residue 146 LYS Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 306 ILE Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 207 SER Chi-restraints excluded: chain M residue 222 LYS Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain M residue 344 LYS Chi-restraints excluded: chain M residue 345 ASP Chi-restraints excluded: chain M residue 347 LYS Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 263 LEU Chi-restraints excluded: chain O residue 222 SER Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 142 THR Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 88 THR Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 98 GLU Chi-restraints excluded: chain R residue 118 ASP Chi-restraints excluded: chain S residue 59 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 185 optimal weight: 6.9990 chunk 369 optimal weight: 6.9990 chunk 267 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 308 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 ASN B 339 ASN E 38 ASN F 131 GLN G 91 ASN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 191 ASN M 339 ASN N 73 HIS N 261 ASN P 38 ASN Q 131 GLN R 91 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.188536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.147354 restraints weight = 30182.752| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.40 r_work: 0.3472 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.203 33143 Z= 0.123 Angle : 0.589 11.847 44973 Z= 0.292 Chirality : 0.042 0.183 4877 Planarity : 0.004 0.057 5688 Dihedral : 13.995 158.367 4798 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.51 % Rotamer: Outliers : 1.47 % Allowed : 14.16 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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: 0.19 (0.13), residues: 3952 helix: 1.01 (0.12), residues: 1978 sheet: 0.51 (0.27), residues: 340 loop : -1.05 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 119 TYR 0.020 0.001 TYR S 68 PHE 0.016 0.001 PHE L 315 TRP 0.016 0.001 TRP E 176 HIS 0.006 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00262 (33131) covalent geometry : angle 0.58800 (44967) SS BOND : bond 0.00238 ( 2) SS BOND : angle 1.10393 ( 4) hydrogen bonds : bond 0.05660 ( 1475) hydrogen bonds : angle 4.10077 ( 4176) metal coordination : bond 0.00644 ( 4) metal coordination : angle 3.93931 ( 2) Misc. bond : bond 0.12229 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13233.76 seconds wall clock time: 225 minutes 13.67 seconds (13513.67 seconds total)