Starting phenix.real_space_refine on Tue May 5 18:36:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yio_39324/05_2026/8yio_39324.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yio_39324/05_2026/8yio_39324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yio_39324/05_2026/8yio_39324.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yio_39324/05_2026/8yio_39324.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yio_39324/05_2026/8yio_39324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yio_39324/05_2026/8yio_39324.map" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.394 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 6 7.16 5 P 12 5.49 5 S 110 5.16 5 C 20987 2.51 5 N 5321 2.21 5 O 5934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 161 residue(s): 0.04s 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: 32370 Number of models: 1 Model: "" Number of chains: 24 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: "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: "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: "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: "N" 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: "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: "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: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 342 Unusual residues: {'8PE': 1, '9PE': 1, 'AZO': 1, '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: "N" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 341 Unusual residues: {'6PH': 1, '8PE': 1, '9PE': 1, 'AZO': 1, 'CN3': 1, 'HEM': 2, 'UQ6': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'6PH': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.68, per 1000 atoms: 0.24 Number of scatterers: 32370 At special positions: 0 Unit cell: (141.12, 131.52, 168.96, 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 6 26.01 S 110 16.00 P 12 15.00 O 5934 8.00 N 5321 7.00 C 20987 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=2.74 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.80 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: 2.76 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 199 helices and 20 sheets defined 57.5% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 removed outlier: 3.573A pdb=" N GLU A 62 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 78 removed outlier: 3.552A pdb=" N ASN A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.812A pdb=" N GLU A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 123 removed outlier: 3.551A pdb=" N SER A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 155 removed outlier: 3.634A pdb=" N ALA A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 169 Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.841A pdb=" N LEU A 176 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 removed outlier: 3.737A pdb=" N GLU A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 201 removed outlier: 3.694A pdb=" N LEU A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.637A 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 Processing helix chain 'A' and resid 274 through 286 removed outlier: 3.527A pdb=" N LYS A 279 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.841A pdb=" N GLN A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.834A pdb=" N GLU A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.521A pdb=" N LEU A 343 " --> pdb=" O MET A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 359 through 379 removed outlier: 3.588A pdb=" N VAL A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 398 removed outlier: 3.737A pdb=" N ILE A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.616A pdb=" N LYS A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 412 " --> pdb=" O LYS A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 426 removed outlier: 3.696A pdb=" N LYS A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.562A 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 'C' and resid 2 through 7 Processing helix chain 'C' and resid 9 through 18 removed outlier: 3.754A pdb=" N VAL C 13 " --> pdb=" O TYR C 9 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 30 Processing helix chain 'C' and resid 31 through 52 removed outlier: 3.531A pdb=" N LEU C 35 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY C 37 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 Processing helix chain 'C' and resid 74 through 103 removed outlier: 3.758A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 removed outlier: 3.551A pdb=" N CYS C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 149 Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.520A pdb=" N ALA C 153 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE C 154 " --> pdb=" O PHE C 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 150 through 154' Processing helix chain 'C' and resid 157 through 167 removed outlier: 4.168A pdb=" N SER C 163 " --> pdb=" O ASN C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 205 removed outlier: 3.505A pdb=" N ALA C 181 " --> pdb=" O GLN C 177 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) Proline residue: C 187 - end of helix removed outlier: 3.631A pdb=" N ILE C 203 " --> pdb=" O MET C 199 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N HIS C 204 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 247 removed outlier: 3.802A pdb=" N VAL C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 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: 3.569A pdb=" N VAL C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 Processing helix chain 'C' and resid 319 through 340 removed outlier: 3.506A pdb=" N PHE C 327 " --> pdb=" O LYS C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 365 removed outlier: 4.156A pdb=" N PHE C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 381 removed outlier: 3.516A pdb=" N TYR C 379 " --> pdb=" O ASN C 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 42 Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 63 through 75 removed outlier: 3.703A pdb=" N LEU B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 112 removed outlier: 3.856A pdb=" N TYR B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 103 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 137 through 152 Processing helix chain 'B' and resid 168 through 180 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: 3.691A pdb=" N ARG B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.578A pdb=" N SER B 207 " --> pdb=" O SER B 204 " (cutoff:3.500A) 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 261 removed outlier: 3.820A pdb=" N THR B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 311 removed outlier: 3.510A pdb=" N VAL B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B 311 " --> pdb=" O ASP B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 329 Processing helix chain 'B' and resid 358 through 362 removed outlier: 3.609A pdb=" N LEU B 362 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'D' and resid 86 through 100 removed outlier: 3.704A pdb=" N GLN D 95 " --> pdb=" O ARG D 91 " (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 Processing helix chain 'D' and resid 161 through 168 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: 3.577A pdb=" N ARG D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 3.566A 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 'N' and resid 2 through 7 Processing helix chain 'N' and resid 9 through 18 removed outlier: 3.755A pdb=" N VAL N 13 " --> pdb=" O TYR N 9 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR N 16 " --> pdb=" O LEU N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 30 Processing helix chain 'N' and resid 31 through 52 removed outlier: 3.531A pdb=" N LEU N 35 " --> pdb=" O ASN N 31 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY N 37 " --> pdb=" O GLY N 33 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 71 Processing helix chain 'N' and resid 74 through 103 removed outlier: 3.758A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 removed outlier: 3.551A pdb=" N CYS N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 149 Processing helix chain 'N' and resid 150 through 154 removed outlier: 3.520A pdb=" N ALA N 153 " --> pdb=" O LEU N 150 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE N 154 " --> pdb=" O PHE N 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 150 through 154' Processing helix chain 'N' and resid 157 through 167 removed outlier: 4.168A pdb=" N SER N 163 " --> pdb=" O ASN N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 205 removed outlier: 3.505A pdb=" N ALA N 181 " --> pdb=" O GLN N 177 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU N 185 " --> pdb=" O ALA N 181 " (cutoff:3.500A) Proline residue: N 187 - end of helix removed outlier: 3.630A pdb=" N ILE N 203 " --> pdb=" O MET N 199 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N HIS N 204 " --> pdb=" O ALA N 200 " (cutoff:3.500A) Processing helix chain 'N' and resid 224 through 247 removed outlier: 3.802A pdb=" N VAL N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR N 232 " --> pdb=" O LYS N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 258 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 Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.570A pdb=" N VAL N 292 " --> pdb=" O LYS N 288 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 304 through 309 Processing helix chain 'N' and resid 319 through 340 removed outlier: 3.505A pdb=" N PHE N 327 " --> pdb=" O LYS N 323 " (cutoff:3.500A) Processing helix chain 'N' and resid 347 through 365 removed outlier: 4.156A pdb=" N PHE N 363 " --> pdb=" O TYR N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 365 through 381 removed outlier: 3.516A pdb=" N TYR N 379 " --> pdb=" O ASN N 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 80 removed outlier: 3.571A pdb=" N GLY E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG E 53 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER E 54 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET E 59 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER E 73 " --> pdb=" O ALA E 69 " (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 90 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.792A pdb=" N ALA E 100 " --> pdb=" O ASN E 97 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE E 101 " --> pdb=" O LEU E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 110 through 114 Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.860A pdb=" N ALA E 136 " --> pdb=" O ASP E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'F' and resid 76 through 86 Processing helix chain 'F' and resid 88 through 109 removed outlier: 3.768A pdb=" N ALA F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS F 101 " --> pdb=" O HIS F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 139 removed outlier: 3.559A pdb=" N THR F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA F 137 " --> pdb=" O TYR F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'G' and resid 4 through 18 removed outlier: 3.507A pdb=" N TYR G 14 " --> pdb=" O ARG G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 37 removed outlier: 3.718A pdb=" N LEU G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL G 26 " --> pdb=" O SER G 22 " (cutoff:3.500A) Proline residue: G 27 - end of helix removed outlier: 3.611A pdb=" N GLY G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) 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: 3.512A pdb=" N ALA G 70 " --> pdb=" O ASP G 66 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 93 removed outlier: 3.674A pdb=" N TRP G 93 " --> pdb=" O ARG G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 99 Processing helix chain 'G' and resid 103 through 122 removed outlier: 3.545A pdb=" N ASN G 122 " --> pdb=" O ASP G 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 34 Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.574A pdb=" N ASN H 43 " --> pdb=" O GLY H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 54 removed outlier: 3.669A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG H 51 " --> pdb=" O ASN H 47 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE H 52 " --> pdb=" O SER H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 81 removed outlier: 3.666A pdb=" N ILE H 61 " --> pdb=" O LEU H 57 " (cutoff:3.500A) Proline residue: H 62 - end of helix removed outlier: 3.555A pdb=" N TYR H 81 " --> pdb=" O ASN H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 93 removed outlier: 3.689A pdb=" N GLU H 90 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 44 removed outlier: 3.770A pdb=" N ILE I 21 " --> pdb=" O PHE I 17 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA I 25 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE I 26 " --> pdb=" O PHE I 22 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL I 27 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN I 29 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR I 30 " --> pdb=" O PHE I 26 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL I 31 " --> pdb=" O VAL I 27 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN I 44 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 54 Processing helix chain 'L' and resid 58 through 62 removed outlier: 3.574A pdb=" N GLU L 62 " --> pdb=" O ALA L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 78 removed outlier: 3.553A pdb=" N ASN L 75 " --> pdb=" O ASN L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 90 removed outlier: 3.812A pdb=" N GLU L 89 " --> pdb=" O VAL L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 123 removed outlier: 3.551A pdb=" N SER L 116 " --> pdb=" O SER L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 155 removed outlier: 3.633A pdb=" N ALA L 139 " --> pdb=" O SER L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 155 through 169 Processing helix chain 'L' and resid 172 through 176 removed outlier: 3.840A pdb=" N LEU L 176 " --> pdb=" O PRO L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 186 removed outlier: 3.737A pdb=" N GLU L 186 " --> pdb=" O LEU L 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 201 removed outlier: 3.694A pdb=" N LEU L 193 " --> pdb=" O VAL L 189 " (cutoff:3.500A) removed outlier: 3.637A 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 Processing helix chain 'L' and resid 274 through 286 removed outlier: 3.527A pdb=" N LYS L 279 " --> pdb=" O TYR L 275 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE L 285 " --> pdb=" O ALA L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 298 removed outlier: 3.839A pdb=" N GLN L 298 " --> pdb=" O SER L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 302 through 310 removed outlier: 3.835A pdb=" N GLU L 308 " --> pdb=" O ASP L 304 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR L 309 " --> pdb=" O ASN L 305 " (cutoff:3.500A) Processing helix chain 'L' and resid 339 through 352 removed outlier: 3.520A pdb=" N LEU L 343 " --> pdb=" O MET L 339 " (cutoff:3.500A) Processing helix chain 'L' and resid 352 through 357 Processing helix chain 'L' and resid 359 through 379 removed outlier: 3.588A pdb=" N VAL L 363 " --> pdb=" O THR L 359 " (cutoff:3.500A) Processing helix chain 'L' and resid 382 through 398 removed outlier: 3.736A pdb=" N ILE L 396 " --> pdb=" O ALA L 392 " (cutoff:3.500A) Processing helix chain 'L' and resid 402 through 412 removed outlier: 3.615A pdb=" N LYS L 408 " --> pdb=" O GLY L 404 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA L 412 " --> pdb=" O LYS L 408 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 426 removed outlier: 3.697A pdb=" N LYS L 424 " --> pdb=" O ALA L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 444 through 450 removed outlier: 3.563A 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 Processing helix chain 'M' and resid 63 through 75 removed outlier: 3.702A pdb=" N LEU M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU M 74 " --> pdb=" O GLU M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 112 removed outlier: 3.856A pdb=" N TYR M 101 " --> pdb=" O ASP M 97 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN M 103 " --> pdb=" O PRO M 99 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL M 108 " --> pdb=" O ALA M 104 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU M 109 " --> pdb=" O LEU M 105 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR M 112 " --> pdb=" O VAL M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 122 Processing helix chain 'M' and resid 122 through 135 Processing helix chain 'M' and resid 137 through 152 Processing helix chain 'M' and resid 168 through 180 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: 3.690A pdb=" N ARG M 199 " --> pdb=" O ALA M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 204 through 209 removed outlier: 3.579A pdb=" N SER M 207 " --> pdb=" O SER M 204 " (cutoff:3.500A) 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 261 removed outlier: 3.820A pdb=" N THR M 261 " --> pdb=" O ALA M 257 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 311 removed outlier: 3.510A pdb=" N VAL M 297 " --> pdb=" O ASP M 293 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS M 302 " --> pdb=" O SER M 298 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS M 303 " --> pdb=" O SER M 299 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS M 310 " --> pdb=" O ALA M 306 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY M 311 " --> pdb=" O ASP M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 317 through 329 Processing helix chain 'M' and resid 358 through 362 removed outlier: 3.610A pdb=" N LEU M 362 " --> pdb=" O VAL M 359 " (cutoff:3.500A) Processing helix chain 'M' and resid 364 through 368 Processing helix chain 'O' and resid 63 through 68 Processing helix chain 'O' and resid 86 through 100 removed outlier: 3.704A pdb=" N GLN O 95 " --> pdb=" O ARG O 91 " (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 Processing helix chain 'O' and resid 161 through 168 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: 3.578A pdb=" N ARG O 268 " --> pdb=" O ASP O 264 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS O 272 " --> pdb=" O ARG O 268 " (cutoff:3.500A) removed outlier: 3.566A 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 48 through 80 removed outlier: 3.572A pdb=" N GLY P 52 " --> pdb=" O ASP P 48 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG P 53 " --> pdb=" O ALA P 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER P 54 " --> pdb=" O ASP P 50 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA P 56 " --> pdb=" O GLY P 52 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET P 59 " --> pdb=" O TYR P 55 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER P 73 " --> pdb=" O ALA P 69 " (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 90 Processing helix chain 'P' and resid 97 through 101 removed outlier: 3.791A pdb=" N ALA P 100 " --> pdb=" O ASN P 97 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE P 101 " --> pdb=" O LEU P 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 101' Processing helix chain 'P' and resid 110 through 114 Processing helix chain 'P' and resid 122 through 126 removed outlier: 4.024A pdb=" N GLU P 125 " --> pdb=" O THR P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 133 through 137 removed outlier: 3.859A pdb=" N ALA P 136 " --> pdb=" O ASP P 133 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 147 Processing helix chain 'Q' and resid 76 through 85 Processing helix chain 'Q' and resid 90 through 109 removed outlier: 3.513A pdb=" N ARG Q 104 " --> pdb=" O GLU Q 100 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS Q 106 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE Q 107 " --> pdb=" O GLU Q 103 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN Q 109 " --> pdb=" O VAL Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 139 removed outlier: 3.586A pdb=" N THR Q 136 " --> pdb=" O HIS Q 132 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Q 137 " --> pdb=" O TYR Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 142 through 146 removed outlier: 3.694A pdb=" N LEU Q 146 " --> pdb=" O PHE Q 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 18 removed outlier: 3.507A pdb=" N TYR R 14 " --> pdb=" O ARG R 10 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 37 removed outlier: 3.717A pdb=" N LEU R 24 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL R 26 " --> pdb=" O SER R 22 " (cutoff:3.500A) Proline residue: R 27 - end of helix removed outlier: 3.611A pdb=" N GLY R 37 " --> pdb=" O ILE R 33 " (cutoff:3.500A) 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: 3.512A pdb=" N ALA R 70 " --> pdb=" O ASP R 66 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR R 84 " --> pdb=" O GLN R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 93 removed outlier: 3.674A pdb=" N TRP R 93 " --> pdb=" O ARG R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 99 Processing helix chain 'R' and resid 103 through 122 removed outlier: 3.544A pdb=" N ASN R 122 " --> pdb=" O ASP R 118 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 34 Processing helix chain 'S' and resid 46 through 54 removed outlier: 3.669A pdb=" N ARG S 50 " --> pdb=" O PHE S 46 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG S 51 " --> pdb=" O ASN S 47 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE S 52 " --> pdb=" O SER S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 56 through 81 removed outlier: 3.667A pdb=" N ILE S 61 " --> pdb=" O LEU S 57 " (cutoff:3.500A) Proline residue: S 62 - end of helix removed outlier: 3.554A pdb=" N TYR S 81 " --> pdb=" O ASN S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 93 removed outlier: 3.687A pdb=" N GLU S 90 " --> pdb=" O ARG S 86 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG S 91 " --> pdb=" O GLU S 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 11 removed outlier: 4.097A pdb=" N PHE T 10 " --> pdb=" O LEU T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 16 through 44 removed outlier: 4.281A pdb=" N ALA T 25 " --> pdb=" O ILE T 21 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE T 26 " --> pdb=" O PHE T 22 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL T 27 " --> pdb=" O ALA T 23 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR T 30 " --> pdb=" O PHE T 26 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL T 31 " --> pdb=" O VAL T 27 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN T 44 " --> pdb=" O TYR T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 57 removed outlier: 3.565A pdb=" N ALA T 54 " --> pdb=" O LYS T 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG T 55 " --> pdb=" O ASP T 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 28 No H-bonds generated for 'chain 'U' and resid 26 through 28' Processing helix chain 'U' and resid 29 through 38 removed outlier: 3.772A pdb=" N GLY U 35 " --> pdb=" O MET U 31 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER U 37 " --> pdb=" O TRP U 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 20 through 25 removed outlier: 3.549A pdb=" N ALA V 25 " --> pdb=" O ARG V 21 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 39 removed outlier: 3.569A pdb=" N SER V 37 " --> pdb=" O TRP V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 39 through 44 removed outlier: 3.507A pdb=" N VAL V 43 " --> pdb=" O LEU V 39 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 33 removed outlier: 4.767A pdb=" N VAL A 37 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 212 " --> pdb=" O GLU A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 287 through 289 removed outlier: 3.604A pdb=" N ASN A 314 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG A 252 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE H 24 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 22 removed outlier: 6.144A pdb=" N THR B 18 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N GLY B 189 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N SER B 20 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 228 through 232 removed outlier: 3.537A pdb=" N SER B 273 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 312 through 313 Processing sheet with id=AA7, first strand: chain 'D' and resid 133 through 135 Processing sheet with id=AA8, first strand: chain 'D' and resid 213 through 214 Processing sheet with id=AA9, first strand: chain 'N' and resid 21 through 23 Processing sheet with id=AB1, first strand: chain 'E' and resid 94 through 96 removed outlier: 3.853A pdb=" N VAL E 96 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL E 212 " --> pdb=" O VAL E 96 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 177 through 178 Processing sheet with id=AB3, first strand: chain 'L' and resid 29 through 33 removed outlier: 4.767A pdb=" N VAL L 37 " --> pdb=" O ALA L 206 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY L 212 " --> pdb=" O GLU L 41 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 287 through 289 removed outlier: 3.604A pdb=" N ASN L 314 " --> pdb=" O ALA L 333 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG L 252 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.783A 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: 6.144A pdb=" N THR M 18 " --> pdb=" O VAL M 187 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N GLY M 189 " --> pdb=" O THR M 18 " (cutoff:3.500A) removed outlier: 6.971A 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: 3.537A 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 'O' and resid 133 through 135 Processing sheet with id=AB9, first strand: chain 'O' and resid 213 through 214 Processing sheet with id=AC1, first strand: chain 'P' and resid 94 through 96 removed outlier: 3.853A pdb=" N VAL P 96 " --> pdb=" O VAL P 212 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL P 212 " --> pdb=" O VAL P 96 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 177 through 178 1577 hydrogen bonds defined for protein. 4461 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: 5.45 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.33: 6027 1.33 - 1.52: 16299 1.52 - 1.71: 10659 1.71 - 1.90: 186 1.90 - 2.09: 24 Bond restraints: 33195 Sorted by residual: bond pdb=" O11 6PH N 402 " pdb=" P 6PH N 402 " ideal model delta sigma weight residual 2.292 1.646 0.646 2.00e-02 2.50e+03 1.04e+03 bond pdb=" O11 6PH O 401 " pdb=" P 6PH O 401 " ideal model delta sigma weight residual 2.292 1.647 0.645 2.00e-02 2.50e+03 1.04e+03 bond pdb=" C PRO S 36 " pdb=" N LEU S 37 " ideal model delta sigma weight residual 1.333 1.598 -0.265 1.29e-02 6.01e+03 4.23e+02 bond pdb=" C THR G 84 " pdb=" N HIS G 85 " ideal model delta sigma weight residual 1.333 1.529 -0.196 1.45e-02 4.76e+03 1.83e+02 bond pdb=" O13 6PH O 401 " pdb=" P 6PH O 401 " ideal model delta sigma weight residual 1.757 1.508 0.249 2.00e-02 2.50e+03 1.55e+02 ... (remaining 33190 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.35: 44966 9.35 - 18.70: 74 18.70 - 28.04: 7 28.04 - 37.39: 4 37.39 - 46.74: 2 Bond angle restraints: 45053 Sorted by residual: angle pdb=" O THR P 122 " pdb=" C THR P 122 " pdb=" N PRO P 123 " ideal model delta sigma weight residual 121.32 96.06 25.26 1.15e+00 7.56e-01 4.82e+02 angle pdb=" C THR P 122 " pdb=" N PRO P 123 " pdb=" CA PRO P 123 " ideal model delta sigma weight residual 119.28 141.87 -22.59 1.10e+00 8.26e-01 4.22e+02 angle pdb=" O11 6PH O 401 " pdb=" P 6PH O 401 " pdb=" O13 6PH O 401 " ideal model delta sigma weight residual 62.77 109.51 -46.74 3.00e+00 1.11e-01 2.43e+02 angle pdb=" O11 6PH N 402 " pdb=" P 6PH N 402 " pdb=" O13 6PH N 402 " ideal model delta sigma weight residual 62.77 109.03 -46.26 3.00e+00 1.11e-01 2.38e+02 angle pdb=" CA THR P 122 " pdb=" C THR P 122 " pdb=" N PRO P 123 " ideal model delta sigma weight residual 118.44 142.54 -24.10 1.59e+00 3.96e-01 2.30e+02 ... (remaining 45048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 19044 35.21 - 70.43: 520 70.43 - 105.64: 88 105.64 - 140.85: 10 140.85 - 176.06: 10 Dihedral angle restraints: 19672 sinusoidal: 8073 harmonic: 11599 Sorted by residual: dihedral pdb=" CA ILE E 191 " pdb=" C ILE E 191 " pdb=" N ARG E 192 " pdb=" CA ARG E 192 " ideal model delta harmonic sigma weight residual -180.00 -136.89 -43.11 0 5.00e+00 4.00e-02 7.43e+01 dihedral pdb=" CA ILE P 191 " pdb=" C ILE P 191 " pdb=" N ARG P 192 " pdb=" CA ARG P 192 " ideal model delta harmonic sigma weight residual -180.00 -139.23 -40.77 0 5.00e+00 4.00e-02 6.65e+01 dihedral pdb=" CA ARG P 192 " pdb=" C ARG P 192 " pdb=" N LYS P 193 " pdb=" CA LYS P 193 " ideal model delta harmonic sigma weight residual 180.00 147.51 32.49 0 5.00e+00 4.00e-02 4.22e+01 ... (remaining 19669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4196 0.074 - 0.149: 617 0.149 - 0.223: 54 0.223 - 0.298: 6 0.298 - 0.372: 4 Chirality restraints: 4877 Sorted by residual: chirality pdb=" CA CYS E 159 " pdb=" N CYS E 159 " pdb=" C CYS E 159 " pdb=" CB CYS E 159 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CB CN3 N 403 " pdb=" CA CN3 N 403 " pdb=" CC CN3 N 403 " pdb=" OA CN3 N 403 " both_signs ideal model delta sigma weight residual False -2.30 -2.64 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CB THR L 172 " pdb=" CA THR L 172 " pdb=" OG1 THR L 172 " pdb=" CG2 THR L 172 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.34 2.00e-01 2.50e+01 2.83e+00 ... (remaining 4874 not shown) Planarity restraints: 5699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 AZO N 401 " 0.021 2.00e-02 2.50e+03 1.41e-01 2.50e+02 pdb=" C18 AZO N 401 " 0.026 2.00e-02 2.50e+03 pdb=" C19 AZO N 401 " -0.111 2.00e-02 2.50e+03 pdb=" C21 AZO N 401 " 0.237 2.00e-02 2.50e+03 pdb=" O5 AZO N 401 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 AZO C 401 " 0.021 2.00e-02 2.50e+03 1.41e-01 2.49e+02 pdb=" C18 AZO C 401 " 0.026 2.00e-02 2.50e+03 pdb=" C19 AZO C 401 " -0.111 2.00e-02 2.50e+03 pdb=" C21 AZO C 401 " 0.237 2.00e-02 2.50e+03 pdb=" O5 AZO C 401 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS P 124 " -0.054 2.00e-02 2.50e+03 1.08e-01 1.16e+02 pdb=" C HIS P 124 " 0.186 2.00e-02 2.50e+03 pdb=" O HIS P 124 " -0.076 2.00e-02 2.50e+03 pdb=" N GLU P 125 " -0.057 2.00e-02 2.50e+03 ... (remaining 5696 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 9690 2.83 - 3.35: 26257 3.35 - 3.87: 50884 3.87 - 4.38: 61997 4.38 - 4.90: 102715 Nonbonded interactions: 251543 Sorted by model distance: nonbonded pdb=" O ASN G 122 " pdb=" OG1 THR U 11 " model vdw 2.314 3.040 nonbonded pdb=" OG SER C 247 " pdb=" OG1 THR C 250 " model vdw 2.317 3.040 nonbonded pdb=" OG SER N 247 " pdb=" OG1 THR N 250 " model vdw 2.318 3.040 nonbonded pdb=" N GLY U 34 " pdb=" N GLY U 35 " model vdw 2.360 2.560 nonbonded pdb=" O3' CN3 N 403 " pdb=" OA CN3 N 403 " model vdw 2.381 2.432 ... (remaining 251538 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' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and (resid 1 through 401 or resid 404 through 405)) selection = (chain 'N' and (resid 1 through 401 or resid 404 through 405)) } ncs_group { reference = (chain 'D' and resid 62 through 309) selection = (chain 'O' and resid 62 through 309) } ncs_group { reference = chain 'E' selection = chain 'P' } 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 28.450 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 : 0.013 0.772 33203 Z= 0.554 Angle : 1.232 46.740 45057 Z= 0.618 Chirality : 0.055 0.372 4877 Planarity : 0.010 0.380 5699 Dihedral : 17.351 176.062 12202 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.82 % Favored : 96.08 % Rotamer: Outliers : 2.00 % Allowed : 3.40 % Favored : 94.60 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.39 (0.10), residues: 3952 helix: -3.88 (0.05), residues: 1965 sheet: -0.08 (0.28), residues: 274 loop : -1.97 (0.13), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 13 TYR 0.037 0.002 TYR V 26 PHE 0.060 0.003 PHE S 41 TRP 0.020 0.002 TRP V 48 HIS 0.012 0.002 HIS P 124 Details of bonding type rmsd covalent geometry : bond 0.00880 (33195) covalent geometry : angle 1.22883 (45053) SS BOND : bond 0.74182 ( 2) SS BOND : angle 10.12989 ( 4) hydrogen bonds : bond 0.33460 ( 1577) hydrogen bonds : angle 8.39514 ( 4461) Misc. bond : bond 0.54601 ( 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 563 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 495 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.6647 (mm-30) cc_final: 0.6382 (mm-30) REVERT: B 96 ASP cc_start: 0.7768 (m-30) cc_final: 0.7436 (m-30) REVERT: D 128 MET cc_start: 0.8637 (mtm) cc_final: 0.8262 (mtm) REVERT: D 145 LYS cc_start: 0.7543 (mtmt) cc_final: 0.7203 (mtpp) REVERT: E 51 LYS cc_start: 0.6008 (OUTLIER) cc_final: 0.5265 (mtpp) REVERT: E 76 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7823 (mt-10) REVERT: E 91 MET cc_start: 0.8398 (mmm) cc_final: 0.8090 (mmm) REVERT: E 169 GLU cc_start: 0.2779 (OUTLIER) cc_final: 0.2357 (mm-30) REVERT: F 82 ARG cc_start: 0.7944 (mtt180) cc_final: 0.7643 (mtt180) REVERT: H 16 MET cc_start: 0.8738 (tpp) cc_final: 0.8358 (tpp) REVERT: L 217 GLU cc_start: 0.6662 (mm-30) cc_final: 0.6427 (mm-30) REVERT: M 96 ASP cc_start: 0.7831 (m-30) cc_final: 0.7508 (m-30) REVERT: O 128 MET cc_start: 0.8623 (mtm) cc_final: 0.8251 (mtm) REVERT: O 145 LYS cc_start: 0.7505 (mtmt) cc_final: 0.7163 (mtpp) REVERT: P 65 LEU cc_start: 0.8272 (tp) cc_final: 0.7985 (tm) REVERT: P 73 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8341 (p) REVERT: P 76 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7605 (mt-10) REVERT: P 79 ILE cc_start: 0.8532 (mm) cc_final: 0.8312 (mt) REVERT: P 82 MET cc_start: 0.8838 (mtp) cc_final: 0.8621 (mtp) REVERT: P 93 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6920 (mptt) REVERT: P 110 LYS cc_start: 0.4897 (OUTLIER) cc_final: 0.4551 (ttpt) REVERT: P 130 ASN cc_start: 0.0585 (OUTLIER) cc_final: 0.0121 (t0) REVERT: P 146 ARG cc_start: 0.3529 (OUTLIER) cc_final: 0.1763 (ttt180) REVERT: P 159 CYS cc_start: 0.0186 (OUTLIER) cc_final: -0.0137 (m) REVERT: P 193 LYS cc_start: 0.2956 (OUTLIER) cc_final: 0.2080 (mmtm) REVERT: Q 141 ARG cc_start: 0.8040 (ptp-170) cc_final: 0.7840 (ptp-170) REVERT: S 16 MET cc_start: 0.8731 (tpp) cc_final: 0.8353 (tpp) REVERT: U 38 MET cc_start: 0.1272 (mtm) cc_final: 0.0258 (tpt) outliers start: 68 outliers final: 14 residues processed: 561 average time/residue: 0.7212 time to fit residues: 470.8870 Evaluate side-chains 432 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 409 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 141 GLN Chi-restraints excluded: chain E residue 146 ARG Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain P residue 73 SER Chi-restraints excluded: chain P residue 93 LYS Chi-restraints excluded: chain P residue 110 LYS Chi-restraints excluded: chain P residue 130 ASN Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 141 GLN Chi-restraints excluded: chain P residue 146 ARG Chi-restraints excluded: chain P residue 158 ILE Chi-restraints excluded: chain P residue 159 CYS Chi-restraints excluded: chain P residue 192 ARG Chi-restraints excluded: chain P residue 193 LYS Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain U residue 21 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 102 GLN A 149 GLN A 271 ASN A 307 GLN A 350 GLN C 22 GLN C 73 HIS C 183 HIS C 332 ASN B 52 ASN B 55 ASN B 136 GLN B 145 GLN B 328 GLN B 339 ASN N 22 GLN N 73 HIS N 183 HIS N 332 ASN G 34 ASN G 53 ASN G 57 GLN G 79 HIS G 86 HIS H 38 GLN L 61 ASN L 102 GLN L 149 GLN L 271 ASN L 307 GLN M 52 ASN M 55 ASN M 136 GLN M 328 GLN M 339 ASN R 34 ASN R 53 ASN R 79 HIS S 38 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.166322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.122120 restraints weight = 27449.529| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.44 r_work: 0.3003 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.206 33203 Z= 0.194 Angle : 0.757 13.746 45057 Z= 0.391 Chirality : 0.048 0.216 4877 Planarity : 0.006 0.131 5699 Dihedral : 16.064 151.426 4878 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.52 % Favored : 96.38 % Rotamer: Outliers : 2.00 % Allowed : 7.81 % Favored : 90.20 % 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: -1.19 (0.12), residues: 3952 helix: -0.36 (0.11), residues: 1970 sheet: 0.35 (0.27), residues: 294 loop : -1.43 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 314 TYR 0.020 0.002 TYR O 94 PHE 0.027 0.002 PHE G 45 TRP 0.013 0.002 TRP U 33 HIS 0.011 0.001 HIS N 197 Details of bonding type rmsd covalent geometry : bond 0.00387 (33195) covalent geometry : angle 0.75685 (45053) SS BOND : bond 0.00727 ( 2) SS BOND : angle 2.37690 ( 4) hydrogen bonds : bond 0.09269 ( 1577) hydrogen bonds : angle 4.74186 ( 4461) Misc. bond : bond 0.13558 ( 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 486 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 418 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: A 241 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7375 (tmtp) REVERT: A 455 MET cc_start: 0.6786 (ttt) cc_final: 0.6354 (mtp) REVERT: B 54 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.8048 (t80) REVERT: B 96 ASP cc_start: 0.8311 (m-30) cc_final: 0.7989 (m-30) REVERT: B 183 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8294 (mp0) REVERT: D 128 MET cc_start: 0.8919 (mtm) cc_final: 0.8622 (mtm) REVERT: D 145 LYS cc_start: 0.7649 (mtmt) cc_final: 0.7266 (mtpp) REVERT: E 91 MET cc_start: 0.8605 (mmm) cc_final: 0.8392 (mmm) REVERT: E 108 VAL cc_start: 0.3086 (OUTLIER) cc_final: 0.2810 (t) REVERT: E 155 MET cc_start: 0.2816 (ppp) cc_final: 0.2390 (ppp) REVERT: H 16 MET cc_start: 0.8644 (tpp) cc_final: 0.8430 (tpp) REVERT: H 78 GLU cc_start: 0.7873 (tt0) cc_final: 0.7607 (mt-10) REVERT: I 6 LEU cc_start: 0.0876 (OUTLIER) cc_final: -0.0198 (pp) REVERT: I 41 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8327 (mt-10) REVERT: L 194 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: L 241 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7373 (tmtp) REVERT: M 54 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8047 (t80) REVERT: M 96 ASP cc_start: 0.8295 (m-30) cc_final: 0.7969 (m-30) REVERT: M 183 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: O 128 MET cc_start: 0.8922 (mtm) cc_final: 0.8621 (mtm) REVERT: O 145 LYS cc_start: 0.7654 (mtmt) cc_final: 0.7283 (mtpp) REVERT: P 108 VAL cc_start: 0.2615 (OUTLIER) cc_final: 0.2407 (t) REVERT: P 130 ASN cc_start: 0.0936 (OUTLIER) cc_final: 0.0391 (t0) REVERT: P 158 ILE cc_start: 0.3123 (OUTLIER) cc_final: 0.2823 (pt) REVERT: Q 141 ARG cc_start: 0.8171 (ptp-170) cc_final: 0.7952 (ptp-170) REVERT: S 16 MET cc_start: 0.8636 (tpp) cc_final: 0.8422 (tpp) REVERT: S 78 GLU cc_start: 0.7819 (tt0) cc_final: 0.7560 (mt-10) REVERT: T 41 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8330 (mt-10) REVERT: U 38 MET cc_start: 0.1193 (mtm) cc_final: 0.0299 (tpt) outliers start: 68 outliers final: 24 residues processed: 462 average time/residue: 0.7516 time to fit residues: 402.1253 Evaluate side-chains 451 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 412 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain N residue 221 MET Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 215 LYS Chi-restraints excluded: chain L residue 241 LYS Chi-restraints excluded: chain L residue 408 LYS Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 183 GLU Chi-restraints excluded: chain P residue 73 SER Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 130 ASN Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 146 ARG Chi-restraints excluded: chain P residue 158 ILE Chi-restraints excluded: chain P residue 192 ARG Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 41 GLU Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 31 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 387 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 304 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 chunk 382 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 149 GLN A 198 ASN A 271 ASN B 36 HIS B 136 GLN E 199 ASN G 34 ASN G 86 HIS H 43 ASN L 122 GLN L 149 GLN L 198 ASN L 271 ASN M 136 GLN Q 109 GLN R 34 ASN U 52 GLN V 29 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.163592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.121977 restraints weight = 27268.775| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.16 r_work: 0.2978 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.165 33203 Z= 0.342 Angle : 0.970 13.824 45057 Z= 0.503 Chirality : 0.061 0.337 4877 Planarity : 0.008 0.126 5699 Dihedral : 16.135 165.942 4838 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Rotamer: Outliers : 2.91 % Allowed : 7.78 % Favored : 89.32 % 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: -0.58 (0.13), residues: 3952 helix: 0.25 (0.11), residues: 1985 sheet: 0.95 (0.29), residues: 258 loop : -1.33 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG C 314 TYR 0.028 0.004 TYR D 94 PHE 0.037 0.004 PHE G 45 TRP 0.022 0.003 TRP C 273 HIS 0.012 0.002 HIS D 263 Details of bonding type rmsd covalent geometry : bond 0.00763 (33195) covalent geometry : angle 0.96984 (45053) SS BOND : bond 0.01062 ( 2) SS BOND : angle 2.33391 ( 4) hydrogen bonds : bond 0.11790 ( 1577) hydrogen bonds : angle 4.95129 ( 4461) Misc. bond : bond 0.11607 ( 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 510 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 411 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: A 241 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7714 (tmtp) REVERT: A 455 MET cc_start: 0.6714 (ttt) cc_final: 0.6463 (mtp) REVERT: C 283 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8402 (mtp180) REVERT: B 96 ASP cc_start: 0.8323 (m-30) cc_final: 0.8023 (m-30) REVERT: B 183 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8547 (mp0) REVERT: B 338 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5776 (mt) REVERT: D 145 LYS cc_start: 0.7731 (mtmt) cc_final: 0.7256 (mtpm) REVERT: E 79 ILE cc_start: 0.8640 (mm) cc_final: 0.8385 (OUTLIER) REVERT: E 108 VAL cc_start: 0.3415 (OUTLIER) cc_final: 0.3163 (t) REVERT: G 118 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8366 (t70) REVERT: H 16 MET cc_start: 0.8777 (tpp) cc_final: 0.8560 (tpp) REVERT: I 6 LEU cc_start: 0.0983 (OUTLIER) cc_final: -0.0198 (pp) REVERT: I 41 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: L 217 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: L 241 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7742 (tmtp) REVERT: M 96 ASP cc_start: 0.8292 (m-30) cc_final: 0.7985 (m-30) REVERT: M 183 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8563 (mp0) REVERT: M 338 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.5780 (mt) REVERT: O 145 LYS cc_start: 0.7764 (mtmt) cc_final: 0.7296 (mtpm) REVERT: P 134 MET cc_start: 0.3808 (tmm) cc_final: 0.3182 (tpt) REVERT: P 146 ARG cc_start: 0.3775 (OUTLIER) cc_final: 0.2811 (mtp85) REVERT: S 16 MET cc_start: 0.8756 (tpp) cc_final: 0.8543 (tpp) REVERT: S 43 ASN cc_start: 0.1299 (OUTLIER) cc_final: 0.0873 (p0) REVERT: T 41 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8328 (mt-10) REVERT: U 38 MET cc_start: 0.1445 (mtm) cc_final: 0.0367 (tpt) outliers start: 99 outliers final: 44 residues processed: 472 average time/residue: 0.7438 time to fit residues: 407.5957 Evaluate side-chains 476 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 417 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 221 MET Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain L residue 215 LYS Chi-restraints excluded: chain L residue 217 GLU Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 241 LYS Chi-restraints excluded: chain L residue 373 GLN Chi-restraints excluded: chain L residue 399 SER Chi-restraints excluded: chain L residue 408 LYS Chi-restraints excluded: chain L residue 436 THR Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 183 GLU Chi-restraints excluded: chain M residue 222 LYS Chi-restraints excluded: chain M residue 338 LEU Chi-restraints excluded: chain O residue 213 ASN Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 146 ARG Chi-restraints excluded: chain P residue 192 ARG Chi-restraints excluded: chain S residue 43 ASN Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 41 GLU Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 31 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 253 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 375 optimal weight: 4.9990 chunk 296 optimal weight: 6.9990 chunk 219 optimal weight: 0.0020 chunk 122 optimal weight: 0.9980 chunk 283 optimal weight: 4.9990 chunk 319 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 271 ASN C 73 HIS B 136 GLN N 73 HIS E 124 HIS G 34 ASN G 86 HIS L 67 ASN L 198 ASN L 271 ASN M 136 GLN R 34 ASN R 57 GLN R 86 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.167291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.125950 restraints weight = 27403.905| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.14 r_work: 0.3042 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.178 33203 Z= 0.180 Angle : 0.705 11.427 45057 Z= 0.365 Chirality : 0.047 0.284 4877 Planarity : 0.005 0.103 5699 Dihedral : 15.068 157.579 4831 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.69 % Favored : 96.26 % Rotamer: Outliers : 2.11 % Allowed : 9.13 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.16 (0.13), residues: 3952 helix: 0.94 (0.12), residues: 1983 sheet: 1.03 (0.28), residues: 296 loop : -1.06 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 166 TYR 0.021 0.002 TYR M 101 PHE 0.024 0.002 PHE G 45 TRP 0.013 0.002 TRP D 257 HIS 0.010 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00361 (33195) covalent geometry : angle 0.70445 (45053) SS BOND : bond 0.00546 ( 2) SS BOND : angle 1.60924 ( 4) hydrogen bonds : bond 0.08107 ( 1577) hydrogen bonds : angle 4.52760 ( 4461) Misc. bond : bond 0.11613 ( 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 492 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 420 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: A 217 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6660 (mp0) REVERT: C 283 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8508 (mtp180) REVERT: B 54 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8116 (t80) REVERT: B 96 ASP cc_start: 0.8427 (m-30) cc_final: 0.8177 (m-30) REVERT: B 183 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8396 (mp0) REVERT: B 338 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5904 (mt) REVERT: D 145 LYS cc_start: 0.7690 (mtmt) cc_final: 0.7223 (mtpm) REVERT: E 159 CYS cc_start: 0.0348 (OUTLIER) cc_final: -0.0125 (m) REVERT: G 118 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8224 (t70) REVERT: I 6 LEU cc_start: 0.0727 (OUTLIER) cc_final: -0.0125 (pp) REVERT: I 41 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8293 (mt-10) REVERT: L 194 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: L 217 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: M 54 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8116 (t80) REVERT: M 96 ASP cc_start: 0.8364 (m-30) cc_final: 0.8099 (m-30) REVERT: M 183 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8410 (mp0) REVERT: M 338 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5905 (mt) REVERT: O 145 LYS cc_start: 0.7723 (mtmt) cc_final: 0.7256 (mtpm) REVERT: P 134 MET cc_start: 0.3546 (tmm) cc_final: 0.2997 (tpt) REVERT: Q 90 GLU cc_start: 0.7404 (tt0) cc_final: 0.7160 (tt0) REVERT: S 43 ASN cc_start: 0.1521 (OUTLIER) cc_final: 0.1113 (p0) REVERT: T 41 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8330 (mt-10) REVERT: U 38 MET cc_start: 0.1161 (mtm) cc_final: 0.0032 (tpt) REVERT: U 43 VAL cc_start: 0.0782 (OUTLIER) cc_final: 0.0533 (p) outliers start: 72 outliers final: 29 residues processed: 461 average time/residue: 0.7505 time to fit residues: 401.3312 Evaluate side-chains 445 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 398 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 221 MET Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 215 LYS Chi-restraints excluded: chain L residue 217 GLU Chi-restraints excluded: chain L residue 373 GLN Chi-restraints excluded: chain L residue 408 LYS Chi-restraints excluded: chain L residue 436 THR Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 183 GLU Chi-restraints excluded: chain M residue 222 LYS Chi-restraints excluded: chain M residue 338 LEU Chi-restraints excluded: chain O residue 213 ASN Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain P residue 192 ARG Chi-restraints excluded: chain S residue 43 ASN Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 41 GLU Chi-restraints excluded: chain U residue 31 MET Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain V residue 59 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 22 optimal weight: 0.9980 chunk 188 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 292 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 chunk 256 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 267 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 122 GLN A 149 GLN A 198 ASN A 271 ASN C 73 HIS B 136 GLN N 73 HIS G 34 ASN G 86 HIS H 93 ASN L 122 GLN L 149 GLN L 198 ASN L 271 ASN M 136 GLN M 145 GLN R 34 ASN R 86 HIS S 93 ASN V 14 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.173051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.134508 restraints weight = 27951.558| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.19 r_work: 0.3137 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.172 33203 Z= 0.121 Angle : 0.576 11.950 45057 Z= 0.294 Chirality : 0.042 0.225 4877 Planarity : 0.004 0.099 5699 Dihedral : 13.642 166.433 4823 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.34 % Favored : 96.61 % Rotamer: Outliers : 1.79 % Allowed : 10.86 % Favored : 87.35 % 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: 0.77 (0.14), residues: 3952 helix: 1.46 (0.12), residues: 2002 sheet: 1.11 (0.27), residues: 324 loop : -0.82 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 166 TYR 0.013 0.001 TYR D 94 PHE 0.012 0.001 PHE A 315 TRP 0.013 0.001 TRP O 257 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00242 (33195) covalent geometry : angle 0.57584 (45053) SS BOND : bond 0.00333 ( 2) SS BOND : angle 1.11085 ( 4) hydrogen bonds : bond 0.05340 ( 1577) hydrogen bonds : angle 4.13130 ( 4461) Misc. bond : bond 0.11146 ( 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 475 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 414 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7213 (mt-10) REVERT: A 239 LYS cc_start: 0.7313 (mmpt) cc_final: 0.6603 (ttmm) REVERT: C 31 ASN cc_start: 0.9083 (m-40) cc_final: 0.8865 (m110) REVERT: C 229 ASP cc_start: 0.7922 (m-30) cc_final: 0.7710 (m-30) REVERT: B 54 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8286 (t80) REVERT: B 96 ASP cc_start: 0.8370 (m-30) cc_final: 0.8114 (m-30) REVERT: B 183 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: D 145 LYS cc_start: 0.7653 (mtmt) cc_final: 0.7309 (mtpp) REVERT: N 219 ILE cc_start: 0.8508 (pt) cc_final: 0.8283 (mp) REVERT: E 134 MET cc_start: 0.3457 (tmm) cc_final: 0.3167 (tpp) REVERT: E 198 LEU cc_start: 0.3721 (OUTLIER) cc_final: 0.3450 (tp) REVERT: H 78 GLU cc_start: 0.7815 (tt0) cc_final: 0.7534 (tp30) REVERT: I 41 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8201 (mt-10) REVERT: L 186 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7221 (mt-10) REVERT: L 239 LYS cc_start: 0.7305 (mmpt) cc_final: 0.7086 (mmmm) REVERT: M 54 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8286 (t80) REVERT: M 96 ASP cc_start: 0.8340 (m-30) cc_final: 0.8084 (m-30) REVERT: M 183 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8161 (mp0) REVERT: O 145 LYS cc_start: 0.7662 (mtmt) cc_final: 0.7324 (mtpp) REVERT: P 134 MET cc_start: 0.3359 (tmm) cc_final: 0.2817 (tpt) REVERT: S 78 GLU cc_start: 0.7840 (tt0) cc_final: 0.7547 (tp30) REVERT: T 41 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8282 (mt-10) REVERT: U 38 MET cc_start: 0.0603 (mtm) cc_final: -0.0224 (tpt) REVERT: V 14 HIS cc_start: 0.2238 (OUTLIER) cc_final: 0.1991 (m90) outliers start: 61 outliers final: 17 residues processed: 454 average time/residue: 0.7352 time to fit residues: 388.0079 Evaluate side-chains 417 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 392 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 221 MET Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain L residue 408 LYS Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 183 GLU Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain P residue 192 ARG Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 41 GLU Chi-restraints excluded: chain V residue 14 HIS Chi-restraints excluded: chain V residue 59 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 172 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 364 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 chunk 225 optimal weight: 8.9990 chunk 349 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS A 122 GLN A 198 ASN A 271 ASN A 382 ASN B 136 GLN B 325 ASN G 34 ASN G 57 GLN L 122 GLN L 198 ASN L 271 ASN L 382 ASN M 136 GLN M 325 ASN R 34 ASN R 57 GLN S 43 ASN V 14 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.165146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123135 restraints weight = 27297.291| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.18 r_work: 0.3013 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.170 33203 Z= 0.253 Angle : 0.814 12.115 45057 Z= 0.421 Chirality : 0.053 0.210 4877 Planarity : 0.006 0.099 5699 Dihedral : 14.453 161.340 4822 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.10 % Rotamer: Outliers : 2.05 % Allowed : 11.27 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.03 (0.12), residues: 1992 sheet: 0.82 (0.29), residues: 300 loop : -1.02 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 166 TYR 0.025 0.003 TYR D 94 PHE 0.031 0.003 PHE R 45 TRP 0.016 0.002 TRP N 273 HIS 0.013 0.002 HIS O 263 Details of bonding type rmsd covalent geometry : bond 0.00542 (33195) covalent geometry : angle 0.81437 (45053) SS BOND : bond 0.00764 ( 2) SS BOND : angle 1.53761 ( 4) hydrogen bonds : bond 0.09961 ( 1577) hydrogen bonds : angle 4.64435 ( 4461) Misc. bond : bond 0.11864 ( 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 478 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 408 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: C 79 ARG cc_start: 0.9425 (OUTLIER) cc_final: 0.8622 (tmt90) REVERT: C 163 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.8131 (t) REVERT: B 96 ASP cc_start: 0.8404 (m-30) cc_final: 0.8115 (m-30) REVERT: B 183 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8506 (mp0) REVERT: B 368 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6644 (pp) REVERT: D 145 LYS cc_start: 0.7714 (mtmt) cc_final: 0.7233 (mtpm) REVERT: N 79 ARG cc_start: 0.9418 (OUTLIER) cc_final: 0.8608 (tmt90) REVERT: N 163 SER cc_start: 0.8344 (OUTLIER) cc_final: 0.8102 (t) REVERT: E 134 MET cc_start: 0.3807 (tmm) cc_final: 0.3424 (tpp) REVERT: E 198 LEU cc_start: 0.3681 (OUTLIER) cc_final: 0.3352 (tp) REVERT: F 103 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: I 6 LEU cc_start: 0.0724 (OUTLIER) cc_final: -0.0026 (pp) REVERT: I 41 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8485 (mt-10) REVERT: L 194 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8160 (mt-10) REVERT: M 96 ASP cc_start: 0.8392 (m-30) cc_final: 0.8100 (m-30) REVERT: M 183 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8521 (mp0) REVERT: M 368 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6639 (pp) REVERT: O 145 LYS cc_start: 0.7728 (mtmt) cc_final: 0.7266 (mtpm) REVERT: P 44 LYS cc_start: 0.6897 (mtmt) cc_final: 0.6693 (mtpt) REVERT: P 134 MET cc_start: 0.3762 (tmm) cc_final: 0.3235 (tpt) REVERT: T 41 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8450 (mt-10) REVERT: U 38 MET cc_start: 0.0761 (mtm) cc_final: -0.0130 (tpt) outliers start: 70 outliers final: 35 residues processed: 447 average time/residue: 0.7793 time to fit residues: 402.7472 Evaluate side-chains 449 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 399 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 79 ARG Chi-restraints excluded: chain N residue 163 SER Chi-restraints excluded: chain N residue 221 MET Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 373 GLN Chi-restraints excluded: chain L residue 408 LYS Chi-restraints excluded: chain L residue 436 THR Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 183 GLU Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 222 LYS Chi-restraints excluded: chain M residue 368 LEU Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain P residue 192 ARG Chi-restraints excluded: chain T residue 10 PHE Chi-restraints excluded: chain T residue 41 GLU Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 31 MET Chi-restraints excluded: chain V residue 59 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 177 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 321 optimal weight: 0.0020 chunk 229 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 324 optimal weight: 2.9990 chunk 370 optimal weight: 6.9990 chunk 295 optimal weight: 7.9990 chunk 386 optimal weight: 0.0170 overall best weight: 3.0032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS A 198 ASN A 271 ASN B 136 GLN G 34 ASN G 57 GLN L 42 HIS L 198 ASN L 271 ASN M 136 GLN R 34 ASN R 57 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.166785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.117685 restraints weight = 27504.172| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.28 r_work: 0.3008 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 33203 Z= 0.189 Angle : 0.710 10.841 45057 Z= 0.367 Chirality : 0.048 0.204 4877 Planarity : 0.005 0.099 5699 Dihedral : 14.046 152.353 4822 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.69 % Favored : 96.26 % Rotamer: Outliers : 1.94 % Allowed : 11.83 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.13), residues: 3952 helix: 1.21 (0.12), residues: 1983 sheet: 0.91 (0.29), residues: 296 loop : -0.92 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 166 TYR 0.021 0.002 TYR M 101 PHE 0.026 0.002 PHE G 45 TRP 0.012 0.002 TRP D 257 HIS 0.010 0.002 HIS N 197 Details of bonding type rmsd covalent geometry : bond 0.00385 (33195) covalent geometry : angle 0.71007 (45053) SS BOND : bond 0.00583 ( 2) SS BOND : angle 1.37387 ( 4) hydrogen bonds : bond 0.08301 ( 1577) hydrogen bonds : angle 4.47888 ( 4461) Misc. bond : bond 0.11194 ( 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 458 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 392 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: C 79 ARG cc_start: 0.9419 (OUTLIER) cc_final: 0.8593 (tmt90) REVERT: B 54 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8105 (t80) REVERT: B 96 ASP cc_start: 0.8372 (m-30) cc_final: 0.8099 (m-30) REVERT: B 183 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8412 (mp0) REVERT: D 133 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8047 (mp0) REVERT: D 145 LYS cc_start: 0.7587 (mtmt) cc_final: 0.7055 (mtpm) REVERT: D 235 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7701 (tm-30) REVERT: N 79 ARG cc_start: 0.9414 (OUTLIER) cc_final: 0.8576 (tmt90) REVERT: E 44 LYS cc_start: 0.6786 (mtmt) cc_final: 0.6550 (mtpt) REVERT: E 134 MET cc_start: 0.3425 (tmm) cc_final: 0.3076 (tpp) REVERT: E 198 LEU cc_start: 0.3273 (OUTLIER) cc_final: 0.3065 (tp) REVERT: F 103 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6872 (mt-10) REVERT: G 118 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8156 (t70) REVERT: I 6 LEU cc_start: 0.0368 (OUTLIER) cc_final: -0.0260 (pp) REVERT: I 41 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: L 194 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: L 217 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: M 54 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.8104 (t80) REVERT: M 96 ASP cc_start: 0.8362 (m-30) cc_final: 0.8089 (m-30) REVERT: M 183 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: O 133 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8034 (mp0) REVERT: O 145 LYS cc_start: 0.7591 (mtmt) cc_final: 0.7066 (mtpm) REVERT: P 44 LYS cc_start: 0.6870 (mtmt) cc_final: 0.6605 (mtpt) REVERT: P 134 MET cc_start: 0.3258 (tmm) cc_final: 0.2789 (tpt) REVERT: T 41 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8259 (mt-10) REVERT: U 38 MET cc_start: 0.0682 (mtm) cc_final: -0.0037 (tpt) outliers start: 66 outliers final: 35 residues processed: 427 average time/residue: 0.7605 time to fit residues: 375.7927 Evaluate side-chains 439 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 389 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 79 ARG Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 221 MET Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 217 GLU Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 373 GLN Chi-restraints excluded: chain L residue 408 LYS Chi-restraints excluded: chain L residue 436 THR Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 183 GLU Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 222 LYS Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain T residue 10 PHE Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 41 GLU Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 31 MET Chi-restraints excluded: chain V residue 59 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 249 optimal weight: 20.0000 chunk 254 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 357 optimal weight: 0.5980 chunk 384 optimal weight: 10.0000 chunk 130 optimal weight: 0.0050 chunk 215 optimal weight: 7.9990 chunk 64 optimal weight: 0.0000 chunk 101 optimal weight: 0.0980 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS A 198 ASN A 271 ASN B 136 GLN G 34 ASN G 57 GLN L 122 GLN L 149 GLN L 198 ASN L 271 ASN M 136 GLN R 34 ASN R 57 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.172933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.132250 restraints weight = 27898.738| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.28 r_work: 0.3131 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.164 33203 Z= 0.119 Angle : 0.574 12.224 45057 Z= 0.292 Chirality : 0.042 0.206 4877 Planarity : 0.004 0.100 5699 Dihedral : 13.090 148.747 4818 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 1.38 % Allowed : 12.42 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.97 (0.14), residues: 3952 helix: 1.65 (0.12), residues: 1994 sheet: 0.94 (0.27), residues: 324 loop : -0.67 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 166 TYR 0.013 0.001 TYR D 94 PHE 0.013 0.001 PHE L 315 TRP 0.015 0.001 TRP D 257 HIS 0.007 0.001 HIS D 263 Details of bonding type rmsd covalent geometry : bond 0.00237 (33195) covalent geometry : angle 0.57385 (45053) SS BOND : bond 0.00316 ( 2) SS BOND : angle 1.05230 ( 4) hydrogen bonds : bond 0.05238 ( 1577) hydrogen bonds : angle 4.11875 ( 4461) Misc. bond : bond 0.11154 ( 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 436 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 389 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7350 (mt-10) REVERT: A 194 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7998 (mt-10) REVERT: A 239 LYS cc_start: 0.7407 (mmpt) cc_final: 0.7139 (mmmm) REVERT: C 237 MET cc_start: 0.9213 (mtt) cc_final: 0.8982 (mtm) REVERT: B 54 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8279 (t80) REVERT: B 96 ASP cc_start: 0.8357 (m-30) cc_final: 0.8145 (m-30) REVERT: B 183 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8210 (mp0) REVERT: D 133 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8195 (mp0) REVERT: D 145 LYS cc_start: 0.7609 (mtmt) cc_final: 0.7132 (mtpm) REVERT: D 265 GLU cc_start: 0.8302 (tt0) cc_final: 0.8048 (pt0) REVERT: E 44 LYS cc_start: 0.6711 (mtmt) cc_final: 0.6492 (mtpt) REVERT: E 134 MET cc_start: 0.3615 (tmm) cc_final: 0.3292 (tpp) REVERT: E 198 LEU cc_start: 0.3423 (OUTLIER) cc_final: 0.3150 (tp) REVERT: F 103 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6801 (pt0) REVERT: H 78 GLU cc_start: 0.7928 (tt0) cc_final: 0.7604 (tp30) REVERT: I 41 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8267 (mt-10) REVERT: L 186 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7358 (mt-10) REVERT: L 239 LYS cc_start: 0.7409 (mmpt) cc_final: 0.7146 (mmmm) REVERT: M 54 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8276 (t80) REVERT: M 183 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8230 (mp0) REVERT: O 133 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8184 (mp0) REVERT: O 145 LYS cc_start: 0.7664 (mtmt) cc_final: 0.7183 (mtpm) REVERT: O 265 GLU cc_start: 0.8277 (tt0) cc_final: 0.8013 (pt0) REVERT: P 44 LYS cc_start: 0.6819 (mtmt) cc_final: 0.6568 (mtpt) REVERT: P 134 MET cc_start: 0.3491 (tmm) cc_final: 0.3047 (tpt) REVERT: S 78 GLU cc_start: 0.7959 (tt0) cc_final: 0.7612 (tp30) REVERT: T 41 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8315 (mt-10) REVERT: U 38 MET cc_start: 0.0415 (mtm) cc_final: -0.0200 (tpt) outliers start: 47 outliers final: 15 residues processed: 419 average time/residue: 0.7646 time to fit residues: 370.7274 Evaluate side-chains 409 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 385 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain N residue 221 MET Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 183 GLU Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain T residue 10 PHE Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 41 GLU Chi-restraints excluded: chain V residue 59 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 74 optimal weight: 6.9990 chunk 224 optimal weight: 8.9990 chunk 130 optimal weight: 0.0010 chunk 88 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 283 optimal weight: 7.9990 chunk 284 optimal weight: 1.9990 chunk 267 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 142 optimal weight: 0.7980 overall best weight: 3.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 149 GLN A 271 ASN B 136 GLN G 34 ASN L 122 GLN L 271 ASN M 136 GLN R 34 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.166409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.123877 restraints weight = 27336.403| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.29 r_work: 0.3012 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.175 33203 Z= 0.206 Angle : 0.732 10.802 45057 Z= 0.377 Chirality : 0.049 0.276 4877 Planarity : 0.005 0.101 5699 Dihedral : 13.618 154.566 4818 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.28 % Rotamer: Outliers : 1.29 % Allowed : 12.33 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.13), residues: 3952 helix: 1.34 (0.12), residues: 1987 sheet: 0.98 (0.29), residues: 296 loop : -0.82 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 166 TYR 0.022 0.003 TYR O 94 PHE 0.027 0.002 PHE G 45 TRP 0.014 0.002 TRP C 164 HIS 0.012 0.002 HIS O 263 Details of bonding type rmsd covalent geometry : bond 0.00429 (33195) covalent geometry : angle 0.73220 (45053) SS BOND : bond 0.00649 ( 2) SS BOND : angle 1.35792 ( 4) hydrogen bonds : bond 0.08721 ( 1577) hydrogen bonds : angle 4.47373 ( 4461) Misc. bond : bond 0.11656 ( 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 434 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 390 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 HIS cc_start: 0.8633 (t-90) cc_final: 0.8417 (t70) REVERT: A 186 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7406 (mt-10) REVERT: A 194 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: C 79 ARG cc_start: 0.9414 (OUTLIER) cc_final: 0.8598 (tmt90) REVERT: C 163 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8197 (t) REVERT: B 54 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8170 (t80) REVERT: B 96 ASP cc_start: 0.8406 (m-30) cc_final: 0.8137 (m-30) REVERT: B 183 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: D 133 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8246 (mp0) REVERT: D 145 LYS cc_start: 0.7687 (mtmt) cc_final: 0.7182 (mtpm) REVERT: N 219 ILE cc_start: 0.8832 (mp) cc_final: 0.8566 (mm) REVERT: E 44 LYS cc_start: 0.6806 (mtmt) cc_final: 0.6570 (mtpt) REVERT: E 134 MET cc_start: 0.3647 (tmm) cc_final: 0.3275 (tpp) REVERT: E 198 LEU cc_start: 0.3445 (OUTLIER) cc_final: 0.3178 (tt) REVERT: I 6 LEU cc_start: 0.0218 (OUTLIER) cc_final: -0.0252 (pp) REVERT: I 41 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8341 (mt-10) REVERT: L 42 HIS cc_start: 0.8629 (t-90) cc_final: 0.8368 (t70) REVERT: L 186 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7387 (mt-10) REVERT: L 194 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: M 54 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.8167 (t80) REVERT: M 96 ASP cc_start: 0.8388 (m-30) cc_final: 0.8115 (m-30) REVERT: M 183 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8430 (mp0) REVERT: O 133 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8247 (mp0) REVERT: O 145 LYS cc_start: 0.7694 (mtmt) cc_final: 0.7195 (mtpm) REVERT: P 44 LYS cc_start: 0.6896 (mtmt) cc_final: 0.6624 (mtpt) REVERT: P 134 MET cc_start: 0.3416 (tmm) cc_final: 0.2957 (tpt) REVERT: T 41 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8376 (mt-10) REVERT: U 38 MET cc_start: 0.0518 (mtm) cc_final: -0.0111 (tpt) outliers start: 44 outliers final: 20 residues processed: 417 average time/residue: 0.7574 time to fit residues: 366.7141 Evaluate side-chains 420 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 388 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 163 SER Chi-restraints excluded: chain N residue 221 MET Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 183 GLU Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain T residue 10 PHE Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 41 GLU Chi-restraints excluded: chain V residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 135 optimal weight: 6.9990 chunk 367 optimal weight: 2.9990 chunk 311 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 275 optimal weight: 4.9990 chunk 95 optimal weight: 0.0060 chunk 223 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 198 ASN A 271 ASN B 136 GLN G 34 ASN L 122 GLN L 198 ASN L 271 ASN M 136 GLN R 34 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.170030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.128160 restraints weight = 27873.166| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.34 r_work: 0.3063 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.170 33203 Z= 0.138 Angle : 0.617 11.674 45057 Z= 0.315 Chirality : 0.044 0.239 4877 Planarity : 0.005 0.102 5699 Dihedral : 13.116 151.291 4818 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.66 % Rotamer: Outliers : 1.06 % Allowed : 12.50 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.89 (0.14), residues: 3952 helix: 1.58 (0.12), residues: 1994 sheet: 0.94 (0.27), residues: 328 loop : -0.72 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 166 TYR 0.016 0.002 TYR B 101 PHE 0.018 0.001 PHE R 45 TRP 0.018 0.001 TRP C 164 HIS 0.008 0.001 HIS N 197 Details of bonding type rmsd covalent geometry : bond 0.00271 (33195) covalent geometry : angle 0.61679 (45053) SS BOND : bond 0.00400 ( 2) SS BOND : angle 1.16524 ( 4) hydrogen bonds : bond 0.06403 ( 1577) hydrogen bonds : angle 4.24067 ( 4461) Misc. bond : bond 0.11387 ( 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 421 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 385 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 HIS cc_start: 0.8562 (t-90) cc_final: 0.8333 (t70) REVERT: A 186 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7343 (mt-10) REVERT: A 194 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: C 163 SER cc_start: 0.8416 (OUTLIER) cc_final: 0.8165 (t) REVERT: B 54 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.8238 (t80) REVERT: B 96 ASP cc_start: 0.8375 (m-30) cc_final: 0.8152 (m-30) REVERT: B 183 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: D 133 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8240 (mp0) REVERT: D 145 LYS cc_start: 0.7674 (mtmt) cc_final: 0.7174 (mtpm) REVERT: N 163 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.8146 (t) REVERT: N 219 ILE cc_start: 0.8796 (mp) cc_final: 0.8571 (mm) REVERT: E 44 LYS cc_start: 0.6750 (mtmt) cc_final: 0.6528 (mtpt) REVERT: E 134 MET cc_start: 0.3650 (tmm) cc_final: 0.3234 (tpp) REVERT: E 198 LEU cc_start: 0.3306 (OUTLIER) cc_final: 0.3036 (tp) REVERT: F 103 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6561 (pt0) REVERT: I 6 LEU cc_start: 0.0177 (OUTLIER) cc_final: -0.0303 (pp) REVERT: I 41 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8318 (mt-10) REVERT: L 42 HIS cc_start: 0.8573 (t-90) cc_final: 0.8341 (t70) REVERT: L 186 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7337 (mt-10) REVERT: L 194 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8066 (mt-10) REVERT: M 54 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8236 (t80) REVERT: M 183 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8301 (mp0) REVERT: O 133 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8220 (mp0) REVERT: O 145 LYS cc_start: 0.7684 (mtmt) cc_final: 0.7194 (mtpm) REVERT: O 265 GLU cc_start: 0.8222 (tt0) cc_final: 0.8018 (pt0) REVERT: P 44 LYS cc_start: 0.6842 (mtmt) cc_final: 0.6580 (mtpt) REVERT: P 134 MET cc_start: 0.3341 (tmm) cc_final: 0.2905 (tpt) REVERT: T 41 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8374 (mt-10) REVERT: U 38 MET cc_start: 0.0428 (mtm) cc_final: -0.0183 (tpt) outliers start: 36 outliers final: 22 residues processed: 407 average time/residue: 0.7481 time to fit residues: 353.9596 Evaluate side-chains 414 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 380 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 163 SER Chi-restraints excluded: chain N residue 221 MET Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 183 GLU Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain P residue 158 ILE Chi-restraints excluded: chain T residue 10 PHE Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 41 GLU Chi-restraints excluded: chain V residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 170 optimal weight: 2.9990 chunk 220 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 chunk 341 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 365 optimal weight: 0.0570 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 271 ASN B 136 GLN G 34 ASN L 198 ASN L 271 ASN M 136 GLN R 34 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.169761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.127454 restraints weight = 27691.931| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.23 r_work: 0.3098 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.175 33203 Z= 0.144 Angle : 0.625 11.181 45057 Z= 0.319 Chirality : 0.044 0.236 4877 Planarity : 0.005 0.107 5699 Dihedral : 12.992 151.509 4818 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.39 % Favored : 96.56 % Rotamer: Outliers : 1.14 % Allowed : 12.50 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.95 (0.14), residues: 3952 helix: 1.64 (0.12), residues: 1990 sheet: 1.12 (0.27), residues: 332 loop : -0.76 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 166 TYR 0.016 0.002 TYR D 94 PHE 0.019 0.002 PHE R 45 TRP 0.020 0.001 TRP C 164 HIS 0.011 0.001 HIS E 120 Details of bonding type rmsd covalent geometry : bond 0.00283 (33195) covalent geometry : angle 0.62510 (45053) SS BOND : bond 0.00422 ( 2) SS BOND : angle 1.15801 ( 4) hydrogen bonds : bond 0.06628 ( 1577) hydrogen bonds : angle 4.23447 ( 4461) Misc. bond : bond 0.11250 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13427.33 seconds wall clock time: 228 minutes 12.61 seconds (13692.61 seconds total)