Starting phenix.real_space_refine on Sat Feb 7 03:35:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vkp_65138/02_2026/9vkp_65138.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vkp_65138/02_2026/9vkp_65138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vkp_65138/02_2026/9vkp_65138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vkp_65138/02_2026/9vkp_65138.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vkp_65138/02_2026/9vkp_65138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vkp_65138/02_2026/9vkp_65138.map" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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 P 16 5.49 5 Mg 5 5.21 5 S 72 5.16 5 C 18404 2.51 5 N 5143 2.21 5 O 5827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29467 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 3959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3959 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 500} Chain: "C" Number of atoms: 3938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3938 Classifications: {'peptide': 520} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 496} Chain: "D" Number of atoms: 3566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3566 Classifications: {'peptide': 465} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 439} Chain: "E" Number of atoms: 3561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3561 Classifications: {'peptide': 465} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 439} Chain: "F" Number of atoms: 3566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3566 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 440} Chain: "G" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2315 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 11, 'TRANS': 294} Chain: "H" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "b" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 588 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "d" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2850 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 10, 'TRANS': 371} Chain: "A" Number of atoms: 4021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4021 Classifications: {'peptide': 531} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Chain breaks: 1 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.71, per 1000 atoms: 0.23 Number of scatterers: 29467 At special positions: 0 Unit cell: (127.68, 155.04, 178.6, 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) S 72 16.00 P 16 15.00 Mg 5 11.99 O 5827 8.00 N 5143 7.00 C 18404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.5 seconds 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7068 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 26 sheets defined 51.5% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'B' and resid 7 through 22 removed outlier: 3.927A pdb=" N PHE B 22 " --> pdb=" O TYR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 removed outlier: 4.074A pdb=" N PHE B 106 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 107 " --> pdb=" O ASP B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 107' Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.709A pdb=" N GLN B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.536A pdb=" N VAL B 181 " --> pdb=" O GLY B 177 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS B 182 " --> pdb=" O LYS B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 4.351A pdb=" N GLY B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 225 Processing helix chain 'B' and resid 226 through 230 removed outlier: 6.143A pdb=" N LEU B 229 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU B 230 " --> pdb=" O GLY B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 230' Processing helix chain 'B' and resid 242 through 262 Proline residue: B 250 - end of helix removed outlier: 3.671A pdb=" N GLY B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.924A pdb=" N GLN B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 300 through 310 removed outlier: 3.593A pdb=" N HIS B 305 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 363 Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.929A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 381 " --> pdb=" O GLY B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 392 through 403 Processing helix chain 'B' and resid 414 through 431 removed outlier: 3.604A pdb=" N GLU B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 463 through 478 Processing helix chain 'B' and resid 479 through 490 removed outlier: 3.927A pdb=" N LEU B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 509 removed outlier: 3.899A pdb=" N LYS B 509 " --> pdb=" O ASN B 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 22 Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.865A pdb=" N PHE C 106 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 removed outlier: 3.513A pdb=" N SER C 158 " --> pdb=" O LYS C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 188 removed outlier: 3.500A pdb=" N VAL C 181 " --> pdb=" O GLY C 177 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 4.129A pdb=" N GLY C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 removed outlier: 3.514A pdb=" N ALA C 226 " --> pdb=" O THR C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 230 removed outlier: 4.083A pdb=" N GLU C 230 " --> pdb=" O GLY C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 242 through 262 removed outlier: 3.658A pdb=" N LYS C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) Proline residue: C 250 - end of helix removed outlier: 3.514A pdb=" N GLY C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.942A pdb=" N GLN C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 278 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 300 through 310 removed outlier: 3.792A pdb=" N HIS C 305 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 339 through 347 removed outlier: 3.644A pdb=" N THR C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 363 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 392 through 402 Processing helix chain 'C' and resid 414 through 431 removed outlier: 3.611A pdb=" N ARG C 426 " --> pdb=" O GLU C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 removed outlier: 3.808A pdb=" N GLY C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 479 Processing helix chain 'C' and resid 479 through 490 removed outlier: 3.798A pdb=" N LEU C 483 " --> pdb=" O HIS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 509 removed outlier: 3.927A pdb=" N LYS C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 47 removed outlier: 3.703A pdb=" N ALA D 47 " --> pdb=" O GLU D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 96 removed outlier: 3.964A pdb=" N VAL D 95 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS D 96 " --> pdb=" O ASP D 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 92 through 96' Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 142 through 148 Processing helix chain 'D' and resid 167 through 179 Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 230 through 245 Processing helix chain 'D' and resid 257 through 272 removed outlier: 3.895A pdb=" N THR D 261 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR D 269 " --> pdb=" O SER D 265 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 280 Processing helix chain 'D' and resid 283 through 293 Processing helix chain 'D' and resid 312 through 315 Processing helix chain 'D' and resid 318 through 325 removed outlier: 3.637A pdb=" N THR D 324 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE D 325 " --> pdb=" O PRO D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 328 No H-bonds generated for 'chain 'D' and resid 326 through 328' Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 358 through 363 Processing helix chain 'D' and resid 364 through 383 removed outlier: 3.695A pdb=" N LEU D 383 " --> pdb=" O ARG D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 391 Processing helix chain 'D' and resid 396 through 413 removed outlier: 3.754A pdb=" N ARG D 408 " --> pdb=" O GLY D 404 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG D 411 " --> pdb=" O ARG D 407 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 421 Processing helix chain 'D' and resid 432 through 445 Processing helix chain 'D' and resid 452 through 457 removed outlier: 3.841A pdb=" N PHE D 457 " --> pdb=" O GLN D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 472 Processing helix chain 'E' and resid 26 through 30 removed outlier: 4.232A pdb=" N VAL E 30 " --> pdb=" O ARG E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 47 removed outlier: 3.782A pdb=" N ALA E 47 " --> pdb=" O GLU E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.819A pdb=" N VAL E 95 " --> pdb=" O GLY E 92 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS E 96 " --> pdb=" O ASP E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 96' Processing helix chain 'E' and resid 127 through 131 Processing helix chain 'E' and resid 142 through 149 Processing helix chain 'E' and resid 166 through 179 Processing helix chain 'E' and resid 194 through 207 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 224 through 229 removed outlier: 3.513A pdb=" N ARG E 228 " --> pdb=" O PRO E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 245 removed outlier: 3.569A pdb=" N SER E 234 " --> pdb=" O ARG E 230 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 272 removed outlier: 4.051A pdb=" N THR E 261 " --> pdb=" O ILE E 257 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY E 272 " --> pdb=" O SER E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 280 Processing helix chain 'E' and resid 283 through 293 Processing helix chain 'E' and resid 312 through 315 Processing helix chain 'E' and resid 318 through 323 Processing helix chain 'E' and resid 324 through 328 removed outlier: 3.846A pdb=" N LEU E 328 " --> pdb=" O PHE E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 358 through 363 Processing helix chain 'E' and resid 364 through 383 Processing helix chain 'E' and resid 383 through 390 removed outlier: 3.805A pdb=" N ILE E 387 " --> pdb=" O LEU E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 395 removed outlier: 3.600A pdb=" N LEU E 395 " --> pdb=" O ILE E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 414 removed outlier: 3.919A pdb=" N SER E 414 " --> pdb=" O GLU E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 421 Processing helix chain 'E' and resid 432 through 446 removed outlier: 3.528A pdb=" N LYS E 445 " --> pdb=" O ASP E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 456 removed outlier: 3.864A pdb=" N PHE E 456 " --> pdb=" O GLU E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 472 Processing helix chain 'F' and resid 92 through 96 removed outlier: 3.850A pdb=" N VAL F 95 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS F 96 " --> pdb=" O ASP F 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 92 through 96' Processing helix chain 'F' and resid 127 through 131 removed outlier: 3.503A pdb=" N LEU F 131 " --> pdb=" O PHE F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 149 Processing helix chain 'F' and resid 166 through 182 removed outlier: 3.652A pdb=" N PHE F 182 " --> pdb=" O ILE F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 208 removed outlier: 3.507A pdb=" N ALA F 206 " --> pdb=" O TRP F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 224 through 229 removed outlier: 3.739A pdb=" N ARG F 228 " --> pdb=" O PRO F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 247 removed outlier: 3.650A pdb=" N GLN F 246 " --> pdb=" O PHE F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 272 removed outlier: 3.567A pdb=" N PHE F 260 " --> pdb=" O ASN F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 280 Processing helix chain 'F' and resid 283 through 293 removed outlier: 3.562A pdb=" N LEU F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 318 through 325 Processing helix chain 'F' and resid 335 through 342 removed outlier: 3.696A pdb=" N PHE F 339 " --> pdb=" O SER F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 383 Processing helix chain 'F' and resid 384 through 390 Processing helix chain 'F' and resid 396 through 412 removed outlier: 3.527A pdb=" N ARG F 407 " --> pdb=" O VAL F 403 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG F 408 " --> pdb=" O GLY F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 421 removed outlier: 3.799A pdb=" N GLU F 421 " --> pdb=" O MET F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 445 Processing helix chain 'F' and resid 453 through 457 removed outlier: 3.878A pdb=" N PHE F 456 " --> pdb=" O GLU F 453 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE F 457 " --> pdb=" O GLN F 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 453 through 457' Processing helix chain 'F' and resid 461 through 472 Processing helix chain 'G' and resid 3 through 43 removed outlier: 3.829A pdb=" N ALA G 43 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 59 removed outlier: 4.135A pdb=" N ALA G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 92 through 111 Processing helix chain 'G' and resid 120 through 130 Processing helix chain 'G' and resid 146 through 167 Processing helix chain 'G' and resid 226 through 307 removed outlier: 4.038A pdb=" N LEU G 235 " --> pdb=" O PHE G 231 " (cutoff:3.500A) Proline residue: G 236 - end of helix removed outlier: 3.586A pdb=" N ALA G 251 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA G 252 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG G 260 " --> pdb=" O ALA G 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 101 removed outlier: 3.903A pdb=" N ASP H 98 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 117 removed outlier: 3.705A pdb=" N ALA H 108 " --> pdb=" O PRO H 104 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) Processing helix chain 'b' and resid 90 through 148 removed outlier: 3.900A pdb=" N GLY b 146 " --> pdb=" O GLU b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 165 Processing helix chain 'd' and resid 67 through 137 removed outlier: 3.546A pdb=" N ARG d 88 " --> pdb=" O SER d 84 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU d 108 " --> pdb=" O GLU d 104 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN d 109 " --> pdb=" O GLN d 105 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG d 110 " --> pdb=" O ILE d 106 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 156 removed outlier: 3.759A pdb=" N ALA d 145 " --> pdb=" O SER d 141 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR d 146 " --> pdb=" O ALA d 142 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL d 147 " --> pdb=" O GLN d 143 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN d 156 " --> pdb=" O ASP d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 177 through 194 removed outlier: 3.926A pdb=" N GLU d 181 " --> pdb=" O ALA d 177 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU d 192 " --> pdb=" O SER d 188 " (cutoff:3.500A) Processing helix chain 'd' and resid 198 through 219 Processing helix chain 'd' and resid 220 through 228 Processing helix chain 'd' and resid 234 through 243 Processing helix chain 'd' and resid 251 through 263 Processing helix chain 'd' and resid 269 through 291 removed outlier: 4.476A pdb=" N ILE d 273 " --> pdb=" O SER d 269 " (cutoff:3.500A) Processing helix chain 'd' and resid 293 through 310 Processing helix chain 'd' and resid 311 through 320 Processing helix chain 'd' and resid 324 through 337 Processing helix chain 'd' and resid 341 through 354 removed outlier: 3.523A pdb=" N LEU d 354 " --> pdb=" O GLN d 350 " (cutoff:3.500A) Processing helix chain 'd' and resid 359 through 377 removed outlier: 3.615A pdb=" N LEU d 365 " --> pdb=" O GLU d 361 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU d 377 " --> pdb=" O ALA d 373 " (cutoff:3.500A) Processing helix chain 'd' and resid 389 through 405 removed outlier: 3.663A pdb=" N ARG d 393 " --> pdb=" O THR d 389 " (cutoff:3.500A) Processing helix chain 'd' and resid 416 through 419 Processing helix chain 'd' and resid 434 through 445 Processing helix chain 'A' and resid 7 through 21 removed outlier: 3.964A pdb=" N ALA A 14 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ILE A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 103 through 107 removed outlier: 4.060A pdb=" N PHE A 106 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 107 " --> pdb=" O ASP A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 107' Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 177 through 188 removed outlier: 3.602A pdb=" N VAL A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS A 182 " --> pdb=" O LYS A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.856A pdb=" N GLY A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 removed outlier: 3.656A pdb=" N ALA A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 removed outlier: 4.064A pdb=" N GLU A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 262 removed outlier: 3.592A pdb=" N LYS A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 273 through 288 removed outlier: 4.049A pdb=" N GLN A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.593A pdb=" N HIS A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 339 through 347 removed outlier: 3.574A pdb=" N THR A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.741A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 381 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 382 " --> pdb=" O GLY A 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 382' Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 392 through 407 Processing helix chain 'A' and resid 414 through 431 Processing helix chain 'A' and resid 440 through 453 removed outlier: 3.649A pdb=" N GLY A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 478 Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.883A pdb=" N LEU A 483 " --> pdb=" O HIS A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 509 Processing sheet with id=AA1, first strand: chain 'B' and resid 63 through 69 removed outlier: 3.709A pdb=" N GLY B 64 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU B 54 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLU B 96 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N GLU B 57 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N THR B 94 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N HIS B 43 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA B 37 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU B 69 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG F 64 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N HIS F 57 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU F 62 " --> pdb=" O HIS F 57 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL F 16 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP F 22 " --> pdb=" O VAL F 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 99 through 102 Processing sheet with id=AA3, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.355A pdb=" N ILE B 111 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG B 203 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N VAL B 270 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE B 205 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP B 272 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 207 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU B 169 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU B 355 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE B 171 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 63 through 69 removed outlier: 4.291A pdb=" N GLU C 54 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU C 55 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 94 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N HIS C 43 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA C 37 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU C 63 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASP D 79 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU D 40 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA D 39 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG D 64 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N HIS D 57 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU D 62 " --> pdb=" O HIS D 57 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL D 16 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASP D 22 " --> pdb=" O VAL D 14 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AA6, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.240A pdb=" N ARG C 203 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL C 270 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 205 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ASP C 272 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL C 207 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 271 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU C 169 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU C 355 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE C 171 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 88 through 91 removed outlier: 3.935A pdb=" N GLU D 117 " --> pdb=" O VAL D 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 99 through 100 removed outlier: 6.616A pdb=" N VAL D 250 " --> pdb=" O THR D 304 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N MET D 306 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU D 252 " --> pdb=" O MET D 306 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ALA D 308 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE D 254 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N TYR D 310 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE D 157 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL D 309 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU D 159 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 137 through 138 removed outlier: 3.988A pdb=" N TYR D 151 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 17 removed outlier: 6.631A pdb=" N ASP E 22 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL E 16 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU E 62 " --> pdb=" O HIS E 57 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N HIS E 57 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG E 64 " --> pdb=" O ALA E 55 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU E 40 " --> pdb=" O ASP E 79 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP E 79 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 80 " --> pdb=" O GLY E 11 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 63 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY A 75 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA A 37 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N HIS A 43 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 94 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU A 55 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU A 54 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 88 through 91 removed outlier: 4.175A pdb=" N GLU E 117 " --> pdb=" O VAL E 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 99 through 100 removed outlier: 6.766A pdb=" N ILE E 157 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL E 309 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU E 159 " --> pdb=" O VAL E 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 137 through 138 removed outlier: 4.301A pdb=" N TYR E 151 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 88 through 91 removed outlier: 4.276A pdb=" N GLU F 117 " --> pdb=" O VAL F 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AB7, first strand: chain 'F' and resid 99 through 101 removed outlier: 6.169A pdb=" N ILE F 157 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LYS F 156 " --> pdb=" O ALA F 330 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N THR F 332 " --> pdb=" O LYS F 156 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA F 158 " --> pdb=" O THR F 332 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N LEU F 334 " --> pdb=" O ALA F 158 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE F 160 " --> pdb=" O LEU F 334 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 137 through 138 removed outlier: 3.597A pdb=" N LEU F 138 " --> pdb=" O TYR F 151 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR F 151 " --> pdb=" O LEU F 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'G' and resid 136 through 138 removed outlier: 4.104A pdb=" N GLU G 136 " --> pdb=" O VAL G 116 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N HIS G 184 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLY G 78 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N VAL G 82 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 11.751A pdb=" N PHE G 190 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU G 183 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 9.461A pdb=" N GLY A 535 " --> pdb=" O ALA G 198 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ALA G 200 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N GLU A 537 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ARG G 202 " --> pdb=" O GLU A 537 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N VAL A 539 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 14.015A pdb=" N ALA G 204 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 15.490A pdb=" N VAL A 541 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 15.093A pdb=" N MET G 206 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 14 through 20 removed outlier: 3.626A pdb=" N TRP H 16 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL H 77 " --> pdb=" O ASP H 5 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE H 79 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL H 9 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA H 81 " --> pdb=" O VAL H 9 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE H 69 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU H 70 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 22 through 23 Processing sheet with id=AC3, first strand: chain 'H' and resid 64 through 65 removed outlier: 4.278A pdb=" N GLN H 85 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'd' and resid 379 through 380 removed outlier: 3.662A pdb=" N ALA d 380 " --> pdb=" O ALA d 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'd' and resid 383 through 384 Processing sheet with id=AC6, first strand: chain 'd' and resid 423 through 426 Processing sheet with id=AC7, first strand: chain 'A' and resid 99 through 102 Processing sheet with id=AC8, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.393A pdb=" N ILE A 111 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG A 203 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL A 270 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 205 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASP A 272 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 207 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 267 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU A 327 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE A 269 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE A 329 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE A 271 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N GLU A 331 " --> pdb=" O PHE A 271 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU A 169 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU A 355 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE A 171 " --> pdb=" O LEU A 355 " (cutoff:3.500A) 1532 hydrogen bonds defined for protein. 4377 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: 6.14 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5207 1.31 - 1.44: 7158 1.44 - 1.56: 17402 1.56 - 1.68: 26 1.68 - 1.81: 128 Bond restraints: 29921 Sorted by residual: bond pdb=" C4 ADP E 600 " pdb=" C5 ADP E 600 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" N ILE C 118 " pdb=" CA ILE C 118 " ideal model delta sigma weight residual 1.457 1.496 -0.040 9.30e-03 1.16e+04 1.81e+01 bond pdb=" C5 ADP D 600 " pdb=" C6 ADP D 600 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C5 ADP E 600 " pdb=" C6 ADP E 600 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 29916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 40221 2.60 - 5.21: 372 5.21 - 7.81: 33 7.81 - 10.42: 8 10.42 - 13.02: 2 Bond angle restraints: 40636 Sorted by residual: angle pdb=" PB ATP F 600 " pdb=" O3B ATP F 600 " pdb=" PG ATP F 600 " ideal model delta sigma weight residual 139.87 132.09 7.78 1.00e+00 1.00e+00 6.05e+01 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 132.34 7.53 1.00e+00 1.00e+00 5.67e+01 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 132.97 6.90 1.00e+00 1.00e+00 4.76e+01 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 130.70 6.13 1.00e+00 1.00e+00 3.75e+01 angle pdb=" PA ATP F 600 " pdb=" O3A ATP F 600 " pdb=" PB ATP F 600 " ideal model delta sigma weight residual 136.83 130.82 6.01 1.00e+00 1.00e+00 3.61e+01 ... (remaining 40631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.92: 17590 20.92 - 41.84: 498 41.84 - 62.76: 105 62.76 - 83.69: 23 83.69 - 104.61: 5 Dihedral angle restraints: 18221 sinusoidal: 7225 harmonic: 10996 Sorted by residual: dihedral pdb=" O1B ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PB ADP E 600 " pdb=" PA ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 -164.61 104.61 1 2.00e+01 2.50e-03 3.01e+01 dihedral pdb=" CA PHE D 218 " pdb=" C PHE D 218 " pdb=" N GLY D 219 " pdb=" CA GLY D 219 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CB GLU D 293 " pdb=" CG GLU D 293 " pdb=" CD GLU D 293 " pdb=" OE1 GLU D 293 " ideal model delta sinusoidal sigma weight residual 0.00 -86.52 86.52 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 18218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4073 0.057 - 0.115: 561 0.115 - 0.172: 81 0.172 - 0.230: 10 0.230 - 0.287: 4 Chirality restraints: 4729 Sorted by residual: chirality pdb=" CA ILE H 72 " pdb=" N ILE H 72 " pdb=" C ILE H 72 " pdb=" CB ILE H 72 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ILE E 295 " pdb=" N ILE E 295 " pdb=" C ILE E 295 " pdb=" CB ILE E 295 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA VAL d 133 " pdb=" N VAL d 133 " pdb=" C VAL d 133 " pdb=" CB VAL d 133 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 4726 not shown) Planarity restraints: 5341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 167 " -0.277 9.50e-02 1.11e+02 1.24e-01 9.48e+00 pdb=" NE ARG A 167 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 167 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 167 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 167 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 295 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C ILE E 295 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE E 295 " -0.019 2.00e-02 2.50e+03 pdb=" N THR E 296 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 540 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.09e+00 pdb=" C GLN A 540 " 0.046 2.00e-02 2.50e+03 pdb=" O GLN A 540 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL A 541 " -0.016 2.00e-02 2.50e+03 ... (remaining 5338 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 16 2.53 - 3.12: 23293 3.12 - 3.72: 42099 3.72 - 4.31: 60743 4.31 - 4.90: 106507 Nonbonded interactions: 232658 Sorted by model distance: nonbonded pdb=" OG1 THR B 179 " pdb="MG MG B 601 " model vdw 1.938 2.170 nonbonded pdb=" OG1 THR C 179 " pdb="MG MG C 601 " model vdw 2.150 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 2.242 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 2.274 2.170 nonbonded pdb=" O2B ADP E 600 " pdb="MG MG E 601 " model vdw 2.313 2.170 ... (remaining 232653 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' and (resid 4 through 514 or resid 530 or resid 532 or resid 534 or re \ sid 537 or resid 541 or resid 600 through 601)) selection = (chain 'B' and (resid 4 through 515 or resid 517 or resid 519 through 521 or res \ id 600 through 601)) selection = (chain 'C' and (resid 4 through 515 or resid 517 or resid 519 through 601)) } ncs_group { reference = (chain 'D' and resid 9 through 472) selection = (chain 'E' and resid 9 through 472) selection = (chain 'F' and resid 9 through 472) } 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: 26.120 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 27.330 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 29921 Z= 0.218 Angle : 0.577 13.022 40636 Z= 0.355 Chirality : 0.042 0.287 4729 Planarity : 0.004 0.124 5341 Dihedral : 10.741 104.608 11153 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.23 % Allowed : 2.97 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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: 1.00 (0.14), residues: 3837 helix: 2.21 (0.13), residues: 1687 sheet: 0.21 (0.23), residues: 542 loop : -0.88 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 97 TYR 0.010 0.001 TYR B 303 PHE 0.009 0.001 PHE B 406 TRP 0.019 0.001 TRP H 62 HIS 0.002 0.000 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00343 (29921) covalent geometry : angle 0.57726 (40636) hydrogen bonds : bond 0.17740 ( 1512) hydrogen bonds : angle 6.51192 ( 4377) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 311 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7203 (pt0) REVERT: B 505 ASN cc_start: 0.8759 (m-40) cc_final: 0.8454 (m-40) REVERT: C 461 VAL cc_start: 0.8516 (p) cc_final: 0.8245 (t) REVERT: G 40 VAL cc_start: 0.8008 (p) cc_final: 0.7806 (t) REVERT: G 65 HIS cc_start: 0.7003 (t-90) cc_final: 0.6737 (t-90) REVERT: H 8 ILE cc_start: 0.5818 (mt) cc_final: 0.5618 (mp) REVERT: H 59 ASP cc_start: 0.6001 (m-30) cc_final: 0.5735 (p0) REVERT: H 89 ASP cc_start: 0.5711 (t0) cc_final: 0.4778 (p0) REVERT: H 98 ASP cc_start: 0.6833 (m-30) cc_final: 0.6549 (t0) REVERT: d 106 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7683 (tp) REVERT: A 436 ASN cc_start: 0.8005 (t0) cc_final: 0.7779 (t0) outliers start: 7 outliers final: 2 residues processed: 317 average time/residue: 0.8104 time to fit residues: 293.6327 Evaluate side-chains 174 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 171 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain d residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 9.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN B 369 ASN C 399 GLN E 209 ASN E 248 GLN E 422 GLN F 454 GLN A 201 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.081017 restraints weight = 45629.390| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.07 r_work: 0.2850 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29921 Z= 0.133 Angle : 0.550 9.829 40636 Z= 0.283 Chirality : 0.042 0.156 4729 Planarity : 0.004 0.045 5341 Dihedral : 6.940 83.348 4335 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.20 % Allowed : 7.40 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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: 1.07 (0.14), residues: 3837 helix: 2.24 (0.13), residues: 1694 sheet: 0.59 (0.23), residues: 511 loop : -0.93 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 134 TYR 0.012 0.001 TYR G 92 PHE 0.014 0.001 PHE D 260 TRP 0.012 0.001 TRP H 62 HIS 0.003 0.001 HIS F 450 Details of bonding type rmsd covalent geometry : bond 0.00293 (29921) covalent geometry : angle 0.54959 (40636) hydrogen bonds : bond 0.05429 ( 1512) hydrogen bonds : angle 4.65747 ( 4377) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 29 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6657 (pt0) REVERT: B 505 ASN cc_start: 0.8780 (m-40) cc_final: 0.8357 (m-40) REVERT: B 509 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7927 (mtpt) REVERT: C 494 GLU cc_start: 0.7969 (mp0) cc_final: 0.7675 (mm-30) REVERT: F 46 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8188 (mtp) REVERT: G 40 VAL cc_start: 0.7686 (p) cc_final: 0.7481 (t) REVERT: G 65 HIS cc_start: 0.7358 (t-90) cc_final: 0.7049 (t70) REVERT: G 206 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6518 (mtt) REVERT: H 4 ILE cc_start: 0.3981 (mp) cc_final: 0.2902 (tp) REVERT: H 59 ASP cc_start: 0.6173 (m-30) cc_final: 0.5907 (p0) REVERT: H 89 ASP cc_start: 0.6189 (t0) cc_final: 0.5210 (p0) REVERT: H 106 VAL cc_start: 0.7435 (p) cc_final: 0.7201 (m) REVERT: b 131 GLU cc_start: 0.7618 (tp30) cc_final: 0.7236 (mm-30) REVERT: d 110 ARG cc_start: 0.8421 (ttp80) cc_final: 0.7740 (ttm-80) REVERT: d 128 ARG cc_start: 0.7821 (tpp80) cc_final: 0.7316 (mpp80) REVERT: d 175 MET cc_start: 0.8515 (mtt) cc_final: 0.7984 (mtt) REVERT: d 419 LEU cc_start: 0.8251 (tt) cc_final: 0.7908 (tt) REVERT: A 420 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.8054 (mt0) REVERT: A 436 ASN cc_start: 0.8686 (t0) cc_final: 0.8317 (t0) outliers start: 37 outliers final: 11 residues processed: 216 average time/residue: 0.7562 time to fit residues: 187.3067 Evaluate side-chains 184 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 300 ASN Chi-restraints excluded: chain d residue 106 ILE Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 420 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 175 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 300 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN B 369 ASN B 479 HIS E 209 ASN F 454 GLN A 68 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.077261 restraints weight = 45798.381| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.03 r_work: 0.2782 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 29921 Z= 0.216 Angle : 0.605 9.850 40636 Z= 0.313 Chirality : 0.046 0.162 4729 Planarity : 0.005 0.045 5341 Dihedral : 6.971 86.108 4333 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.68 % Allowed : 8.02 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.14), residues: 3837 helix: 1.98 (0.13), residues: 1691 sheet: 0.43 (0.23), residues: 522 loop : -0.99 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 105 TYR 0.019 0.002 TYR G 92 PHE 0.022 0.002 PHE D 260 TRP 0.010 0.002 TRP A 247 HIS 0.004 0.001 HIS D 366 Details of bonding type rmsd covalent geometry : bond 0.00533 (29921) covalent geometry : angle 0.60503 (40636) hydrogen bonds : bond 0.06736 ( 1512) hydrogen bonds : angle 4.69452 ( 4377) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: B 29 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6715 (pt0) REVERT: D 181 ASN cc_start: 0.7956 (p0) cc_final: 0.7685 (p0) REVERT: D 385 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: E 27 ARG cc_start: 0.7247 (tpm170) cc_final: 0.7008 (tpm170) REVERT: F 379 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7481 (mtp-110) REVERT: F 454 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8507 (mm-40) REVERT: G 40 VAL cc_start: 0.8021 (p) cc_final: 0.7767 (t) REVERT: G 65 HIS cc_start: 0.7310 (t-90) cc_final: 0.7002 (t70) REVERT: H 1 MET cc_start: 0.5146 (pmm) cc_final: 0.4694 (ttp) REVERT: H 4 ILE cc_start: 0.4445 (mp) cc_final: 0.3479 (tp) REVERT: d 110 ARG cc_start: 0.8410 (ttp80) cc_final: 0.7724 (ttm-80) REVERT: d 128 ARG cc_start: 0.7787 (tpp80) cc_final: 0.7541 (tpp80) REVERT: d 175 MET cc_start: 0.8655 (mtt) cc_final: 0.8202 (mtt) REVERT: d 228 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: A 436 ASN cc_start: 0.8735 (t0) cc_final: 0.8395 (t0) REVERT: A 469 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7254 (mp10) outliers start: 52 outliers final: 17 residues processed: 208 average time/residue: 0.7685 time to fit residues: 184.2641 Evaluate side-chains 178 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 379 ARG Chi-restraints excluded: chain F residue 454 GLN Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain d residue 106 ILE Chi-restraints excluded: chain d residue 228 GLU Chi-restraints excluded: chain d residue 358 VAL Chi-restraints excluded: chain d residue 426 ILE Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 509 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 100 optimal weight: 0.9990 chunk 267 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 302 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 257 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 329 optimal weight: 0.9980 chunk 312 optimal weight: 4.9990 chunk 106 optimal weight: 0.0770 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 GLN E 209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.113778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.080126 restraints weight = 45382.381| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.03 r_work: 0.2836 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29921 Z= 0.110 Angle : 0.500 14.239 40636 Z= 0.259 Chirality : 0.041 0.143 4729 Planarity : 0.004 0.051 5341 Dihedral : 6.506 88.746 4333 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.16 % Allowed : 9.28 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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: 1.10 (0.14), residues: 3837 helix: 2.26 (0.13), residues: 1683 sheet: 0.54 (0.23), residues: 516 loop : -0.89 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 134 TYR 0.017 0.001 TYR F 380 PHE 0.011 0.001 PHE D 260 TRP 0.009 0.001 TRP H 62 HIS 0.003 0.000 HIS C 474 Details of bonding type rmsd covalent geometry : bond 0.00230 (29921) covalent geometry : angle 0.49970 (40636) hydrogen bonds : bond 0.05047 ( 1512) hydrogen bonds : angle 4.31073 ( 4377) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: B 29 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6640 (pt0) REVERT: B 505 ASN cc_start: 0.8721 (m-40) cc_final: 0.8323 (m-40) REVERT: B 509 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8120 (mtpt) REVERT: C 494 GLU cc_start: 0.8002 (mp0) cc_final: 0.7787 (mm-30) REVERT: D 181 ASN cc_start: 0.7958 (p0) cc_final: 0.7690 (p0) REVERT: D 385 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: F 379 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7422 (mtp-110) REVERT: F 454 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8444 (mm-40) REVERT: F 457 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.7948 (t80) REVERT: G 65 HIS cc_start: 0.7307 (t-90) cc_final: 0.6965 (t70) REVERT: G 206 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6458 (mmt) REVERT: H 4 ILE cc_start: 0.4397 (mp) cc_final: 0.3356 (tp) REVERT: b 131 GLU cc_start: 0.7713 (tp30) cc_final: 0.7208 (mm-30) REVERT: d 110 ARG cc_start: 0.8411 (ttp80) cc_final: 0.7754 (ttm-80) REVERT: d 181 GLU cc_start: 0.8206 (mp0) cc_final: 0.7611 (mp0) REVERT: d 228 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: d 419 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7919 (tt) REVERT: A 436 ASN cc_start: 0.8666 (t0) cc_final: 0.8355 (t0) REVERT: A 469 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7256 (mp10) outliers start: 36 outliers final: 9 residues processed: 196 average time/residue: 0.7870 time to fit residues: 177.3330 Evaluate side-chains 175 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 379 ARG Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 454 GLN Chi-restraints excluded: chain F residue 457 PHE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain d residue 106 ILE Chi-restraints excluded: chain d residue 228 GLU Chi-restraints excluded: chain d residue 419 LEU Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 469 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 57 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 327 optimal weight: 0.0870 chunk 172 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 303 optimal weight: 0.9980 chunk 246 optimal weight: 3.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 GLN F 454 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.078279 restraints weight = 45657.120| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.05 r_work: 0.2804 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 29921 Z= 0.153 Angle : 0.523 12.699 40636 Z= 0.271 Chirality : 0.042 0.149 4729 Planarity : 0.004 0.048 5341 Dihedral : 6.402 85.142 4333 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 1.45 % Allowed : 9.73 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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: 1.04 (0.14), residues: 3837 helix: 2.20 (0.13), residues: 1680 sheet: 0.53 (0.23), residues: 516 loop : -0.90 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 72 TYR 0.014 0.001 TYR G 92 PHE 0.016 0.001 PHE B 409 TRP 0.008 0.001 TRP H 62 HIS 0.003 0.001 HIS C 474 Details of bonding type rmsd covalent geometry : bond 0.00367 (29921) covalent geometry : angle 0.52319 (40636) hydrogen bonds : bond 0.05515 ( 1512) hydrogen bonds : angle 4.32608 ( 4377) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: B 29 GLU cc_start: 0.7412 (mm-30) cc_final: 0.6683 (pt0) REVERT: C 245 PHE cc_start: 0.9472 (OUTLIER) cc_final: 0.9087 (m-10) REVERT: C 494 GLU cc_start: 0.8044 (mp0) cc_final: 0.7787 (mm-30) REVERT: D 385 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: F 46 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8008 (mtm) REVERT: F 379 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7427 (mtp-110) REVERT: F 457 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.7910 (t80) REVERT: G 65 HIS cc_start: 0.7303 (t-90) cc_final: 0.6949 (t70) REVERT: G 206 MET cc_start: 0.6837 (OUTLIER) cc_final: 0.6499 (mtt) REVERT: H 1 MET cc_start: 0.4995 (pmm) cc_final: 0.4524 (ttp) REVERT: d 110 ARG cc_start: 0.8381 (ttp80) cc_final: 0.7754 (ttm-80) REVERT: d 181 GLU cc_start: 0.8280 (mp0) cc_final: 0.7686 (mp0) REVERT: d 228 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: d 419 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7933 (tt) REVERT: A 436 ASN cc_start: 0.8655 (t0) cc_final: 0.8351 (t0) REVERT: A 469 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7238 (mp10) outliers start: 45 outliers final: 18 residues processed: 189 average time/residue: 0.8268 time to fit residues: 179.9362 Evaluate side-chains 183 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 379 ARG Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 457 PHE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain d residue 106 ILE Chi-restraints excluded: chain d residue 228 GLU Chi-restraints excluded: chain d residue 419 LEU Chi-restraints excluded: chain d residue 426 ILE Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 469 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 76 optimal weight: 1.9990 chunk 316 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 234 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 340 optimal weight: 5.9990 chunk 267 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 363 optimal weight: 0.7980 chunk 261 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 GLN F 454 GLN G 125 ASN A 335 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.077166 restraints weight = 45466.047| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.02 r_work: 0.2779 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 29921 Z= 0.198 Angle : 0.564 12.046 40636 Z= 0.292 Chirality : 0.044 0.154 4729 Planarity : 0.004 0.053 5341 Dihedral : 6.601 80.513 4333 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.28 % Favored : 96.66 % Rotamer: Outliers : 1.71 % Allowed : 9.89 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.14), residues: 3837 helix: 2.04 (0.13), residues: 1686 sheet: 0.47 (0.22), residues: 514 loop : -0.99 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 394 TYR 0.015 0.001 TYR G 92 PHE 0.019 0.002 PHE D 260 TRP 0.010 0.001 TRP A 247 HIS 0.004 0.001 HIS E 327 Details of bonding type rmsd covalent geometry : bond 0.00490 (29921) covalent geometry : angle 0.56415 (40636) hydrogen bonds : bond 0.06128 ( 1512) hydrogen bonds : angle 4.44168 ( 4377) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 160 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: B 29 GLU cc_start: 0.7456 (mm-30) cc_final: 0.6704 (pt0) REVERT: C 245 PHE cc_start: 0.9484 (OUTLIER) cc_final: 0.9098 (m-10) REVERT: D 385 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.7876 (m-30) REVERT: F 379 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7420 (mtp-110) REVERT: F 457 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7956 (t80) REVERT: G 65 HIS cc_start: 0.7280 (t-90) cc_final: 0.6924 (t70) REVERT: G 206 MET cc_start: 0.6837 (OUTLIER) cc_final: 0.6503 (mtt) REVERT: H 1 MET cc_start: 0.5032 (pmm) cc_final: 0.4391 (ttp) REVERT: H 4 ILE cc_start: 0.4470 (mp) cc_final: 0.3516 (tp) REVERT: d 110 ARG cc_start: 0.8355 (ttp80) cc_final: 0.7684 (ttm-80) REVERT: d 128 ARG cc_start: 0.7607 (tpp80) cc_final: 0.7210 (tpp80) REVERT: d 181 GLU cc_start: 0.8328 (mp0) cc_final: 0.7726 (mp0) REVERT: d 228 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7180 (tm-30) REVERT: d 419 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8013 (tt) REVERT: A 436 ASN cc_start: 0.8684 (t0) cc_final: 0.8397 (t0) REVERT: A 469 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7285 (mp10) outliers start: 53 outliers final: 25 residues processed: 205 average time/residue: 0.8109 time to fit residues: 192.6579 Evaluate side-chains 191 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 379 ARG Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 454 GLN Chi-restraints excluded: chain F residue 457 PHE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain b residue 117 ASP Chi-restraints excluded: chain d residue 106 ILE Chi-restraints excluded: chain d residue 228 GLU Chi-restraints excluded: chain d residue 358 VAL Chi-restraints excluded: chain d residue 419 LEU Chi-restraints excluded: chain d residue 426 ILE Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 469 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 18 optimal weight: 0.9990 chunk 344 optimal weight: 1.9990 chunk 325 optimal weight: 0.6980 chunk 173 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 106 optimal weight: 0.0870 chunk 41 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 270 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 271 optimal weight: 2.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.079294 restraints weight = 45402.879| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.99 r_work: 0.2827 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29921 Z= 0.117 Angle : 0.497 11.679 40636 Z= 0.259 Chirality : 0.041 0.141 4729 Planarity : 0.004 0.052 5341 Dihedral : 6.285 83.707 4333 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.87 % Favored : 97.08 % Rotamer: Outliers : 1.65 % Allowed : 10.44 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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: 1.10 (0.14), residues: 3837 helix: 2.24 (0.13), residues: 1689 sheet: 0.56 (0.23), residues: 515 loop : -0.88 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 394 TYR 0.013 0.001 TYR G 92 PHE 0.016 0.001 PHE B 409 TRP 0.008 0.001 TRP A 247 HIS 0.002 0.000 HIS C 474 Details of bonding type rmsd covalent geometry : bond 0.00256 (29921) covalent geometry : angle 0.49704 (40636) hydrogen bonds : bond 0.05000 ( 1512) hydrogen bonds : angle 4.20849 ( 4377) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 165 time to evaluate : 1.384 Fit side-chains revert: symmetry clash REVERT: B 29 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6696 (pt0) REVERT: D 385 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.7894 (m-30) REVERT: F 379 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7380 (mtp-110) REVERT: F 453 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: F 457 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.7898 (t80) REVERT: G 65 HIS cc_start: 0.7211 (t-90) cc_final: 0.6856 (t70) REVERT: G 206 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.6571 (mtt) REVERT: H 1 MET cc_start: 0.5048 (pmm) cc_final: 0.4403 (ttp) REVERT: H 4 ILE cc_start: 0.4400 (mp) cc_final: 0.3443 (tp) REVERT: b 117 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7446 (p0) REVERT: b 118 MET cc_start: 0.6686 (ttm) cc_final: 0.6204 (tmm) REVERT: b 131 GLU cc_start: 0.7738 (tp30) cc_final: 0.7147 (mm-30) REVERT: d 181 GLU cc_start: 0.8309 (mp0) cc_final: 0.7721 (mp0) REVERT: d 228 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: d 419 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7965 (tt) REVERT: A 436 ASN cc_start: 0.8665 (t0) cc_final: 0.8370 (t0) REVERT: A 469 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7301 (mp10) outliers start: 51 outliers final: 24 residues processed: 206 average time/residue: 0.7942 time to fit residues: 189.3657 Evaluate side-chains 191 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 379 ARG Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 457 PHE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain b residue 117 ASP Chi-restraints excluded: chain d residue 106 ILE Chi-restraints excluded: chain d residue 228 GLU Chi-restraints excluded: chain d residue 294 ILE Chi-restraints excluded: chain d residue 358 VAL Chi-restraints excluded: chain d residue 419 LEU Chi-restraints excluded: chain d residue 426 ILE Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 469 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 246 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 377 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 157 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 213 optimal weight: 5.9990 chunk 214 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 454 GLN G 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.114266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.080439 restraints weight = 45433.965| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.99 r_work: 0.2842 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 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 : 0.002 0.032 29921 Z= 0.107 Angle : 0.487 11.018 40636 Z= 0.252 Chirality : 0.040 0.145 4729 Planarity : 0.004 0.058 5341 Dihedral : 6.085 86.173 4333 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.03 % Rotamer: Outliers : 1.36 % Allowed : 11.05 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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: 1.27 (0.14), residues: 3837 helix: 2.41 (0.13), residues: 1683 sheet: 0.67 (0.23), residues: 513 loop : -0.81 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 394 TYR 0.011 0.001 TYR G 92 PHE 0.022 0.001 PHE B 409 TRP 0.007 0.001 TRP d 266 HIS 0.006 0.001 HIS d 101 Details of bonding type rmsd covalent geometry : bond 0.00229 (29921) covalent geometry : angle 0.48701 (40636) hydrogen bonds : bond 0.04682 ( 1512) hydrogen bonds : angle 4.08886 ( 4377) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: B 29 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6703 (pt0) REVERT: B 409 PHE cc_start: 0.7976 (m-10) cc_final: 0.7674 (m-80) REVERT: B 505 ASN cc_start: 0.8706 (m-40) cc_final: 0.8326 (m-40) REVERT: F 379 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7378 (mtp-110) REVERT: F 457 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.7926 (t80) REVERT: F 472 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7586 (mp) REVERT: G 65 HIS cc_start: 0.7186 (t-90) cc_final: 0.6829 (t70) REVERT: H 1 MET cc_start: 0.4939 (pmm) cc_final: 0.4372 (ttp) REVERT: H 4 ILE cc_start: 0.4256 (mp) cc_final: 0.3374 (tp) REVERT: b 117 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7504 (p0) REVERT: b 118 MET cc_start: 0.6598 (ttm) cc_final: 0.6169 (tmm) REVERT: d 181 GLU cc_start: 0.8313 (mp0) cc_final: 0.7735 (mp0) REVERT: d 228 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7142 (tm-30) REVERT: d 419 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7951 (tt) REVERT: A 436 ASN cc_start: 0.8650 (t0) cc_final: 0.8371 (t0) REVERT: A 469 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7284 (mp10) outliers start: 42 outliers final: 22 residues processed: 198 average time/residue: 0.8210 time to fit residues: 187.5417 Evaluate side-chains 184 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 379 ARG Chi-restraints excluded: chain F residue 454 GLN Chi-restraints excluded: chain F residue 457 PHE Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain b residue 117 ASP Chi-restraints excluded: chain d residue 106 ILE Chi-restraints excluded: chain d residue 224 LYS Chi-restraints excluded: chain d residue 228 GLU Chi-restraints excluded: chain d residue 294 ILE Chi-restraints excluded: chain d residue 358 VAL Chi-restraints excluded: chain d residue 419 LEU Chi-restraints excluded: chain d residue 426 ILE Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 469 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 381 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 289 optimal weight: 8.9990 chunk 255 optimal weight: 10.0000 chunk 378 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 15 optimal weight: 0.0470 chunk 160 optimal weight: 0.7980 chunk 188 optimal weight: 0.9980 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 454 GLN d 101 HIS d 425 ASN A 135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.080424 restraints weight = 45273.609| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.99 r_work: 0.2841 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29921 Z= 0.113 Angle : 0.492 11.858 40636 Z= 0.254 Chirality : 0.041 0.142 4729 Planarity : 0.004 0.065 5341 Dihedral : 6.052 86.741 4333 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.87 % Favored : 97.08 % Rotamer: Outliers : 1.26 % Allowed : 11.15 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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: 1.28 (0.14), residues: 3837 helix: 2.42 (0.13), residues: 1683 sheet: 0.69 (0.23), residues: 513 loop : -0.80 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 134 TYR 0.012 0.001 TYR G 92 PHE 0.014 0.001 PHE G 190 TRP 0.008 0.001 TRP A 247 HIS 0.002 0.001 HIS C 474 Details of bonding type rmsd covalent geometry : bond 0.00252 (29921) covalent geometry : angle 0.49231 (40636) hydrogen bonds : bond 0.04702 ( 1512) hydrogen bonds : angle 4.07830 ( 4377) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 1.178 Fit side-chains REVERT: B 29 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6702 (pt0) REVERT: B 72 ARG cc_start: 0.7980 (mmt90) cc_final: 0.7745 (tpp-160) REVERT: B 409 PHE cc_start: 0.7970 (m-10) cc_final: 0.7650 (m-80) REVERT: B 505 ASN cc_start: 0.8689 (m-40) cc_final: 0.8307 (m-40) REVERT: F 379 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7386 (mtp-110) REVERT: F 457 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.7911 (t80) REVERT: F 472 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7602 (mp) REVERT: G 51 THR cc_start: 0.7817 (m) cc_final: 0.7492 (p) REVERT: G 65 HIS cc_start: 0.7185 (t-90) cc_final: 0.6856 (t70) REVERT: H 1 MET cc_start: 0.4948 (pmm) cc_final: 0.4370 (ttp) REVERT: b 117 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7536 (p0) REVERT: b 118 MET cc_start: 0.6541 (ttm) cc_final: 0.6121 (tmm) REVERT: b 131 GLU cc_start: 0.7743 (tp30) cc_final: 0.7152 (mm-30) REVERT: d 181 GLU cc_start: 0.8314 (mp0) cc_final: 0.7740 (mp0) REVERT: d 228 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7291 (tm-30) REVERT: d 419 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7947 (tt) REVERT: A 436 ASN cc_start: 0.8638 (t0) cc_final: 0.8362 (t0) REVERT: A 469 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7279 (mp10) outliers start: 39 outliers final: 21 residues processed: 183 average time/residue: 0.7676 time to fit residues: 161.3057 Evaluate side-chains 174 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 379 ARG Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 454 GLN Chi-restraints excluded: chain F residue 457 PHE Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain b residue 117 ASP Chi-restraints excluded: chain d residue 106 ILE Chi-restraints excluded: chain d residue 228 GLU Chi-restraints excluded: chain d residue 294 ILE Chi-restraints excluded: chain d residue 358 VAL Chi-restraints excluded: chain d residue 419 LEU Chi-restraints excluded: chain d residue 426 ILE Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 469 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 chunk 306 optimal weight: 0.9990 chunk 240 optimal weight: 0.1980 chunk 282 optimal weight: 0.9980 chunk 375 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 330 optimal weight: 10.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 454 GLN G 125 ASN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.114524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.080795 restraints weight = 45170.097| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.04 r_work: 0.2844 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29921 Z= 0.107 Angle : 0.488 10.927 40636 Z= 0.252 Chirality : 0.040 0.140 4729 Planarity : 0.004 0.067 5341 Dihedral : 5.957 87.471 4331 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.11 % Rotamer: Outliers : 1.13 % Allowed : 11.31 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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: 1.33 (0.14), residues: 3837 helix: 2.46 (0.13), residues: 1683 sheet: 0.72 (0.23), residues: 513 loop : -0.79 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 134 TYR 0.011 0.001 TYR G 92 PHE 0.016 0.001 PHE F 456 TRP 0.008 0.001 TRP A 247 HIS 0.006 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00232 (29921) covalent geometry : angle 0.48825 (40636) hydrogen bonds : bond 0.04560 ( 1512) hydrogen bonds : angle 4.04301 ( 4377) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: B 29 GLU cc_start: 0.7452 (mm-30) cc_final: 0.6700 (pt0) REVERT: B 72 ARG cc_start: 0.7986 (mmt90) cc_final: 0.7763 (tpp-160) REVERT: B 409 PHE cc_start: 0.7934 (m-10) cc_final: 0.7621 (m-80) REVERT: B 505 ASN cc_start: 0.8649 (m-40) cc_final: 0.8259 (m-40) REVERT: F 379 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7386 (mtp-110) REVERT: F 457 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.7953 (t80) REVERT: G 51 THR cc_start: 0.7794 (m) cc_final: 0.7449 (p) REVERT: G 65 HIS cc_start: 0.7174 (t-90) cc_final: 0.6834 (t-90) REVERT: H 1 MET cc_start: 0.4950 (pmm) cc_final: 0.4381 (ttp) REVERT: b 117 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7574 (p0) REVERT: b 118 MET cc_start: 0.6447 (ttm) cc_final: 0.6048 (tmm) REVERT: b 131 GLU cc_start: 0.7713 (tp30) cc_final: 0.7101 (mm-30) REVERT: d 181 GLU cc_start: 0.8321 (mp0) cc_final: 0.7774 (mp0) REVERT: d 228 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7287 (tm-30) REVERT: d 419 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7921 (tt) REVERT: A 436 ASN cc_start: 0.8640 (t0) cc_final: 0.8354 (t0) REVERT: A 469 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7277 (mp10) outliers start: 35 outliers final: 19 residues processed: 185 average time/residue: 0.7716 time to fit residues: 164.9993 Evaluate side-chains 173 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 379 ARG Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 457 PHE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain b residue 117 ASP Chi-restraints excluded: chain d residue 106 ILE Chi-restraints excluded: chain d residue 228 GLU Chi-restraints excluded: chain d residue 294 ILE Chi-restraints excluded: chain d residue 358 VAL Chi-restraints excluded: chain d residue 419 LEU Chi-restraints excluded: chain d residue 426 ILE Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 469 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 75 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 118 optimal weight: 0.3980 chunk 256 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 308 optimal weight: 1.9990 chunk 346 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 454 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.080318 restraints weight = 45442.603| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.06 r_work: 0.2836 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29921 Z= 0.115 Angle : 0.493 10.350 40636 Z= 0.255 Chirality : 0.041 0.145 4729 Planarity : 0.004 0.068 5341 Dihedral : 5.957 87.580 4331 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.03 % Rotamer: Outliers : 1.10 % Allowed : 11.51 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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: 1.34 (0.14), residues: 3837 helix: 2.47 (0.13), residues: 1683 sheet: 0.71 (0.23), residues: 523 loop : -0.78 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 134 TYR 0.012 0.001 TYR G 92 PHE 0.015 0.001 PHE G 190 TRP 0.008 0.001 TRP A 247 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00257 (29921) covalent geometry : angle 0.49324 (40636) hydrogen bonds : bond 0.04665 ( 1512) hydrogen bonds : angle 4.05356 ( 4377) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9628.95 seconds wall clock time: 164 minutes 56.53 seconds (9896.53 seconds total)