Starting phenix.real_space_refine on Sat Jul 4 22:49:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l1q_23115/07_2026/7l1q_23115.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l1q_23115/07_2026/7l1q_23115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l1q_23115/07_2026/7l1q_23115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l1q_23115/07_2026/7l1q_23115.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7l1q_23115/07_2026/7l1q_23115.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l1q_23115/07_2026/7l1q_23115.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l1q_23115/07_2026/7l1q_23115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l1q_23115/07_2026/7l1q_23115.map" } resolution = 3.4 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= 0.005 sd= 0.049 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 18 5.49 5 Mg 6 5.21 5 S 78 5.16 5 C 15235 2.51 5 N 4214 2.21 5 O 4653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 250 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24204 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3636 Classifications: {'peptide': 474} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 451} Chain: "B" Number of atoms: 3643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3643 Classifications: {'peptide': 475} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 452} Chain: "C" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3649 Classifications: {'peptide': 476} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 453} Chain: "D" Number of atoms: 3621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3621 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3622 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3629 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2211 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 271} 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} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" 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: "F" 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: 5.51, per 1000 atoms: 0.23 Number of scatterers: 24204 At special positions: 0 Unit cell: (141.12, 120.96, 131.88, 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 78 16.00 P 18 15.00 Mg 6 11.99 O 4653 8.00 N 4214 7.00 C 15235 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: 1.59 Conformation dependent library (CDL) restraints added in 1.1 seconds 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5690 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 22 sheets defined 47.3% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 231 through 253 removed outlier: 3.764A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.508A pdb=" N GLY A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 288 No H-bonds generated for 'chain 'A' and resid 287 through 288' Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.686A pdb=" N ILE A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 372 through 394 removed outlier: 3.728A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 399 removed outlier: 4.429A pdb=" N PHE A 398 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 399 " --> pdb=" O ALA A 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 395 through 399' Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.566A pdb=" N GLN A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 443 through 447 removed outlier: 4.338A pdb=" N ASP A 447 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.658A pdb=" N PHE A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A 457 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 removed outlier: 3.629A pdb=" N LEU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.827A pdb=" N ASN A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LYS A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.595A pdb=" N ARG B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 220 removed outlier: 3.648A pdb=" N TYR B 220 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 removed outlier: 3.503A pdb=" N LEU B 237 " --> pdb=" O PRO B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 253 removed outlier: 3.739A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.570A pdb=" N GLU B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 338 removed outlier: 3.832A pdb=" N ILE B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 358 through 362 Processing helix chain 'B' and resid 372 through 380 removed outlier: 4.013A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 399 removed outlier: 3.825A pdb=" N PHE B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 421 removed outlier: 3.622A pdb=" N ALA B 411 " --> pdb=" O GLN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 449 through 468 removed outlier: 3.888A pdb=" N ARG B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLN B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.627A pdb=" N LYS B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 38 removed outlier: 4.543A pdb=" N GLY C 37 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.891A pdb=" N VAL C 178 " --> pdb=" O GLY C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 217 through 221 removed outlier: 4.166A pdb=" N TYR C 220 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR C 221 " --> pdb=" O LEU C 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 217 through 221' Processing helix chain 'C' and resid 231 through 237 removed outlier: 3.767A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 253 removed outlier: 4.089A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 4.000A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 328 through 338 Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 372 through 397 removed outlier: 3.583A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 429 through 442 removed outlier: 3.796A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 467 removed outlier: 3.626A pdb=" N LYS C 458 " --> pdb=" O ARG C 454 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.535A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 498 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 179 Processing helix chain 'D' and resid 191 through 205 removed outlier: 3.523A pdb=" N GLY D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN D 196 " --> pdb=" O THR D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 211 removed outlier: 4.214A pdb=" N LYS D 210 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR D 211 " --> pdb=" O ILE D 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 207 through 211' Processing helix chain 'D' and resid 221 through 244 removed outlier: 3.605A pdb=" N VAL D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 Processing helix chain 'D' and resid 280 through 291 removed outlier: 3.877A pdb=" N GLU D 284 " --> pdb=" O THR D 280 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 323 removed outlier: 4.288A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.517A pdb=" N ALA D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 379 Processing helix chain 'D' and resid 380 through 387 Processing helix chain 'D' and resid 388 through 392 Processing helix chain 'D' and resid 393 through 410 Processing helix chain 'D' and resid 416 through 421 removed outlier: 4.068A pdb=" N PHE D 420 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 444 through 448 removed outlier: 4.334A pdb=" N HIS D 447 " --> pdb=" O LYS D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 458 through 470 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 164 through 178 Processing helix chain 'E' and resid 191 through 206 Processing helix chain 'E' and resid 221 through 242 removed outlier: 4.381A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 269 Processing helix chain 'E' and resid 280 through 290 removed outlier: 3.654A pdb=" N LEU E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 325 removed outlier: 3.952A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 387 removed outlier: 4.019A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 392 Processing helix chain 'E' and resid 393 through 410 Processing helix chain 'E' and resid 415 through 421 removed outlier: 4.230A pdb=" N GLN E 419 " --> pdb=" O HIS E 415 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE E 420 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 443 Processing helix chain 'E' and resid 444 through 448 removed outlier: 4.362A pdb=" N HIS E 447 " --> pdb=" O LYS E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 454 removed outlier: 3.695A pdb=" N ARG E 454 " --> pdb=" O ASP E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.560A pdb=" N LYS E 467 " --> pdb=" O VAL E 463 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 removed outlier: 3.504A pdb=" N LEU F 92 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 145 Processing helix chain 'F' and resid 163 through 176 removed outlier: 3.666A pdb=" N LEU F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 205 Processing helix chain 'F' and resid 206 through 210 removed outlier: 3.503A pdb=" N SER F 209 " --> pdb=" O GLY F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 243 removed outlier: 3.506A pdb=" N ARG F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.917A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 292 removed outlier: 3.912A pdb=" N GLU F 284 " --> pdb=" O THR F 280 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG F 291 " --> pdb=" O GLN F 287 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE F 292 " --> pdb=" O LEU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 322 removed outlier: 3.634A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 removed outlier: 3.547A pdb=" N ALA F 336 " --> pdb=" O GLU F 332 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 388 removed outlier: 3.748A pdb=" N VAL F 366 " --> pdb=" O GLU F 362 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU F 379 " --> pdb=" O GLN F 375 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 6.161A pdb=" N SER F 393 " --> pdb=" O ASP F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 410 removed outlier: 3.774A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 420 removed outlier: 3.891A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 458 through 469 Processing helix chain 'G' and resid 7 through 62 removed outlier: 4.164A pdb=" N THR G 12 " --> pdb=" O ARG G 8 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) Proline residue: G 47 - end of helix removed outlier: 4.178A pdb=" N GLY G 62 " --> pdb=" O ASN G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 111 removed outlier: 3.764A pdb=" N VAL G 98 " --> pdb=" O TYR G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 148 through 165 removed outlier: 3.676A pdb=" N ILE G 152 " --> pdb=" O SER G 148 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE G 155 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 287 removed outlier: 3.768A pdb=" N CYS G 215 " --> pdb=" O SER G 211 " (cutoff:3.500A) Proline residue: G 221 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 34 removed outlier: 6.305A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 39 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN A 65 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 76 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLY A 61 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.462A pdb=" N VAL A 256 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N LEU A 316 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL A 258 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 35 removed outlier: 6.348A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ARG B 93 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.230A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.344A pdb=" N VAL B 108 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 258 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N PHE B 318 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR B 260 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N GLU B 320 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 28 through 33 removed outlier: 6.090A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN C 65 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 99 Processing sheet with id=AB1, first strand: chain 'C' and resid 107 through 108 removed outlier: 3.998A pdb=" N LEU C 257 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 10 removed outlier: 3.976A pdb=" N ARG D 5 " --> pdb=" O LYS D 17 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB4, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.261A pdb=" N PHE D 96 " --> pdb=" O PHE D 215 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLN D 217 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA D 327 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 3 through 10 removed outlier: 3.696A pdb=" N ARG E 5 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASN E 28 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ALA E 29 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.591A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR E 301 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA E 305 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS E 153 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N THR E 329 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY E 155 " --> pdb=" O THR E 329 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU E 331 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE E 157 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 4 through 10 removed outlier: 4.020A pdb=" N ARG F 5 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE F 44 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS F 34 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 85 through 86 Processing sheet with id=AC1, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.611A pdb=" N PHE F 96 " --> pdb=" O PHE F 215 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N GLN F 217 " --> pdb=" O PHE F 96 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY F 189 " --> pdb=" O GLY F 216 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA F 305 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS F 153 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N THR F 329 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY F 155 " --> pdb=" O THR F 329 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU F 331 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE F 157 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 133 through 134 removed outlier: 4.640A pdb=" N GLU F 133 " --> pdb=" O LYS F 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 136 through 140 removed outlier: 7.916A pdb=" N ILE G 137 " --> pdb=" O TYR G 116 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ILE G 118 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP G 139 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL G 120 " --> pdb=" O ASP G 139 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR G 79 " --> pdb=" O ALA G 117 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE G 119 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N TYR G 81 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE G 121 " --> pdb=" O TYR G 81 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL G 83 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE G 84 " --> pdb=" O TYR G 174 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU G 171 " --> pdb=" O LEU G 191 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 176 through 177 1143 hydrogen bonds defined for protein. 3267 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.31 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4497 1.32 - 1.44: 5579 1.44 - 1.57: 14350 1.57 - 1.69: 28 1.69 - 1.81: 154 Bond restraints: 24608 Sorted by residual: bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.476 -0.088 1.00e-02 1.00e+04 7.83e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.13e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.18e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.93e+01 bond pdb=" C8 ATP B 600 " pdb=" N7 ATP B 600 " ideal model delta sigma weight residual 1.310 1.365 -0.055 1.00e-02 1.00e+04 3.03e+01 ... (remaining 24603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.19: 32987 4.19 - 8.37: 364 8.37 - 12.56: 11 12.56 - 16.74: 3 16.74 - 20.93: 5 Bond angle restraints: 33370 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 118.94 20.93 1.00e+00 1.00e+00 4.38e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.65 20.18 1.00e+00 1.00e+00 4.07e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 121.88 17.99 1.00e+00 1.00e+00 3.24e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 122.90 16.97 1.00e+00 1.00e+00 2.88e+02 angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 122.97 16.90 1.00e+00 1.00e+00 2.86e+02 ... (remaining 33365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.19: 13755 21.19 - 42.39: 945 42.39 - 63.58: 152 63.58 - 84.78: 32 84.78 - 105.97: 5 Dihedral angle restraints: 14889 sinusoidal: 5997 harmonic: 8892 Sorted by residual: dihedral pdb=" C THR B 204 " pdb=" N THR B 204 " pdb=" CA THR B 204 " pdb=" CB THR B 204 " ideal model delta harmonic sigma weight residual -122.00 -137.70 15.70 0 2.50e+00 1.60e-01 3.95e+01 dihedral pdb=" CA GLU C 284 " pdb=" C GLU C 284 " pdb=" N ALA C 285 " pdb=" CA ALA C 285 " ideal model delta harmonic sigma weight residual 180.00 151.59 28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA GLY C 35 " pdb=" C GLY C 35 " pdb=" N ASP C 36 " pdb=" CA ASP C 36 " ideal model delta harmonic sigma weight residual 180.00 151.80 28.20 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 14886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3338 0.101 - 0.203: 466 0.203 - 0.304: 28 0.304 - 0.406: 6 0.406 - 0.507: 2 Chirality restraints: 3840 Sorted by residual: chirality pdb=" CA THR B 204 " pdb=" N THR B 204 " pdb=" C THR B 204 " pdb=" CB THR B 204 " both_signs ideal model delta sigma weight residual False 2.53 2.02 0.51 2.00e-01 2.50e+01 6.42e+00 chirality pdb=" CA HIS A 425 " pdb=" N HIS A 425 " pdb=" C HIS A 425 " pdb=" CB HIS A 425 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CA ARG C 454 " pdb=" N ARG C 454 " pdb=" C ARG C 454 " pdb=" CB ARG C 454 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 3837 not shown) Planarity restraints: 4349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 296 " -0.348 9.50e-02 1.11e+02 1.61e-01 3.64e+01 pdb=" NE ARG B 296 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG B 296 " 0.084 2.00e-02 2.50e+03 pdb=" NH1 ARG B 296 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG B 296 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 435 " 0.336 9.50e-02 1.11e+02 1.55e-01 3.04e+01 pdb=" NE ARG D 435 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG D 435 " -0.074 2.00e-02 2.50e+03 pdb=" NH1 ARG D 435 " 0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG D 435 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 161 " 0.129 9.50e-02 1.11e+02 7.38e-02 2.83e+01 pdb=" NE ARG A 161 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A 161 " 0.087 2.00e-02 2.50e+03 pdb=" NH1 ARG A 161 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG A 161 " -0.024 2.00e-02 2.50e+03 ... (remaining 4346 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 24 2.43 - 3.04: 14858 3.04 - 3.66: 34419 3.66 - 4.28: 51443 4.28 - 4.90: 88052 Nonbonded interactions: 188796 Sorted by model distance: nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.807 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 501 " model vdw 2.058 2.170 nonbonded pdb=" O1G ATP B 600 " pdb="MG MG B 601 " model vdw 2.067 2.170 nonbonded pdb=" OE1 GLU E 194 " pdb="MG MG E 502 " model vdw 2.151 2.170 nonbonded pdb=" O2G ATP E 501 " pdb="MG MG E 502 " model vdw 2.161 2.170 ... (remaining 188791 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 27 through 499) selection = (chain 'B' and resid 27 through 499) selection = (chain 'C' and resid 27 through 499) } ncs_group { reference = (chain 'D' and resid 2 through 470) selection = (chain 'E' and resid 2 through 470) selection = (chain 'F' and resid 2 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.420 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 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 : 0.008 0.105 24608 Z= 0.436 Angle : 1.295 20.929 33370 Z= 0.838 Chirality : 0.068 0.507 3840 Planarity : 0.011 0.161 4349 Dihedral : 14.917 105.970 9199 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.70 % Favored : 96.13 % Rotamer: Outliers : 2.54 % Allowed : 12.24 % Favored : 85.22 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3104 helix: -0.40 (0.13), residues: 1253 sheet: -0.16 (0.22), residues: 500 loop : -0.63 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.089 0.011 ARG A 161 TYR 0.054 0.007 TYR C 438 PHE 0.057 0.005 PHE A 236 HIS 0.013 0.003 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00793 / 0.44 (24608) covalent geometry : angle 1.29484 / 0.84 (33370) hydrogen bonds : bond 0.18499 / 12.65 ( 1143) hydrogen bonds : angle 7.59576 / 5.38 ( 3267) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1127 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 1062 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ILE cc_start: 0.7669 (mm) cc_final: 0.7371 (tt) REVERT: A 190 ASN cc_start: 0.7620 (m-40) cc_final: 0.7233 (m-40) REVERT: A 214 LYS cc_start: 0.7555 (tttt) cc_final: 0.7303 (tttt) REVERT: A 333 ASN cc_start: 0.7541 (t0) cc_final: 0.7302 (t0) REVERT: A 415 ARG cc_start: 0.7852 (mtt90) cc_final: 0.7505 (mtt90) REVERT: A 417 VAL cc_start: 0.8583 (t) cc_final: 0.8352 (m) REVERT: A 420 LEU cc_start: 0.8207 (mp) cc_final: 0.7913 (mt) REVERT: A 432 LYS cc_start: 0.7861 (mttt) cc_final: 0.7135 (mtpp) REVERT: A 456 PHE cc_start: 0.7658 (t80) cc_final: 0.7399 (t80) REVERT: B 32 ILE cc_start: 0.8331 (tt) cc_final: 0.7890 (tt) REVERT: B 45 ASP cc_start: 0.6434 (p0) cc_final: 0.6207 (p0) REVERT: B 88 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7909 (p) REVERT: B 150 ILE cc_start: 0.8228 (mt) cc_final: 0.7342 (mt) REVERT: B 154 ASP cc_start: 0.7528 (m-30) cc_final: 0.7222 (m-30) REVERT: B 175 LYS cc_start: 0.7543 (mtmm) cc_final: 0.7068 (mtmm) REVERT: B 184 ILE cc_start: 0.7744 (mt) cc_final: 0.7507 (tp) REVERT: B 230 GLN cc_start: 0.6724 (mm-40) cc_final: 0.6459 (mm-40) REVERT: B 243 VAL cc_start: 0.7452 (m) cc_final: 0.7236 (t) REVERT: B 373 LYS cc_start: 0.7641 (ttmt) cc_final: 0.7149 (ttmt) REVERT: B 377 LYS cc_start: 0.7910 (mttp) cc_final: 0.7595 (mttp) REVERT: B 424 LEU cc_start: 0.7913 (tp) cc_final: 0.7653 (tp) REVERT: B 452 ASP cc_start: 0.6625 (m-30) cc_final: 0.6386 (t0) REVERT: B 470 HIS cc_start: 0.7689 (p90) cc_final: 0.7415 (p-80) REVERT: C 202 GLU cc_start: 0.6807 (tt0) cc_final: 0.6547 (tt0) REVERT: C 206 ARG cc_start: 0.7191 (ttt180) cc_final: 0.6852 (tpp-160) REVERT: C 227 SER cc_start: 0.7186 (p) cc_final: 0.6580 (p) REVERT: C 434 VAL cc_start: 0.7791 (m) cc_final: 0.7444 (p) REVERT: C 452 ASP cc_start: 0.7178 (m-30) cc_final: 0.6957 (m-30) REVERT: C 474 HIS cc_start: 0.6663 (t70) cc_final: 0.6315 (t70) REVERT: C 480 ASP cc_start: 0.6697 (t0) cc_final: 0.6357 (t0) REVERT: D 18 PHE cc_start: 0.7504 (m-80) cc_final: 0.7131 (m-80) REVERT: D 35 LYS cc_start: 0.7908 (ttmt) cc_final: 0.7699 (ttmt) REVERT: D 44 ILE cc_start: 0.7474 (tp) cc_final: 0.7230 (tp) REVERT: D 45 ASP cc_start: 0.6683 (t0) cc_final: 0.6176 (t0) REVERT: D 66 SER cc_start: 0.6800 (t) cc_final: 0.6523 (m) REVERT: D 104 ASP cc_start: 0.7583 (p0) cc_final: 0.6976 (p0) REVERT: D 191 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6673 (mtt180) REVERT: D 213 MET cc_start: 0.7084 (mtp) cc_final: 0.6865 (mtp) REVERT: D 271 MET cc_start: 0.6352 (mtt) cc_final: 0.5521 (mtt) REVERT: D 275 VAL cc_start: 0.8418 (t) cc_final: 0.8094 (t) REVERT: D 308 VAL cc_start: 0.8668 (t) cc_final: 0.8434 (m) REVERT: D 333 ARG cc_start: 0.6760 (ttm110) cc_final: 0.6558 (ttm110) REVERT: D 334 LYS cc_start: 0.7477 (ttpt) cc_final: 0.7167 (ttpt) REVERT: D 401 HIS cc_start: 0.6358 (t70) cc_final: 0.5404 (t70) REVERT: D 405 ARG cc_start: 0.7057 (mpt180) cc_final: 0.6646 (mpt180) REVERT: D 441 LEU cc_start: 0.8432 (mt) cc_final: 0.8190 (mp) REVERT: D 464 GLU cc_start: 0.7391 (tp30) cc_final: 0.7024 (tp30) REVERT: E 10 MET cc_start: 0.5754 (mtp) cc_final: 0.5433 (mtp) REVERT: E 44 ILE cc_start: 0.6401 (tp) cc_final: 0.6160 (tp) REVERT: E 101 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6552 (mp0) REVERT: E 136 GLU cc_start: 0.5765 (tt0) cc_final: 0.5481 (tt0) REVERT: E 168 ILE cc_start: 0.8685 (mm) cc_final: 0.8454 (mm) REVERT: E 197 ASP cc_start: 0.6279 (t0) cc_final: 0.6020 (t0) REVERT: E 201 GLU cc_start: 0.6676 (tp30) cc_final: 0.6199 (tp30) REVERT: E 207 VAL cc_start: 0.7471 (t) cc_final: 0.7215 (p) REVERT: E 372 GLN cc_start: 0.7623 (mt0) cc_final: 0.7303 (mt0) REVERT: E 389 MET cc_start: 0.7091 (mmm) cc_final: 0.6845 (mmm) REVERT: E 405 ARG cc_start: 0.7391 (mpt180) cc_final: 0.7188 (mpt180) REVERT: E 410 LEU cc_start: 0.8395 (mt) cc_final: 0.8177 (mt) REVERT: E 411 SER cc_start: 0.7834 (m) cc_final: 0.7549 (p) REVERT: E 419 GLN cc_start: 0.7452 (pt0) cc_final: 0.6863 (pm20) REVERT: E 432 GLU cc_start: 0.6463 (mm-30) cc_final: 0.5442 (mm-30) REVERT: E 450 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6321 (pm20) REVERT: E 453 PHE cc_start: 0.7865 (m-80) cc_final: 0.7589 (m-80) REVERT: E 469 MET cc_start: 0.5663 (mmm) cc_final: 0.5354 (mmm) REVERT: F 38 ASN cc_start: 0.7681 (t0) cc_final: 0.7257 (t0) REVERT: F 39 GLU cc_start: 0.6959 (pp20) cc_final: 0.6725 (pp20) REVERT: F 47 THR cc_start: 0.6921 (t) cc_final: 0.6707 (p) REVERT: F 77 ILE cc_start: 0.6162 (OUTLIER) cc_final: 0.5683 (mt) REVERT: F 240 ARG cc_start: 0.5653 (OUTLIER) cc_final: 0.5325 (ppt90) REVERT: F 241 ASP cc_start: 0.7103 (m-30) cc_final: 0.6703 (m-30) REVERT: F 285 MET cc_start: 0.6887 (ttp) cc_final: 0.6530 (ttt) REVERT: F 331 LEU cc_start: 0.7755 (mt) cc_final: 0.7357 (mt) REVERT: F 366 VAL cc_start: 0.7550 (t) cc_final: 0.7017 (p) REVERT: F 377 TYR cc_start: 0.7842 (t80) cc_final: 0.7494 (t80) REVERT: F 438 LYS cc_start: 0.7942 (tttt) cc_final: 0.7652 (tttt) REVERT: F 456 VAL cc_start: 0.6235 (p) cc_final: 0.5742 (m) REVERT: G 12 THR cc_start: 0.8066 (p) cc_final: 0.7845 (t) REVERT: G 19 LYS cc_start: 0.8018 (mptt) cc_final: 0.7732 (mptt) REVERT: G 43 LYS cc_start: 0.8519 (ttpt) cc_final: 0.8252 (ttpt) REVERT: G 48 TYR cc_start: 0.7508 (t80) cc_final: 0.7266 (t80) REVERT: G 49 MET cc_start: 0.7640 (mmt) cc_final: 0.7431 (mmt) REVERT: G 70 MET cc_start: 0.7766 (mmp) cc_final: 0.7474 (mmp) REVERT: G 97 ASN cc_start: 0.7656 (m-40) cc_final: 0.6846 (m-40) REVERT: G 148 SER cc_start: 0.8579 (m) cc_final: 0.8346 (p) REVERT: G 149 PHE cc_start: 0.6840 (t80) cc_final: 0.6640 (t80) REVERT: G 222 GLN cc_start: 0.7570 (mt0) cc_final: 0.7337 (mt0) REVERT: G 265 TYR cc_start: 0.7740 (t80) cc_final: 0.7034 (t80) REVERT: G 269 ARG cc_start: 0.7140 (ttp80) cc_final: 0.6763 (ttp80) REVERT: G 270 GLN cc_start: 0.7319 (mt0) cc_final: 0.6929 (mt0) REVERT: G 275 GLN cc_start: 0.7426 (tp40) cc_final: 0.6321 (tp40) REVERT: G 279 GLU cc_start: 0.6698 (mm-30) cc_final: 0.6452 (mm-30) outliers start: 65 outliers final: 13 residues processed: 1101 average time/residue: 0.1735 time to fit residues: 285.3022 Evaluate side-chains 1004 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 985 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 322 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 0.0770 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 GLN A 113 GLN A 397 GLN A 422 GLN ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN A 470 HIS A 474 HIS B 470 HIS B 474 HIS B 488 ASN C 69 ASN C 185 ASN D 33 GLN D 200 HIS D 259 GLN D 372 GLN E 33 GLN E 174 ASN E 177 GLN E 259 GLN E 287 GLN E 371 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN F 33 GLN F 287 GLN F 304 GLN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN ** F 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN G 95 ASN G 107 GLN G 184 GLN G 266 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.147666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.128992 restraints weight = 40233.236| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.13 r_work: 0.3656 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24608 Z= 0.159 Angle : 0.697 19.359 33370 Z= 0.365 Chirality : 0.048 0.218 3840 Planarity : 0.005 0.061 4349 Dihedral : 7.000 85.296 3454 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.38 % Favored : 97.58 % Rotamer: Outliers : 4.96 % Allowed : 19.55 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.15), residues: 3104 helix: 0.78 (0.14), residues: 1288 sheet: 0.36 (0.23), residues: 483 loop : -0.62 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG A 278 TYR 0.023 0.002 TYR G 103 PHE 0.027 0.002 PHE B 236 HIS 0.009 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (24608) covalent geometry : angle 0.69671 / 0.37 (33370) hydrogen bonds : bond 0.05765 / 3.94 ( 1143) hydrogen bonds : angle 5.50390 / 3.92 ( 3267) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 986 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.7329 (t) cc_final: 0.6793 (m) REVERT: A 57 ASN cc_start: 0.8125 (m-40) cc_final: 0.7921 (m-40) REVERT: A 62 MET cc_start: 0.7440 (ptp) cc_final: 0.6838 (ptm) REVERT: A 87 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6658 (mm-30) REVERT: A 164 ARG cc_start: 0.7130 (mtm110) cc_final: 0.6666 (mtm-85) REVERT: A 172 GLN cc_start: 0.7444 (mm-40) cc_final: 0.7208 (mm-40) REVERT: A 190 ASN cc_start: 0.7788 (m-40) cc_final: 0.7355 (m-40) REVERT: A 191 MET cc_start: 0.6733 (mmm) cc_final: 0.6125 (mmm) REVERT: A 214 LYS cc_start: 0.8360 (tttt) cc_final: 0.8132 (ttpp) REVERT: A 245 MET cc_start: 0.7291 (mtt) cc_final: 0.7077 (mtt) REVERT: A 283 ARG cc_start: 0.7894 (ttm110) cc_final: 0.7402 (mtp85) REVERT: A 284 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7707 (mt-10) REVERT: A 341 GLN cc_start: 0.7905 (pm20) cc_final: 0.7460 (pm20) REVERT: A 363 VAL cc_start: 0.7715 (p) cc_final: 0.7386 (m) REVERT: A 365 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.7000 (mtp85) REVERT: A 377 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7734 (mptt) REVERT: A 397 GLN cc_start: 0.6401 (OUTLIER) cc_final: 0.6051 (pm20) REVERT: A 415 ARG cc_start: 0.8250 (mtt90) cc_final: 0.7885 (mtt90) REVERT: A 432 LYS cc_start: 0.8089 (mttt) cc_final: 0.7438 (mtpp) REVERT: A 456 PHE cc_start: 0.8002 (t80) cc_final: 0.7715 (t80) REVERT: B 80 THR cc_start: 0.8352 (p) cc_final: 0.7897 (m) REVERT: B 87 GLU cc_start: 0.7307 (tt0) cc_final: 0.6752 (tt0) REVERT: B 88 VAL cc_start: 0.8167 (t) cc_final: 0.7816 (p) REVERT: B 93 ARG cc_start: 0.7398 (mmm160) cc_final: 0.6866 (mmm160) REVERT: B 172 GLN cc_start: 0.6367 (mm-40) cc_final: 0.6116 (mm-40) REVERT: B 196 VAL cc_start: 0.7653 (t) cc_final: 0.7384 (m) REVERT: B 230 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7363 (mm-40) REVERT: B 272 GLU cc_start: 0.7771 (tt0) cc_final: 0.7264 (tt0) REVERT: B 305 SER cc_start: 0.7295 (m) cc_final: 0.6914 (m) REVERT: B 321 THR cc_start: 0.7796 (OUTLIER) cc_final: 0.7519 (t) REVERT: B 335 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8169 (tt) REVERT: B 341 GLN cc_start: 0.7311 (pm20) cc_final: 0.6928 (pt0) REVERT: B 373 LYS cc_start: 0.7671 (ttmt) cc_final: 0.7181 (ttmt) REVERT: B 392 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7811 (tp) REVERT: B 470 HIS cc_start: 0.7647 (p-80) cc_final: 0.7374 (p-80) REVERT: C 62 MET cc_start: 0.6864 (tpt) cc_final: 0.6662 (tpt) REVERT: C 173 THR cc_start: 0.8148 (m) cc_final: 0.7835 (p) REVERT: C 206 ARG cc_start: 0.7662 (ttt180) cc_final: 0.7109 (tpp-160) REVERT: C 210 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6774 (mm-30) REVERT: C 265 LYS cc_start: 0.8168 (mttp) cc_final: 0.7953 (mttp) REVERT: C 273 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8164 (mm) REVERT: C 277 LEU cc_start: 0.8095 (mt) cc_final: 0.7857 (mm) REVERT: C 361 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7519 (tp) REVERT: C 375 MET cc_start: 0.7347 (tpp) cc_final: 0.7073 (tpp) REVERT: C 409 LYS cc_start: 0.7962 (tptt) cc_final: 0.7760 (mtpp) REVERT: C 433 GLN cc_start: 0.7999 (mt0) cc_final: 0.7595 (mt0) REVERT: C 480 ASP cc_start: 0.7123 (t0) cc_final: 0.6876 (t0) REVERT: C 484 GLU cc_start: 0.7103 (tt0) cc_final: 0.6844 (tt0) REVERT: D 8 GLN cc_start: 0.7753 (tt0) cc_final: 0.7359 (tt0) REVERT: D 17 LYS cc_start: 0.7666 (tmtt) cc_final: 0.7351 (tmtt) REVERT: D 18 PHE cc_start: 0.7583 (m-80) cc_final: 0.7274 (m-80) REVERT: D 35 LYS cc_start: 0.7938 (ttmt) cc_final: 0.7716 (ttmt) REVERT: D 41 GLU cc_start: 0.6512 (mt-10) cc_final: 0.6295 (mp0) REVERT: D 104 ASP cc_start: 0.7704 (p0) cc_final: 0.7219 (p0) REVERT: D 106 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6958 (mt-10) REVERT: D 120 ARG cc_start: 0.7332 (ttt-90) cc_final: 0.7020 (ptt-90) REVERT: D 124 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.7040 (mtpp) REVERT: D 128 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8029 (tt) REVERT: D 157 PHE cc_start: 0.7472 (m-80) cc_final: 0.7190 (m-80) REVERT: D 202 MET cc_start: 0.7408 (mmt) cc_final: 0.6730 (mmt) REVERT: D 207 VAL cc_start: 0.8485 (t) cc_final: 0.7514 (p) REVERT: D 213 MET cc_start: 0.7988 (mtp) cc_final: 0.7779 (mtp) REVERT: D 243 GLN cc_start: 0.7383 (mm-40) cc_final: 0.7086 (mp10) REVERT: D 256 ARG cc_start: 0.8079 (mtm-85) cc_final: 0.7694 (mtm110) REVERT: D 267 LEU cc_start: 0.8020 (mm) cc_final: 0.7386 (mt) REVERT: D 291 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7128 (mtt180) REVERT: D 294 SER cc_start: 0.7383 (t) cc_final: 0.6711 (p) REVERT: D 308 VAL cc_start: 0.8849 (t) cc_final: 0.8580 (m) REVERT: D 333 ARG cc_start: 0.7430 (ttm110) cc_final: 0.7228 (ttm110) REVERT: D 365 GLN cc_start: 0.7672 (mp10) cc_final: 0.7442 (pm20) REVERT: D 378 LYS cc_start: 0.8283 (tttt) cc_final: 0.7953 (ttmm) REVERT: D 386 ILE cc_start: 0.7961 (pt) cc_final: 0.7685 (mp) REVERT: D 440 ILE cc_start: 0.8682 (mm) cc_final: 0.8458 (tt) REVERT: D 441 LEU cc_start: 0.8763 (mt) cc_final: 0.8405 (mp) REVERT: D 464 GLU cc_start: 0.8089 (tp30) cc_final: 0.7649 (tp30) REVERT: E 10 MET cc_start: 0.7491 (mtp) cc_final: 0.7272 (mtp) REVERT: E 26 ILE cc_start: 0.8801 (mt) cc_final: 0.8451 (tt) REVERT: E 101 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: E 197 ASP cc_start: 0.7174 (t0) cc_final: 0.6828 (t0) REVERT: E 201 GLU cc_start: 0.7587 (tp30) cc_final: 0.6965 (tp30) REVERT: E 203 LYS cc_start: 0.7822 (tppp) cc_final: 0.7495 (tppt) REVERT: E 207 VAL cc_start: 0.7359 (t) cc_final: 0.7051 (m) REVERT: E 210 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7194 (ttpt) REVERT: E 231 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7764 (t) REVERT: E 256 ARG cc_start: 0.8015 (mmt180) cc_final: 0.7679 (tpp-160) REVERT: E 259 GLN cc_start: 0.7928 (tt0) cc_final: 0.7684 (mt0) REVERT: E 275 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8328 (t) REVERT: E 369 LYS cc_start: 0.8277 (mtmm) cc_final: 0.8059 (mttm) REVERT: E 372 GLN cc_start: 0.8060 (mt0) cc_final: 0.7760 (mt0) REVERT: E 380 LEU cc_start: 0.8231 (tp) cc_final: 0.7615 (tp) REVERT: E 384 ILE cc_start: 0.8188 (mt) cc_final: 0.7423 (mt) REVERT: E 410 LEU cc_start: 0.8515 (mt) cc_final: 0.8266 (mt) REVERT: E 412 GLN cc_start: 0.6972 (tp40) cc_final: 0.6549 (tp-100) REVERT: E 419 GLN cc_start: 0.8099 (pt0) cc_final: 0.7595 (pt0) REVERT: E 435 ARG cc_start: 0.6388 (ttp80) cc_final: 0.6032 (ttp80) REVERT: E 458 ARG cc_start: 0.6539 (ttp-110) cc_final: 0.6284 (mtp-110) REVERT: E 469 MET cc_start: 0.6069 (OUTLIER) cc_final: 0.5549 (mmm) REVERT: F 15 ASP cc_start: 0.7473 (m-30) cc_final: 0.7117 (m-30) REVERT: F 38 ASN cc_start: 0.8007 (t0) cc_final: 0.7676 (t0) REVERT: F 39 GLU cc_start: 0.7731 (pp20) cc_final: 0.7462 (pp20) REVERT: F 77 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6607 (mt) REVERT: F 202 MET cc_start: 0.7057 (mmp) cc_final: 0.6435 (mmp) REVERT: F 285 MET cc_start: 0.7366 (ttp) cc_final: 0.6758 (ttp) REVERT: F 331 LEU cc_start: 0.7748 (mt) cc_final: 0.7216 (mp) REVERT: F 332 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7281 (mm-30) REVERT: F 338 MET cc_start: 0.7514 (mtm) cc_final: 0.7156 (mtm) REVERT: F 389 MET cc_start: 0.7439 (mmm) cc_final: 0.6711 (mmm) REVERT: F 409 PHE cc_start: 0.8170 (t80) cc_final: 0.7954 (t80) REVERT: F 415 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.7216 (m-70) REVERT: F 438 LYS cc_start: 0.8281 (tttt) cc_final: 0.8042 (tttt) REVERT: G 15 ASN cc_start: 0.8650 (m-40) cc_final: 0.8379 (m110) REVERT: G 22 GLN cc_start: 0.8617 (tt0) cc_final: 0.8404 (tm-30) REVERT: G 33 SER cc_start: 0.8492 (t) cc_final: 0.8128 (p) REVERT: G 43 LYS cc_start: 0.8574 (ttpt) cc_final: 0.8347 (ttpt) REVERT: G 48 TYR cc_start: 0.7910 (t80) cc_final: 0.7622 (t80) REVERT: G 49 MET cc_start: 0.7880 (mmt) cc_final: 0.7669 (mmt) REVERT: G 94 TYR cc_start: 0.7268 (t80) cc_final: 0.7016 (t80) REVERT: G 97 ASN cc_start: 0.8083 (m-40) cc_final: 0.7854 (m-40) REVERT: G 104 GLN cc_start: 0.8623 (mt0) cc_final: 0.8367 (mt0) REVERT: G 141 THR cc_start: 0.7714 (p) cc_final: 0.7472 (m) REVERT: G 145 ASP cc_start: 0.8038 (m-30) cc_final: 0.7827 (m-30) REVERT: G 148 SER cc_start: 0.8918 (m) cc_final: 0.8614 (p) REVERT: G 190 LYS cc_start: 0.8556 (pttt) cc_final: 0.8330 (pttt) REVERT: G 222 GLN cc_start: 0.8108 (mt0) cc_final: 0.7851 (mt0) REVERT: G 239 GLU cc_start: 0.8202 (tt0) cc_final: 0.7922 (tt0) REVERT: G 269 ARG cc_start: 0.7921 (ttp80) cc_final: 0.7508 (ttp80) REVERT: G 270 GLN cc_start: 0.7870 (mt0) cc_final: 0.7453 (mt0) REVERT: G 275 GLN cc_start: 0.8250 (tp40) cc_final: 0.6823 (tp40) REVERT: G 278 THR cc_start: 0.8253 (p) cc_final: 0.7599 (p) REVERT: G 279 GLU cc_start: 0.7569 (mm-30) cc_final: 0.6942 (mm-30) outliers start: 127 outliers final: 53 residues processed: 1036 average time/residue: 0.1608 time to fit residues: 250.0678 Evaluate side-chains 1019 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 948 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 415 HIS Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 273 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 150 optimal weight: 4.9990 chunk 303 optimal weight: 0.9980 chunk 252 optimal weight: 0.3980 chunk 256 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 307 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 242 optimal weight: 0.9980 chunk 297 optimal weight: 9.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN A 333 ASN A 422 GLN A 426 GLN B 474 HIS C 69 ASN C 143 HIS C 407 GLN C 469 GLN D 200 HIS D 419 GLN ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 HIS E 174 ASN E 219 ASN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN F 196 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 HIS F 371 GLN G 253 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.146303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.127753 restraints weight = 40234.031| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.12 r_work: 0.3633 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24608 Z= 0.148 Angle : 0.638 19.604 33370 Z= 0.331 Chirality : 0.046 0.227 3840 Planarity : 0.005 0.133 4349 Dihedral : 6.165 86.740 3425 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 4.89 % Allowed : 23.49 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.15), residues: 3104 helix: 0.93 (0.14), residues: 1289 sheet: 0.29 (0.23), residues: 491 loop : -0.69 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 415 TYR 0.034 0.002 TYR G 103 PHE 0.024 0.002 PHE B 460 HIS 0.010 0.001 HIS B 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (24608) covalent geometry : angle 0.63783 / 0.33 (33370) hydrogen bonds : bond 0.05347 / 3.67 ( 1143) hydrogen bonds : angle 5.22516 / 3.74 ( 3267) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 971 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.7417 (t) cc_final: 0.6804 (m) REVERT: A 57 ASN cc_start: 0.8149 (m-40) cc_final: 0.7946 (m-40) REVERT: A 62 MET cc_start: 0.7403 (ptp) cc_final: 0.7081 (ptp) REVERT: A 79 TYR cc_start: 0.7339 (p90) cc_final: 0.7005 (p90) REVERT: A 87 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6561 (mm-30) REVERT: A 95 MET cc_start: 0.6881 (tmm) cc_final: 0.6464 (tmm) REVERT: A 125 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6706 (mm-30) REVERT: A 154 ASP cc_start: 0.8122 (m-30) cc_final: 0.7806 (t0) REVERT: A 164 ARG cc_start: 0.7124 (mtm110) cc_final: 0.6800 (mtm110) REVERT: A 170 ASP cc_start: 0.5701 (t0) cc_final: 0.5492 (t0) REVERT: A 172 GLN cc_start: 0.7249 (mm-40) cc_final: 0.6930 (mm-40) REVERT: A 181 ASP cc_start: 0.7673 (m-30) cc_final: 0.7454 (m-30) REVERT: A 190 ASN cc_start: 0.7865 (m-40) cc_final: 0.7394 (m-40) REVERT: A 191 MET cc_start: 0.6757 (mmm) cc_final: 0.6147 (mmm) REVERT: A 193 SER cc_start: 0.7448 (m) cc_final: 0.6755 (t) REVERT: A 213 ARG cc_start: 0.8330 (ttm170) cc_final: 0.8013 (ttm-80) REVERT: A 215 HIS cc_start: 0.7441 (OUTLIER) cc_final: 0.6636 (t-90) REVERT: A 245 MET cc_start: 0.7213 (mtt) cc_final: 0.6967 (mtt) REVERT: A 278 ARG cc_start: 0.8118 (mmp-170) cc_final: 0.7832 (mmp-170) REVERT: A 283 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7409 (mtp85) REVERT: A 284 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7612 (mm-30) REVERT: A 341 GLN cc_start: 0.7883 (pm20) cc_final: 0.7411 (pm20) REVERT: A 363 VAL cc_start: 0.7820 (p) cc_final: 0.7447 (m) REVERT: A 365 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.7165 (mtp85) REVERT: A 377 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7763 (mptt) REVERT: A 415 ARG cc_start: 0.8196 (mtt90) cc_final: 0.7922 (mtt90) REVERT: A 424 LEU cc_start: 0.8008 (tp) cc_final: 0.7510 (tp) REVERT: A 432 LYS cc_start: 0.7964 (mttt) cc_final: 0.7304 (mtpp) REVERT: A 456 PHE cc_start: 0.7973 (t80) cc_final: 0.7645 (t80) REVERT: B 32 ILE cc_start: 0.8130 (tt) cc_final: 0.7758 (mm) REVERT: B 38 ILE cc_start: 0.8176 (mp) cc_final: 0.7940 (mt) REVERT: B 80 THR cc_start: 0.8415 (p) cc_final: 0.8087 (m) REVERT: B 87 GLU cc_start: 0.7487 (tt0) cc_final: 0.6862 (tt0) REVERT: B 88 VAL cc_start: 0.8222 (t) cc_final: 0.7867 (p) REVERT: B 93 ARG cc_start: 0.7494 (mmm160) cc_final: 0.7255 (mmm-85) REVERT: B 96 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7186 (mt-10) REVERT: B 171 ARG cc_start: 0.7079 (mtp-110) cc_final: 0.6716 (mtp85) REVERT: B 172 GLN cc_start: 0.6248 (mm-40) cc_final: 0.6001 (mm-40) REVERT: B 176 THR cc_start: 0.8344 (m) cc_final: 0.8043 (m) REVERT: B 196 VAL cc_start: 0.7694 (t) cc_final: 0.7468 (t) REVERT: B 272 GLU cc_start: 0.7840 (tt0) cc_final: 0.7319 (tt0) REVERT: B 305 SER cc_start: 0.7410 (m) cc_final: 0.7046 (m) REVERT: B 321 THR cc_start: 0.7748 (p) cc_final: 0.7502 (t) REVERT: B 333 ASN cc_start: 0.8085 (t0) cc_final: 0.7868 (t0) REVERT: B 341 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.7075 (pt0) REVERT: B 373 LYS cc_start: 0.7657 (ttmt) cc_final: 0.6978 (ttmt) REVERT: B 377 LYS cc_start: 0.8051 (mttp) cc_final: 0.7633 (mttp) REVERT: B 415 ARG cc_start: 0.7581 (mtt90) cc_final: 0.6152 (mtm-85) REVERT: B 419 VAL cc_start: 0.8520 (t) cc_final: 0.8249 (m) REVERT: B 469 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7661 (mm-40) REVERT: B 470 HIS cc_start: 0.7688 (p-80) cc_final: 0.7484 (p-80) REVERT: C 96 GLU cc_start: 0.6251 (mm-30) cc_final: 0.5944 (mm-30) REVERT: C 143 HIS cc_start: 0.7264 (p90) cc_final: 0.6999 (p90) REVERT: C 206 ARG cc_start: 0.7719 (ttt180) cc_final: 0.7098 (tpp80) REVERT: C 210 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6677 (mm-30) REVERT: C 265 LYS cc_start: 0.8118 (mttp) cc_final: 0.7867 (mttp) REVERT: C 272 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7060 (mt-10) REVERT: C 291 PHE cc_start: 0.7885 (t80) cc_final: 0.7635 (t80) REVERT: C 361 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7789 (tp) REVERT: C 375 MET cc_start: 0.7283 (tpp) cc_final: 0.7029 (tpp) REVERT: C 404 LYS cc_start: 0.8369 (mttt) cc_final: 0.8087 (mmtt) REVERT: C 409 LYS cc_start: 0.8091 (tptt) cc_final: 0.7832 (mtpp) REVERT: C 433 GLN cc_start: 0.8057 (mt0) cc_final: 0.7686 (mt0) REVERT: C 484 GLU cc_start: 0.7027 (tt0) cc_final: 0.6649 (tt0) REVERT: C 488 ASN cc_start: 0.7597 (m110) cc_final: 0.7366 (m110) REVERT: D 17 LYS cc_start: 0.7828 (tmtt) cc_final: 0.7478 (tmtt) REVERT: D 18 PHE cc_start: 0.7620 (m-80) cc_final: 0.7364 (m-80) REVERT: D 35 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7774 (ttmt) REVERT: D 104 ASP cc_start: 0.7418 (p0) cc_final: 0.6941 (p0) REVERT: D 106 GLU cc_start: 0.7446 (mt-10) cc_final: 0.6932 (mt-10) REVERT: D 116 ASP cc_start: 0.6953 (m-30) cc_final: 0.6566 (m-30) REVERT: D 120 ARG cc_start: 0.7321 (ttt-90) cc_final: 0.6963 (ptt-90) REVERT: D 128 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8075 (tt) REVERT: D 154 ILE cc_start: 0.7691 (mm) cc_final: 0.7391 (mt) REVERT: D 157 PHE cc_start: 0.7464 (m-80) cc_final: 0.6988 (m-80) REVERT: D 202 MET cc_start: 0.7581 (mmt) cc_final: 0.6833 (mmt) REVERT: D 207 VAL cc_start: 0.8571 (t) cc_final: 0.7563 (p) REVERT: D 213 MET cc_start: 0.8042 (mtp) cc_final: 0.7825 (mtp) REVERT: D 227 ARG cc_start: 0.6698 (mmt90) cc_final: 0.6391 (mmt90) REVERT: D 263 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7570 (mt-10) REVERT: D 267 LEU cc_start: 0.8016 (mm) cc_final: 0.7410 (mt) REVERT: D 294 SER cc_start: 0.7444 (t) cc_final: 0.6752 (p) REVERT: D 308 VAL cc_start: 0.8880 (t) cc_final: 0.8592 (m) REVERT: D 333 ARG cc_start: 0.7410 (ttm110) cc_final: 0.7198 (ttm110) REVERT: D 338 MET cc_start: 0.7962 (tpp) cc_final: 0.7652 (mtm) REVERT: D 340 ILE cc_start: 0.8483 (pt) cc_final: 0.8096 (mm) REVERT: D 386 ILE cc_start: 0.8056 (pt) cc_final: 0.7799 (mp) REVERT: D 439 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6781 (mm-30) REVERT: D 441 LEU cc_start: 0.8759 (mt) cc_final: 0.8432 (mp) REVERT: D 454 ARG cc_start: 0.7796 (ttm170) cc_final: 0.7511 (ttm170) REVERT: D 464 GLU cc_start: 0.8139 (tp30) cc_final: 0.7753 (tp30) REVERT: E 10 MET cc_start: 0.7388 (mtp) cc_final: 0.7178 (mtp) REVERT: E 30 LEU cc_start: 0.8054 (mt) cc_final: 0.7836 (mm) REVERT: E 52 LEU cc_start: 0.7797 (mt) cc_final: 0.7565 (mp) REVERT: E 101 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: E 188 VAL cc_start: 0.6916 (t) cc_final: 0.6646 (p) REVERT: E 194 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7087 (mm-30) REVERT: E 197 ASP cc_start: 0.7196 (t0) cc_final: 0.6648 (t0) REVERT: E 199 TYR cc_start: 0.8230 (t80) cc_final: 0.7201 (t80) REVERT: E 203 LYS cc_start: 0.7891 (tppp) cc_final: 0.7086 (tppp) REVERT: E 207 VAL cc_start: 0.7411 (t) cc_final: 0.7025 (m) REVERT: E 210 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7221 (ttpt) REVERT: E 231 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7781 (t) REVERT: E 256 ARG cc_start: 0.8085 (mmt180) cc_final: 0.7632 (tpp-160) REVERT: E 291 ARG cc_start: 0.6976 (mtt180) cc_final: 0.6167 (ttt180) REVERT: E 330 ASN cc_start: 0.7290 (m-40) cc_final: 0.6955 (t0) REVERT: E 369 LYS cc_start: 0.8264 (mtmm) cc_final: 0.8009 (mttt) REVERT: E 372 GLN cc_start: 0.8020 (mt0) cc_final: 0.7610 (mt0) REVERT: E 380 LEU cc_start: 0.8277 (tp) cc_final: 0.7809 (pp) REVERT: E 384 ILE cc_start: 0.8095 (mt) cc_final: 0.7714 (mt) REVERT: E 410 LEU cc_start: 0.8538 (mt) cc_final: 0.8249 (mt) REVERT: E 435 ARG cc_start: 0.6477 (ttp80) cc_final: 0.6144 (ttp80) REVERT: E 450 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7015 (pm20) REVERT: E 469 MET cc_start: 0.6008 (mmm) cc_final: 0.5501 (mmm) REVERT: F 15 ASP cc_start: 0.7464 (m-30) cc_final: 0.7136 (m-30) REVERT: F 38 ASN cc_start: 0.7959 (t0) cc_final: 0.7681 (t0) REVERT: F 39 GLU cc_start: 0.7787 (pp20) cc_final: 0.7573 (pp20) REVERT: F 70 LEU cc_start: 0.8478 (mt) cc_final: 0.8266 (mt) REVERT: F 174 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7458 (t0) REVERT: F 202 MET cc_start: 0.7084 (mmp) cc_final: 0.6451 (mmp) REVERT: F 227 ARG cc_start: 0.6560 (mmt180) cc_final: 0.6298 (mmt90) REVERT: F 241 ASP cc_start: 0.7753 (m-30) cc_final: 0.7421 (m-30) REVERT: F 285 MET cc_start: 0.7379 (ttp) cc_final: 0.6769 (ttp) REVERT: F 289 GLN cc_start: 0.7443 (tp-100) cc_final: 0.7177 (tm-30) REVERT: F 331 LEU cc_start: 0.7876 (mt) cc_final: 0.7262 (mp) REVERT: F 332 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7187 (mm-30) REVERT: F 338 MET cc_start: 0.7436 (mtm) cc_final: 0.7146 (mtm) REVERT: F 389 MET cc_start: 0.7482 (mmm) cc_final: 0.6795 (mmm) REVERT: F 431 LYS cc_start: 0.8540 (tmmt) cc_final: 0.8305 (tmmt) REVERT: F 438 LYS cc_start: 0.8395 (tttt) cc_final: 0.8152 (tttt) REVERT: F 442 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7653 (mt-10) REVERT: F 456 VAL cc_start: 0.6762 (p) cc_final: 0.6249 (m) REVERT: G 22 GLN cc_start: 0.8554 (tt0) cc_final: 0.8297 (tm-30) REVERT: G 33 SER cc_start: 0.8470 (t) cc_final: 0.8090 (p) REVERT: G 43 LYS cc_start: 0.8540 (ttpt) cc_final: 0.8258 (ttpt) REVERT: G 48 TYR cc_start: 0.7877 (t80) cc_final: 0.7572 (t80) REVERT: G 105 THR cc_start: 0.8628 (m) cc_final: 0.8382 (t) REVERT: G 107 GLN cc_start: 0.8588 (pt0) cc_final: 0.8346 (mp10) REVERT: G 148 SER cc_start: 0.8874 (m) cc_final: 0.8544 (p) REVERT: G 222 GLN cc_start: 0.8147 (mt0) cc_final: 0.7863 (mt0) REVERT: G 239 GLU cc_start: 0.8180 (tt0) cc_final: 0.7965 (tt0) REVERT: G 267 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8057 (ttm-80) REVERT: G 269 ARG cc_start: 0.7879 (ttp80) cc_final: 0.7444 (ttp80) REVERT: G 275 GLN cc_start: 0.8234 (tp40) cc_final: 0.7713 (tp40) REVERT: G 278 THR cc_start: 0.8266 (p) cc_final: 0.7930 (p) REVERT: G 279 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7198 (mm-30) outliers start: 125 outliers final: 70 residues processed: 1015 average time/residue: 0.1744 time to fit residues: 267.6581 Evaluate side-chains 1036 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 954 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 379 GLU Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 267 ARG Chi-restraints excluded: chain G residue 273 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 154 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 277 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 299 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN A 397 GLN A 422 GLN A 426 GLN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN D 401 HIS ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS F 371 GLN ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.145377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.126704 restraints weight = 39880.056| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 3.13 r_work: 0.3621 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24608 Z= 0.152 Angle : 0.625 19.768 33370 Z= 0.323 Chirality : 0.046 0.249 3840 Planarity : 0.005 0.060 4349 Dihedral : 5.978 82.663 3423 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.80 % Favored : 97.16 % Rotamer: Outliers : 5.00 % Allowed : 25.96 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 3104 helix: 1.00 (0.14), residues: 1283 sheet: 0.29 (0.23), residues: 495 loop : -0.72 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG G 189 TYR 0.021 0.001 TYR G 229 PHE 0.034 0.002 PHE B 460 HIS 0.007 0.001 HIS F 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (24608) covalent geometry : angle 0.62462 / 0.32 (33370) hydrogen bonds : bond 0.05140 / 3.53 ( 1143) hydrogen bonds : angle 5.11030 / 3.66 ( 3267) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 955 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8178 (m-40) cc_final: 0.7949 (m-40) REVERT: A 60 MET cc_start: 0.6858 (mmt) cc_final: 0.6617 (mmp) REVERT: A 62 MET cc_start: 0.7282 (ptp) cc_final: 0.6950 (ptp) REVERT: A 87 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6615 (mm-30) REVERT: A 95 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6526 (tmm) REVERT: A 125 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6872 (mm-30) REVERT: A 154 ASP cc_start: 0.8131 (m-30) cc_final: 0.7804 (t0) REVERT: A 164 ARG cc_start: 0.7105 (mtm110) cc_final: 0.6717 (mtm110) REVERT: A 170 ASP cc_start: 0.6004 (t0) cc_final: 0.5798 (t0) REVERT: A 181 ASP cc_start: 0.7698 (m-30) cc_final: 0.7452 (m-30) REVERT: A 190 ASN cc_start: 0.7896 (m-40) cc_final: 0.7480 (m-40) REVERT: A 191 MET cc_start: 0.6724 (mmm) cc_final: 0.6137 (mmm) REVERT: A 193 SER cc_start: 0.7490 (m) cc_final: 0.6751 (t) REVERT: A 213 ARG cc_start: 0.8291 (ttm170) cc_final: 0.7989 (ttm-80) REVERT: A 215 HIS cc_start: 0.7473 (OUTLIER) cc_final: 0.6489 (t-90) REVERT: A 245 MET cc_start: 0.7183 (mtt) cc_final: 0.6950 (mtt) REVERT: A 283 ARG cc_start: 0.7859 (ttm110) cc_final: 0.7362 (mtp85) REVERT: A 284 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7619 (mm-30) REVERT: A 341 GLN cc_start: 0.7887 (pm20) cc_final: 0.7346 (pm20) REVERT: A 415 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7695 (mtt90) REVERT: A 424 LEU cc_start: 0.7944 (tp) cc_final: 0.7479 (tp) REVERT: A 432 LYS cc_start: 0.8003 (mttt) cc_final: 0.7787 (mttt) REVERT: A 456 PHE cc_start: 0.7951 (t80) cc_final: 0.7620 (t80) REVERT: B 32 ILE cc_start: 0.8111 (tt) cc_final: 0.7745 (mm) REVERT: B 38 ILE cc_start: 0.8256 (mp) cc_final: 0.8056 (mt) REVERT: B 87 GLU cc_start: 0.7545 (tt0) cc_final: 0.6895 (tt0) REVERT: B 88 VAL cc_start: 0.8228 (t) cc_final: 0.7876 (p) REVERT: B 93 ARG cc_start: 0.7548 (mmm160) cc_final: 0.7237 (mmm-85) REVERT: B 96 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7318 (mt-10) REVERT: B 143 HIS cc_start: 0.6425 (m170) cc_final: 0.6013 (m170) REVERT: B 171 ARG cc_start: 0.7029 (mtp-110) cc_final: 0.6688 (mtp85) REVERT: B 172 GLN cc_start: 0.6324 (mm-40) cc_final: 0.6087 (mm-40) REVERT: B 181 ASP cc_start: 0.7829 (t70) cc_final: 0.7483 (t70) REVERT: B 196 VAL cc_start: 0.7682 (t) cc_final: 0.7451 (t) REVERT: B 275 LEU cc_start: 0.8392 (mt) cc_final: 0.8083 (mp) REVERT: B 299 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: B 305 SER cc_start: 0.7532 (m) cc_final: 0.7256 (m) REVERT: B 321 THR cc_start: 0.7867 (p) cc_final: 0.7566 (t) REVERT: B 333 ASN cc_start: 0.8139 (t0) cc_final: 0.7934 (t0) REVERT: B 373 LYS cc_start: 0.7621 (ttmt) cc_final: 0.6823 (ttmt) REVERT: B 377 LYS cc_start: 0.8198 (mttp) cc_final: 0.7778 (mttp) REVERT: B 392 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7768 (tp) REVERT: B 452 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7020 (m-30) REVERT: B 470 HIS cc_start: 0.7766 (p-80) cc_final: 0.7531 (p-80) REVERT: C 95 MET cc_start: 0.6846 (tpt) cc_final: 0.6590 (tpt) REVERT: C 96 GLU cc_start: 0.6317 (mm-30) cc_final: 0.5940 (mm-30) REVERT: C 143 HIS cc_start: 0.7456 (p90) cc_final: 0.7139 (p-80) REVERT: C 161 ARG cc_start: 0.7476 (mtt180) cc_final: 0.6996 (mmt90) REVERT: C 206 ARG cc_start: 0.7835 (ttt180) cc_final: 0.7140 (tpp80) REVERT: C 210 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6699 (mm-30) REVERT: C 265 LYS cc_start: 0.8048 (mttp) cc_final: 0.7836 (mttp) REVERT: C 272 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7114 (mt-10) REVERT: C 375 MET cc_start: 0.7244 (tpp) cc_final: 0.6986 (tpp) REVERT: C 389 TYR cc_start: 0.7843 (t80) cc_final: 0.7485 (t80) REVERT: C 409 LYS cc_start: 0.8123 (tptt) cc_final: 0.7777 (mtpp) REVERT: C 433 GLN cc_start: 0.8110 (mt0) cc_final: 0.7727 (mt0) REVERT: C 435 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8082 (mm) REVERT: C 459 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7344 (mt-10) REVERT: C 484 GLU cc_start: 0.7095 (tt0) cc_final: 0.6622 (tt0) REVERT: C 488 ASN cc_start: 0.7699 (m110) cc_final: 0.7397 (m110) REVERT: D 17 LYS cc_start: 0.7844 (tmtt) cc_final: 0.7467 (tmtt) REVERT: D 35 LYS cc_start: 0.7996 (ttmt) cc_final: 0.7728 (ttmt) REVERT: D 104 ASP cc_start: 0.7217 (p0) cc_final: 0.6672 (p0) REVERT: D 106 GLU cc_start: 0.7475 (mt-10) cc_final: 0.6922 (mt-10) REVERT: D 120 ARG cc_start: 0.7362 (ttt-90) cc_final: 0.6963 (ptt-90) REVERT: D 128 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8099 (tt) REVERT: D 154 ILE cc_start: 0.7706 (mm) cc_final: 0.7407 (mt) REVERT: D 157 PHE cc_start: 0.7462 (m-80) cc_final: 0.6958 (m-80) REVERT: D 202 MET cc_start: 0.7642 (mmt) cc_final: 0.6857 (mmt) REVERT: D 207 VAL cc_start: 0.8605 (t) cc_final: 0.7522 (p) REVERT: D 242 GLU cc_start: 0.6610 (pt0) cc_final: 0.6354 (pt0) REVERT: D 243 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7256 (mm-40) REVERT: D 263 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7516 (mt-10) REVERT: D 267 LEU cc_start: 0.8013 (mm) cc_final: 0.7422 (mt) REVERT: D 294 SER cc_start: 0.7450 (t) cc_final: 0.6648 (p) REVERT: D 308 VAL cc_start: 0.8876 (t) cc_final: 0.8618 (m) REVERT: D 333 ARG cc_start: 0.7400 (ttm110) cc_final: 0.7163 (ttm110) REVERT: D 338 MET cc_start: 0.7903 (tpp) cc_final: 0.7650 (mtm) REVERT: D 340 ILE cc_start: 0.8478 (pt) cc_final: 0.8089 (mm) REVERT: D 365 GLN cc_start: 0.7602 (tm-30) cc_final: 0.7320 (tm-30) REVERT: D 389 MET cc_start: 0.7287 (tmt) cc_final: 0.7055 (tmt) REVERT: D 439 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6878 (mm-30) REVERT: D 441 LEU cc_start: 0.8771 (mt) cc_final: 0.8512 (mp) REVERT: D 464 GLU cc_start: 0.8116 (tp30) cc_final: 0.7727 (tp30) REVERT: E 5 ARG cc_start: 0.7058 (ptm-80) cc_final: 0.6747 (ptm-80) REVERT: E 10 MET cc_start: 0.7360 (mtp) cc_final: 0.7151 (mtp) REVERT: E 26 ILE cc_start: 0.8860 (mt) cc_final: 0.8487 (tt) REVERT: E 30 LEU cc_start: 0.8039 (mt) cc_final: 0.7801 (mm) REVERT: E 101 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: E 188 VAL cc_start: 0.6951 (t) cc_final: 0.6717 (p) REVERT: E 197 ASP cc_start: 0.7194 (t0) cc_final: 0.6790 (t0) REVERT: E 199 TYR cc_start: 0.8270 (t80) cc_final: 0.7267 (t80) REVERT: E 201 GLU cc_start: 0.7725 (tp30) cc_final: 0.6906 (tp30) REVERT: E 203 LYS cc_start: 0.7930 (tppp) cc_final: 0.7101 (tppp) REVERT: E 207 VAL cc_start: 0.7417 (t) cc_final: 0.6973 (m) REVERT: E 210 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7185 (ttpt) REVERT: E 231 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7808 (t) REVERT: E 259 GLN cc_start: 0.7842 (tt0) cc_final: 0.7635 (mt0) REVERT: E 275 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8238 (t) REVERT: E 330 ASN cc_start: 0.7351 (m-40) cc_final: 0.7047 (t0) REVERT: E 369 LYS cc_start: 0.8287 (mtmm) cc_final: 0.8048 (mttm) REVERT: E 372 GLN cc_start: 0.7969 (mt0) cc_final: 0.7574 (mt0) REVERT: E 378 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7913 (tmmm) REVERT: E 380 LEU cc_start: 0.8344 (tp) cc_final: 0.7755 (tp) REVERT: E 410 LEU cc_start: 0.8531 (mt) cc_final: 0.8275 (mt) REVERT: E 419 GLN cc_start: 0.8157 (pt0) cc_final: 0.7231 (pt0) REVERT: E 435 ARG cc_start: 0.6557 (ttp80) cc_final: 0.6231 (ttp80) REVERT: E 450 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7041 (pm20) REVERT: E 469 MET cc_start: 0.5958 (mmm) cc_final: 0.5463 (mmm) REVERT: F 15 ASP cc_start: 0.7494 (m-30) cc_final: 0.7148 (m-30) REVERT: F 38 ASN cc_start: 0.7950 (t0) cc_final: 0.7686 (t0) REVERT: F 144 LEU cc_start: 0.7882 (tp) cc_final: 0.7662 (tp) REVERT: F 174 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.7893 (t0) REVERT: F 202 MET cc_start: 0.7194 (mmp) cc_final: 0.6493 (mmp) REVERT: F 241 ASP cc_start: 0.7747 (m-30) cc_final: 0.7383 (m-30) REVERT: F 285 MET cc_start: 0.7383 (ttp) cc_final: 0.6770 (ttp) REVERT: F 338 MET cc_start: 0.7504 (mtm) cc_final: 0.7252 (mtm) REVERT: F 389 MET cc_start: 0.7691 (mmm) cc_final: 0.7044 (mmm) REVERT: F 438 LYS cc_start: 0.8379 (tttt) cc_final: 0.8131 (tttt) REVERT: G 15 ASN cc_start: 0.8417 (m110) cc_final: 0.8145 (m-40) REVERT: G 29 MET cc_start: 0.8072 (mmm) cc_final: 0.7584 (mmm) REVERT: G 43 LYS cc_start: 0.8482 (ttpt) cc_final: 0.8204 (ttpt) REVERT: G 48 TYR cc_start: 0.7896 (t80) cc_final: 0.7586 (t80) REVERT: G 94 TYR cc_start: 0.7533 (t80) cc_final: 0.7280 (t80) REVERT: G 132 ARG cc_start: 0.8060 (mmp80) cc_final: 0.7141 (mmm-85) REVERT: G 148 SER cc_start: 0.8826 (m) cc_final: 0.8501 (p) REVERT: G 183 GLN cc_start: 0.7621 (pp30) cc_final: 0.6720 (pp30) REVERT: G 188 GLU cc_start: 0.7617 (tt0) cc_final: 0.7246 (tp30) REVERT: G 222 GLN cc_start: 0.8079 (mt0) cc_final: 0.7800 (mt0) REVERT: G 239 GLU cc_start: 0.8198 (tt0) cc_final: 0.7846 (tt0) REVERT: G 267 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8077 (ttm-80) REVERT: G 269 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7467 (ttp80) REVERT: G 275 GLN cc_start: 0.8279 (tp40) cc_final: 0.7750 (tp40) REVERT: G 279 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7201 (mm-30) outliers start: 128 outliers final: 79 residues processed: 1001 average time/residue: 0.1695 time to fit residues: 257.0737 Evaluate side-chains 1033 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 939 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 200 HIS Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 267 ARG Chi-restraints excluded: chain G residue 273 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 221 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 305 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 251 optimal weight: 10.0000 chunk 275 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 72 optimal weight: 0.0670 overall best weight: 4.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN A 294 HIS ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN D 217 GLN ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.139723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.121376 restraints weight = 40170.889| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 3.07 r_work: 0.3540 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 24608 Z= 0.329 Angle : 0.782 17.529 33370 Z= 0.417 Chirality : 0.052 0.281 3840 Planarity : 0.006 0.062 4349 Dihedral : 6.580 88.860 3423 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.80 % Favored : 95.17 % Rotamer: Outliers : 5.94 % Allowed : 26.19 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 3104 helix: 0.17 (0.14), residues: 1305 sheet: -0.03 (0.23), residues: 487 loop : -1.10 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 383 TYR 0.024 0.003 TYR G 178 PHE 0.023 0.003 PHE F 250 HIS 0.013 0.002 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.33 (24608) covalent geometry : angle 0.78178 / 0.42 (33370) hydrogen bonds : bond 0.07135 / 4.85 ( 1143) hydrogen bonds : angle 5.70221 / 4.10 ( 3267) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 1003 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.6861 (mmt) cc_final: 0.6583 (mmp) REVERT: A 62 MET cc_start: 0.7374 (ptp) cc_final: 0.7072 (ptp) REVERT: A 87 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6722 (mm-30) REVERT: A 95 MET cc_start: 0.7015 (mmm) cc_final: 0.6562 (tmm) REVERT: A 139 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7648 (mtt-85) REVERT: A 154 ASP cc_start: 0.8212 (m-30) cc_final: 0.7955 (t0) REVERT: A 164 ARG cc_start: 0.7150 (mtm110) cc_final: 0.6561 (mtm110) REVERT: A 181 ASP cc_start: 0.7825 (m-30) cc_final: 0.7572 (m-30) REVERT: A 190 ASN cc_start: 0.7992 (m-40) cc_final: 0.7625 (m-40) REVERT: A 191 MET cc_start: 0.6835 (mmm) cc_final: 0.6370 (mmm) REVERT: A 193 SER cc_start: 0.7779 (m) cc_final: 0.7042 (t) REVERT: A 207 THR cc_start: 0.7476 (m) cc_final: 0.7268 (t) REVERT: A 245 MET cc_start: 0.7251 (mtt) cc_final: 0.7007 (mtt) REVERT: A 261 ASP cc_start: 0.6383 (OUTLIER) cc_final: 0.6182 (m-30) REVERT: A 262 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.6743 (m-30) REVERT: A 266 GLN cc_start: 0.7769 (tt0) cc_final: 0.7426 (tp40) REVERT: A 341 GLN cc_start: 0.7858 (pm20) cc_final: 0.7377 (pm20) REVERT: A 349 PHE cc_start: 0.8171 (t80) cc_final: 0.7954 (t80) REVERT: A 363 VAL cc_start: 0.7925 (p) cc_final: 0.7705 (t) REVERT: A 365 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.7028 (mmt-90) REVERT: A 420 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7948 (mm) REVERT: A 424 LEU cc_start: 0.7871 (tp) cc_final: 0.7620 (tp) REVERT: A 456 PHE cc_start: 0.8028 (t80) cc_final: 0.7742 (t80) REVERT: B 68 GLU cc_start: 0.7849 (tt0) cc_final: 0.7647 (tt0) REVERT: B 86 ASP cc_start: 0.7266 (m-30) cc_final: 0.6988 (m-30) REVERT: B 87 GLU cc_start: 0.7553 (tt0) cc_final: 0.6871 (tt0) REVERT: B 88 VAL cc_start: 0.8160 (t) cc_final: 0.7838 (p) REVERT: B 93 ARG cc_start: 0.7542 (mmm160) cc_final: 0.7072 (mmm-85) REVERT: B 96 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7085 (mt-10) REVERT: B 126 THR cc_start: 0.7807 (p) cc_final: 0.7531 (t) REVERT: B 171 ARG cc_start: 0.7008 (mtp-110) cc_final: 0.6754 (mtp85) REVERT: B 181 ASP cc_start: 0.7794 (t70) cc_final: 0.7498 (t70) REVERT: B 272 GLU cc_start: 0.8022 (tt0) cc_final: 0.7537 (tt0) REVERT: B 275 LEU cc_start: 0.8501 (mt) cc_final: 0.8201 (mp) REVERT: B 299 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7226 (mt-10) REVERT: B 305 SER cc_start: 0.7735 (m) cc_final: 0.7504 (m) REVERT: B 321 THR cc_start: 0.7909 (p) cc_final: 0.7649 (t) REVERT: B 333 ASN cc_start: 0.8279 (t0) cc_final: 0.7892 (t0) REVERT: B 373 LYS cc_start: 0.7708 (ttmt) cc_final: 0.7053 (ttmt) REVERT: B 377 LYS cc_start: 0.8310 (mttp) cc_final: 0.7921 (mttp) REVERT: B 392 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7947 (tp) REVERT: B 461 TYR cc_start: 0.6906 (m-10) cc_final: 0.6656 (m-10) REVERT: C 54 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6691 (pt0) REVERT: C 95 MET cc_start: 0.7057 (tpt) cc_final: 0.6790 (tpt) REVERT: C 198 ILE cc_start: 0.5725 (OUTLIER) cc_final: 0.5387 (tp) REVERT: C 206 ARG cc_start: 0.7950 (ttt180) cc_final: 0.7245 (tpp80) REVERT: C 210 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6743 (mm-30) REVERT: C 254 LYS cc_start: 0.7311 (mttm) cc_final: 0.7033 (mtmm) REVERT: C 265 LYS cc_start: 0.8191 (mttp) cc_final: 0.7948 (mttp) REVERT: C 272 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7261 (mt-10) REVERT: C 299 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7537 (mt-10) REVERT: C 361 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7934 (tp) REVERT: C 375 MET cc_start: 0.7513 (tpp) cc_final: 0.7290 (tpp) REVERT: C 377 LYS cc_start: 0.8357 (tttp) cc_final: 0.8081 (tttp) REVERT: C 389 TYR cc_start: 0.8078 (t80) cc_final: 0.7673 (t80) REVERT: C 409 LYS cc_start: 0.8251 (tptt) cc_final: 0.7935 (mtpp) REVERT: C 484 GLU cc_start: 0.7431 (tt0) cc_final: 0.6986 (tt0) REVERT: C 488 ASN cc_start: 0.7848 (m110) cc_final: 0.7504 (m110) REVERT: D 8 GLN cc_start: 0.7677 (tt0) cc_final: 0.6999 (tt0) REVERT: D 10 MET cc_start: 0.7611 (mtm) cc_final: 0.7278 (mtm) REVERT: D 17 LYS cc_start: 0.7996 (tmtt) cc_final: 0.7675 (tmtt) REVERT: D 35 LYS cc_start: 0.8098 (ttmt) cc_final: 0.7782 (ttmt) REVERT: D 52 LEU cc_start: 0.7776 (pp) cc_final: 0.7571 (pp) REVERT: D 150 LYS cc_start: 0.7908 (mtpt) cc_final: 0.7488 (mtpt) REVERT: D 154 ILE cc_start: 0.7923 (mm) cc_final: 0.7575 (mt) REVERT: D 174 ASN cc_start: 0.7806 (m-40) cc_final: 0.7434 (t0) REVERT: D 185 PHE cc_start: 0.8344 (t80) cc_final: 0.8077 (t80) REVERT: D 202 MET cc_start: 0.7749 (mmt) cc_final: 0.6965 (mmt) REVERT: D 207 VAL cc_start: 0.8668 (t) cc_final: 0.7430 (p) REVERT: D 220 GLU cc_start: 0.7484 (mp0) cc_final: 0.6707 (mp0) REVERT: D 242 GLU cc_start: 0.6851 (pt0) cc_final: 0.6632 (pt0) REVERT: D 243 GLN cc_start: 0.7496 (mm-40) cc_final: 0.7230 (mm-40) REVERT: D 285 MET cc_start: 0.8074 (ttt) cc_final: 0.7771 (ttp) REVERT: D 294 SER cc_start: 0.7481 (t) cc_final: 0.6849 (p) REVERT: D 340 ILE cc_start: 0.8570 (pt) cc_final: 0.8097 (mm) REVERT: D 345 ASP cc_start: 0.7517 (t0) cc_final: 0.7183 (t0) REVERT: D 347 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7356 (mt) REVERT: D 365 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7547 (tm-30) REVERT: D 378 LYS cc_start: 0.8533 (tttt) cc_final: 0.7681 (mmmm) REVERT: D 381 GLN cc_start: 0.7896 (pm20) cc_final: 0.7587 (pm20) REVERT: D 397 LYS cc_start: 0.8630 (pttm) cc_final: 0.8423 (mtmm) REVERT: D 401 HIS cc_start: 0.7528 (t-90) cc_final: 0.6894 (t-90) REVERT: D 428 VAL cc_start: 0.6346 (OUTLIER) cc_final: 0.5233 (p) REVERT: D 439 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6778 (mm-30) REVERT: D 441 LEU cc_start: 0.8831 (mt) cc_final: 0.8588 (mp) REVERT: D 454 ARG cc_start: 0.7718 (ttm170) cc_final: 0.7240 (mtp85) REVERT: D 464 GLU cc_start: 0.8118 (tp30) cc_final: 0.7723 (tp30) REVERT: E 5 ARG cc_start: 0.7368 (ptm-80) cc_final: 0.7038 (ptm-80) REVERT: E 10 MET cc_start: 0.7480 (mtp) cc_final: 0.7269 (mtp) REVERT: E 101 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: E 115 ARG cc_start: 0.7719 (mmm-85) cc_final: 0.7308 (mmm-85) REVERT: E 199 TYR cc_start: 0.8330 (t80) cc_final: 0.7898 (t80) REVERT: E 201 GLU cc_start: 0.7813 (tp30) cc_final: 0.7320 (tp30) REVERT: E 207 VAL cc_start: 0.7917 (t) cc_final: 0.7569 (m) REVERT: E 210 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7111 (ttpt) REVERT: E 226 MET cc_start: 0.6798 (ttp) cc_final: 0.6550 (ttp) REVERT: E 227 ARG cc_start: 0.6867 (mmt180) cc_final: 0.6326 (mmt180) REVERT: E 315 ASP cc_start: 0.7552 (t0) cc_final: 0.7265 (t0) REVERT: E 378 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7939 (tmmm) REVERT: E 380 LEU cc_start: 0.8304 (tp) cc_final: 0.8101 (tp) REVERT: E 410 LEU cc_start: 0.8545 (mt) cc_final: 0.8318 (mt) REVERT: E 435 ARG cc_start: 0.6719 (ttp80) cc_final: 0.6436 (ttp80) REVERT: E 450 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7141 (pm20) REVERT: E 451 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: E 455 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7760 (mm) REVERT: E 458 ARG cc_start: 0.7179 (ttp-110) cc_final: 0.6814 (mtp-110) REVERT: E 469 MET cc_start: 0.6172 (mmm) cc_final: 0.5805 (mmm) REVERT: F 15 ASP cc_start: 0.7572 (m-30) cc_final: 0.7263 (m-30) REVERT: F 22 HIS cc_start: 0.7456 (m-70) cc_final: 0.7160 (m-70) REVERT: F 38 ASN cc_start: 0.7985 (t0) cc_final: 0.7743 (t0) REVERT: F 84 SER cc_start: 0.7783 (OUTLIER) cc_final: 0.7565 (p) REVERT: F 120 ARG cc_start: 0.6966 (ptm-80) cc_final: 0.6626 (ptm-80) REVERT: F 172 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8494 (tt) REVERT: F 202 MET cc_start: 0.7307 (mmp) cc_final: 0.6715 (mmp) REVERT: F 226 MET cc_start: 0.5558 (OUTLIER) cc_final: 0.5286 (mtm) REVERT: F 227 ARG cc_start: 0.6593 (mmt180) cc_final: 0.6320 (mmt-90) REVERT: F 285 MET cc_start: 0.7386 (ttp) cc_final: 0.6843 (ttp) REVERT: F 338 MET cc_start: 0.7466 (mtm) cc_final: 0.7215 (mtm) REVERT: F 354 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7200 (tp) REVERT: F 391 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7337 (tm-30) REVERT: F 438 LYS cc_start: 0.8618 (tttt) cc_final: 0.8266 (tttt) REVERT: G 15 ASN cc_start: 0.8400 (m110) cc_final: 0.8179 (m-40) REVERT: G 37 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7432 (ttp80) REVERT: G 43 LYS cc_start: 0.8435 (ttpt) cc_final: 0.8148 (ttpt) REVERT: G 48 TYR cc_start: 0.7928 (t80) cc_final: 0.7634 (t80) REVERT: G 70 MET cc_start: 0.8315 (mmp) cc_final: 0.7730 (mmp) REVERT: G 103 TYR cc_start: 0.8188 (t80) cc_final: 0.7935 (t80) REVERT: G 105 THR cc_start: 0.8716 (m) cc_final: 0.8398 (t) REVERT: G 123 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7214 (ttm110) REVERT: G 148 SER cc_start: 0.8754 (m) cc_final: 0.8435 (p) REVERT: G 153 LYS cc_start: 0.8046 (tttm) cc_final: 0.7717 (tttm) REVERT: G 183 GLN cc_start: 0.7786 (pp30) cc_final: 0.7093 (pp30) REVERT: G 189 ARG cc_start: 0.6651 (mpt90) cc_final: 0.6383 (mpt90) REVERT: G 222 GLN cc_start: 0.8191 (mt0) cc_final: 0.7884 (mt0) REVERT: G 239 GLU cc_start: 0.8290 (tt0) cc_final: 0.8083 (tt0) REVERT: G 267 ARG cc_start: 0.8447 (ttm-80) cc_final: 0.8193 (ttm-80) REVERT: G 269 ARG cc_start: 0.7964 (ttp80) cc_final: 0.7536 (ttp80) REVERT: G 279 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7253 (mm-30) outliers start: 152 outliers final: 91 residues processed: 1070 average time/residue: 0.1694 time to fit residues: 273.1086 Evaluate side-chains 1087 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 973 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 365 GLN Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain G residue 123 ARG Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 285 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 111 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 305 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 205 optimal weight: 0.9980 chunk 138 optimal weight: 9.9990 chunk 121 optimal weight: 0.5980 chunk 151 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 GLN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN C 230 GLN C 433 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN F 8 GLN ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN F 324 HIS ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.142576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.124157 restraints weight = 39656.445| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 3.08 r_work: 0.3585 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24608 Z= 0.180 Angle : 0.684 18.929 33370 Z= 0.352 Chirality : 0.047 0.259 3840 Planarity : 0.006 0.111 4349 Dihedral : 6.160 88.901 3421 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.04 % Rotamer: Outliers : 6.22 % Allowed : 28.07 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 3104 helix: 0.54 (0.14), residues: 1301 sheet: 0.15 (0.24), residues: 484 loop : -1.00 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 405 TYR 0.015 0.002 TYR G 265 PHE 0.033 0.002 PHE B 460 HIS 0.014 0.001 HIS F 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (24608) covalent geometry : angle 0.68373 / 0.35 (33370) hydrogen bonds : bond 0.05670 / 3.88 ( 1143) hydrogen bonds : angle 5.24720 / 3.76 ( 3267) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 989 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 VAL cc_start: 0.7972 (OUTLIER) cc_final: 0.7599 (p) REVERT: A 60 MET cc_start: 0.6844 (mmt) cc_final: 0.6535 (mmp) REVERT: A 62 MET cc_start: 0.7365 (ptp) cc_final: 0.7051 (ptp) REVERT: A 87 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6667 (mm-30) REVERT: A 93 ARG cc_start: 0.7791 (ttm-80) cc_final: 0.7282 (ttm-80) REVERT: A 95 MET cc_start: 0.6993 (tmm) cc_final: 0.6641 (tmm) REVERT: A 125 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7120 (mm-30) REVERT: A 139 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7649 (mtt-85) REVERT: A 154 ASP cc_start: 0.8228 (m-30) cc_final: 0.7974 (t0) REVERT: A 164 ARG cc_start: 0.7116 (mtm110) cc_final: 0.6751 (mtm110) REVERT: A 181 ASP cc_start: 0.7712 (m-30) cc_final: 0.7484 (m-30) REVERT: A 190 ASN cc_start: 0.7972 (m-40) cc_final: 0.7618 (m-40) REVERT: A 191 MET cc_start: 0.6798 (mmm) cc_final: 0.6276 (mmm) REVERT: A 193 SER cc_start: 0.7677 (m) cc_final: 0.6946 (t) REVERT: A 215 HIS cc_start: 0.7616 (OUTLIER) cc_final: 0.6577 (t-90) REVERT: A 245 MET cc_start: 0.7217 (mtt) cc_final: 0.6967 (mtt) REVERT: A 262 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6744 (m-30) REVERT: A 266 GLN cc_start: 0.7673 (tt0) cc_final: 0.7304 (tp40) REVERT: A 283 ARG cc_start: 0.7883 (ttm110) cc_final: 0.7361 (mtp85) REVERT: A 341 GLN cc_start: 0.7811 (pm20) cc_final: 0.7369 (pm20) REVERT: A 349 PHE cc_start: 0.8113 (t80) cc_final: 0.7896 (t80) REVERT: A 365 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.7085 (mmt-90) REVERT: A 420 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7829 (mm) REVERT: A 424 LEU cc_start: 0.7769 (tp) cc_final: 0.7531 (tp) REVERT: A 456 PHE cc_start: 0.8009 (t80) cc_final: 0.7717 (t80) REVERT: A 472 LEU cc_start: 0.7534 (tt) cc_final: 0.7325 (tp) REVERT: B 86 ASP cc_start: 0.7242 (m-30) cc_final: 0.7001 (m-30) REVERT: B 88 VAL cc_start: 0.8178 (t) cc_final: 0.7850 (p) REVERT: B 93 ARG cc_start: 0.7481 (mmm160) cc_final: 0.6781 (mmm-85) REVERT: B 96 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7058 (mt-10) REVERT: B 113 GLN cc_start: 0.7359 (tp40) cc_final: 0.7143 (tp-100) REVERT: B 126 THR cc_start: 0.7848 (p) cc_final: 0.7621 (t) REVERT: B 127 ARG cc_start: 0.7424 (ttm-80) cc_final: 0.7186 (tpt-90) REVERT: B 139 ARG cc_start: 0.8485 (mtt90) cc_final: 0.8275 (mtt90) REVERT: B 144 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7261 (tm-30) REVERT: B 181 ASP cc_start: 0.7758 (t70) cc_final: 0.7442 (t70) REVERT: B 191 MET cc_start: 0.7580 (tpp) cc_final: 0.7215 (tpp) REVERT: B 305 SER cc_start: 0.7585 (m) cc_final: 0.7317 (m) REVERT: B 333 ASN cc_start: 0.8232 (t0) cc_final: 0.7917 (t0) REVERT: B 373 LYS cc_start: 0.7664 (ttmt) cc_final: 0.6985 (ttmt) REVERT: B 377 LYS cc_start: 0.8276 (mttp) cc_final: 0.7900 (mttp) REVERT: B 392 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7887 (tp) REVERT: B 458 LYS cc_start: 0.7221 (tmmt) cc_final: 0.6878 (mttp) REVERT: B 461 TYR cc_start: 0.6849 (m-10) cc_final: 0.6487 (m-10) REVERT: C 54 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6713 (pt0) REVERT: C 95 MET cc_start: 0.7016 (tpt) cc_final: 0.6678 (tpt) REVERT: C 161 ARG cc_start: 0.7475 (mtt180) cc_final: 0.6994 (mmt90) REVERT: C 206 ARG cc_start: 0.7876 (ttt180) cc_final: 0.7152 (tpp80) REVERT: C 210 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6666 (mm-30) REVERT: C 254 LYS cc_start: 0.7236 (mttm) cc_final: 0.6969 (mtmm) REVERT: C 272 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7238 (mt-10) REVERT: C 299 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7470 (mt-10) REVERT: C 361 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7910 (tp) REVERT: C 377 LYS cc_start: 0.8324 (tttp) cc_final: 0.8038 (tttp) REVERT: C 389 TYR cc_start: 0.7957 (t80) cc_final: 0.7611 (t80) REVERT: C 409 LYS cc_start: 0.8193 (tptt) cc_final: 0.7891 (mtpp) REVERT: C 484 GLU cc_start: 0.7295 (tt0) cc_final: 0.6792 (tt0) REVERT: C 488 ASN cc_start: 0.7755 (m110) cc_final: 0.7406 (m110) REVERT: D 8 GLN cc_start: 0.7607 (tt0) cc_final: 0.7354 (tt0) REVERT: D 17 LYS cc_start: 0.7995 (tmtt) cc_final: 0.7648 (tmtt) REVERT: D 35 LYS cc_start: 0.8074 (ttmt) cc_final: 0.7729 (ttmt) REVERT: D 120 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6745 (ptt-90) REVERT: D 150 LYS cc_start: 0.7861 (mtpt) cc_final: 0.7455 (mtpt) REVERT: D 154 ILE cc_start: 0.7861 (mm) cc_final: 0.7484 (mt) REVERT: D 157 PHE cc_start: 0.7427 (m-80) cc_final: 0.6958 (m-80) REVERT: D 185 PHE cc_start: 0.8249 (t80) cc_final: 0.8012 (t80) REVERT: D 202 MET cc_start: 0.7660 (mmt) cc_final: 0.6901 (mmt) REVERT: D 207 VAL cc_start: 0.8646 (t) cc_final: 0.7374 (p) REVERT: D 227 ARG cc_start: 0.6912 (mmt90) cc_final: 0.6477 (mmt90) REVERT: D 233 LEU cc_start: 0.7629 (tp) cc_final: 0.7353 (tp) REVERT: D 259 GLN cc_start: 0.7862 (mp10) cc_final: 0.7122 (mp10) REVERT: D 267 LEU cc_start: 0.8062 (mm) cc_final: 0.7475 (mt) REVERT: D 285 MET cc_start: 0.8008 (ttt) cc_final: 0.7697 (ttp) REVERT: D 294 SER cc_start: 0.7396 (t) cc_final: 0.6768 (p) REVERT: D 333 ARG cc_start: 0.7576 (ttm110) cc_final: 0.7342 (ttm110) REVERT: D 365 GLN cc_start: 0.7701 (tm-30) cc_final: 0.7284 (tm-30) REVERT: D 378 LYS cc_start: 0.8516 (tttt) cc_final: 0.8074 (mtpp) REVERT: D 396 ASP cc_start: 0.8197 (m-30) cc_final: 0.7949 (m-30) REVERT: D 428 VAL cc_start: 0.6312 (OUTLIER) cc_final: 0.5210 (p) REVERT: D 439 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6824 (mm-30) REVERT: D 441 LEU cc_start: 0.8811 (mt) cc_final: 0.8552 (mp) REVERT: D 464 GLU cc_start: 0.8125 (tp30) cc_final: 0.7736 (tp30) REVERT: E 5 ARG cc_start: 0.7279 (ptm-80) cc_final: 0.6926 (ptm-80) REVERT: E 112 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.7011 (m-30) REVERT: E 127 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7617 (mt-10) REVERT: E 199 TYR cc_start: 0.8309 (t80) cc_final: 0.7893 (t80) REVERT: E 201 GLU cc_start: 0.7775 (tp30) cc_final: 0.7276 (tp30) REVERT: E 202 MET cc_start: 0.7711 (mtt) cc_final: 0.7343 (ttt) REVERT: E 207 VAL cc_start: 0.7737 (t) cc_final: 0.6988 (m) REVERT: E 210 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.7011 (ttpt) REVERT: E 231 THR cc_start: 0.8005 (m) cc_final: 0.7800 (t) REVERT: E 275 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8198 (t) REVERT: E 322 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7857 (m-80) REVERT: E 333 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.7468 (ttm-80) REVERT: E 369 LYS cc_start: 0.8304 (mttm) cc_final: 0.7950 (mtmm) REVERT: E 380 LEU cc_start: 0.8269 (tp) cc_final: 0.8039 (pp) REVERT: E 391 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5621 (tm-30) REVERT: E 435 ARG cc_start: 0.6643 (ttp80) cc_final: 0.6261 (ttp80) REVERT: E 450 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7144 (pm20) REVERT: E 451 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7387 (m-30) REVERT: E 469 MET cc_start: 0.6169 (mmm) cc_final: 0.5799 (mmm) REVERT: F 15 ASP cc_start: 0.7467 (m-30) cc_final: 0.7166 (m-30) REVERT: F 22 HIS cc_start: 0.7395 (m-70) cc_final: 0.7101 (m-70) REVERT: F 38 ASN cc_start: 0.7897 (t0) cc_final: 0.7647 (t0) REVERT: F 60 ARG cc_start: 0.7968 (ttt180) cc_final: 0.7681 (ttm170) REVERT: F 202 MET cc_start: 0.7208 (mmp) cc_final: 0.6982 (mmp) REVERT: F 278 GLN cc_start: 0.7962 (pm20) cc_final: 0.7581 (pm20) REVERT: F 285 MET cc_start: 0.7379 (ttp) cc_final: 0.6813 (ttp) REVERT: F 338 MET cc_start: 0.7431 (mtm) cc_final: 0.7206 (mtm) REVERT: F 354 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7124 (tp) REVERT: F 391 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7252 (tm-30) REVERT: F 438 LYS cc_start: 0.8534 (tttt) cc_final: 0.8189 (tttt) REVERT: F 458 ARG cc_start: 0.7047 (ttp-110) cc_final: 0.6832 (ttm110) REVERT: G 15 ASN cc_start: 0.8403 (m110) cc_final: 0.8066 (m-40) REVERT: G 37 ARG cc_start: 0.7757 (ttp80) cc_final: 0.7246 (ttp80) REVERT: G 43 LYS cc_start: 0.8364 (ttpt) cc_final: 0.8093 (ttpt) REVERT: G 48 TYR cc_start: 0.7951 (t80) cc_final: 0.7615 (t80) REVERT: G 123 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6930 (ttm110) REVERT: G 146 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7378 (pp30) REVERT: G 148 SER cc_start: 0.8800 (m) cc_final: 0.8469 (p) REVERT: G 153 LYS cc_start: 0.8034 (tttm) cc_final: 0.7637 (tttm) REVERT: G 183 GLN cc_start: 0.7619 (pp30) cc_final: 0.6896 (pp30) REVERT: G 188 GLU cc_start: 0.7669 (tt0) cc_final: 0.7353 (tt0) REVERT: G 222 GLN cc_start: 0.8170 (mt0) cc_final: 0.7871 (mt0) REVERT: G 239 GLU cc_start: 0.8196 (tt0) cc_final: 0.7832 (tt0) REVERT: G 267 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.8073 (ttm-80) REVERT: G 269 ARG cc_start: 0.7898 (ttp80) cc_final: 0.7512 (ttp80) REVERT: G 279 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7126 (mm-30) outliers start: 159 outliers final: 102 residues processed: 1061 average time/residue: 0.1626 time to fit residues: 262.5133 Evaluate side-chains 1078 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 955 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 379 GLU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain G residue 123 ARG Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 273 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 179 optimal weight: 3.9990 chunk 289 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 198 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 180 optimal weight: 0.3980 chunk 46 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 GLN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN B 69 ASN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 230 GLN C 433 GLN D 196 ASN ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN F 40 ASN ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.142163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.123599 restraints weight = 39718.447| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 3.09 r_work: 0.3577 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24608 Z= 0.196 Angle : 0.686 18.205 33370 Z= 0.355 Chirality : 0.048 0.265 3840 Planarity : 0.006 0.095 4349 Dihedral : 6.101 88.477 3418 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.64 % Favored : 95.33 % Rotamer: Outliers : 6.41 % Allowed : 28.73 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 3104 helix: 0.60 (0.14), residues: 1289 sheet: 0.10 (0.24), residues: 484 loop : -0.98 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 3 TYR 0.037 0.002 TYR G 103 PHE 0.025 0.002 PHE B 460 HIS 0.012 0.001 HIS F 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 (24608) covalent geometry : angle 0.68610 / 0.35 (33370) hydrogen bonds : bond 0.05684 / 3.88 ( 1143) hydrogen bonds : angle 5.23133 / 3.75 ( 3267) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1140 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 976 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 VAL cc_start: 0.7953 (OUTLIER) cc_final: 0.7622 (p) REVERT: A 60 MET cc_start: 0.6930 (mmt) cc_final: 0.6642 (mmp) REVERT: A 62 MET cc_start: 0.7338 (ptp) cc_final: 0.7030 (ptp) REVERT: A 87 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6697 (mm-30) REVERT: A 93 ARG cc_start: 0.7823 (ttm-80) cc_final: 0.7301 (ttm-80) REVERT: A 95 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6634 (tmm) REVERT: A 113 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7432 (mm-40) REVERT: A 139 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7650 (mtt-85) REVERT: A 154 ASP cc_start: 0.8222 (m-30) cc_final: 0.7991 (t0) REVERT: A 164 ARG cc_start: 0.7126 (mtm110) cc_final: 0.6714 (mtm110) REVERT: A 170 ASP cc_start: 0.6171 (t0) cc_final: 0.5968 (t0) REVERT: A 181 ASP cc_start: 0.7735 (m-30) cc_final: 0.7513 (m-30) REVERT: A 190 ASN cc_start: 0.8008 (m-40) cc_final: 0.7641 (m-40) REVERT: A 191 MET cc_start: 0.6819 (mmm) cc_final: 0.6305 (mmm) REVERT: A 193 SER cc_start: 0.7739 (m) cc_final: 0.7030 (t) REVERT: A 245 MET cc_start: 0.7183 (mtt) cc_final: 0.6919 (mtt) REVERT: A 262 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6821 (m-30) REVERT: A 266 GLN cc_start: 0.7659 (tt0) cc_final: 0.7290 (tp40) REVERT: A 317 PRO cc_start: 0.8151 (Cg_endo) cc_final: 0.7905 (Cg_exo) REVERT: A 341 GLN cc_start: 0.7763 (pm20) cc_final: 0.7396 (pm20) REVERT: A 365 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6978 (mmt-90) REVERT: A 376 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7719 (mtmt) REVERT: A 391 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7092 (pt0) REVERT: A 420 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7849 (mm) REVERT: A 432 LYS cc_start: 0.8022 (mttt) cc_final: 0.7791 (mttt) REVERT: A 456 PHE cc_start: 0.8008 (t80) cc_final: 0.7737 (t80) REVERT: B 86 ASP cc_start: 0.7209 (m-30) cc_final: 0.6983 (m-30) REVERT: B 88 VAL cc_start: 0.8147 (t) cc_final: 0.7827 (p) REVERT: B 93 ARG cc_start: 0.7466 (mmm160) cc_final: 0.7102 (mmm-85) REVERT: B 96 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7003 (mt-10) REVERT: B 127 ARG cc_start: 0.7439 (ttm-80) cc_final: 0.7145 (ttm-80) REVERT: B 136 VAL cc_start: 0.6773 (p) cc_final: 0.5586 (m) REVERT: B 144 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7450 (tm-30) REVERT: B 171 ARG cc_start: 0.6949 (mtp-110) cc_final: 0.6714 (mtp85) REVERT: B 175 LYS cc_start: 0.7863 (mtmm) cc_final: 0.7581 (mtmm) REVERT: B 181 ASP cc_start: 0.7731 (t70) cc_final: 0.7408 (t70) REVERT: B 191 MET cc_start: 0.7632 (tpp) cc_final: 0.7271 (tpp) REVERT: B 272 GLU cc_start: 0.7937 (tt0) cc_final: 0.7231 (tt0) REVERT: B 305 SER cc_start: 0.7562 (m) cc_final: 0.7283 (m) REVERT: B 333 ASN cc_start: 0.8263 (t0) cc_final: 0.7947 (t0) REVERT: B 341 GLN cc_start: 0.7304 (pt0) cc_final: 0.6836 (pt0) REVERT: B 373 LYS cc_start: 0.7641 (ttmt) cc_final: 0.7017 (ttmt) REVERT: B 377 LYS cc_start: 0.8291 (mttp) cc_final: 0.7915 (mttp) REVERT: B 392 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7927 (tp) REVERT: B 432 LYS cc_start: 0.8698 (mttt) cc_final: 0.8258 (mttt) REVERT: B 436 ILE cc_start: 0.8188 (mm) cc_final: 0.7955 (tp) REVERT: B 458 LYS cc_start: 0.7207 (tmmt) cc_final: 0.6844 (mttp) REVERT: C 54 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6672 (pt0) REVERT: C 95 MET cc_start: 0.7042 (tpt) cc_final: 0.6790 (tpt) REVERT: C 161 ARG cc_start: 0.7469 (mtt180) cc_final: 0.7006 (mmt90) REVERT: C 202 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7164 (tt0) REVERT: C 206 ARG cc_start: 0.7862 (ttt180) cc_final: 0.7144 (ttm170) REVERT: C 214 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8307 (mtpt) REVERT: C 272 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7237 (mt-10) REVERT: C 299 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7474 (mt-10) REVERT: C 353 VAL cc_start: 0.8401 (t) cc_final: 0.7987 (p) REVERT: C 361 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7901 (tp) REVERT: C 376 LYS cc_start: 0.7614 (mmmt) cc_final: 0.7386 (mmmm) REVERT: C 377 LYS cc_start: 0.8434 (tttp) cc_final: 0.8090 (tttp) REVERT: C 389 TYR cc_start: 0.8003 (t80) cc_final: 0.7384 (t80) REVERT: C 409 LYS cc_start: 0.8175 (tptt) cc_final: 0.7595 (tptt) REVERT: C 435 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8123 (mm) REVERT: C 484 GLU cc_start: 0.7343 (tt0) cc_final: 0.6850 (tt0) REVERT: C 488 ASN cc_start: 0.7810 (m110) cc_final: 0.7474 (m110) REVERT: D 8 GLN cc_start: 0.7608 (tt0) cc_final: 0.6842 (tt0) REVERT: D 10 MET cc_start: 0.7517 (mtm) cc_final: 0.7221 (mtm) REVERT: D 17 LYS cc_start: 0.8031 (tmtt) cc_final: 0.7690 (tmtt) REVERT: D 35 LYS cc_start: 0.8085 (ttmt) cc_final: 0.7738 (ttmt) REVERT: D 115 ARG cc_start: 0.6959 (mtt-85) cc_final: 0.6515 (mtt-85) REVERT: D 120 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6599 (ptt-90) REVERT: D 154 ILE cc_start: 0.7904 (mm) cc_final: 0.7519 (mt) REVERT: D 157 PHE cc_start: 0.7363 (m-80) cc_final: 0.6985 (m-80) REVERT: D 202 MET cc_start: 0.7616 (mmt) cc_final: 0.7099 (mmt) REVERT: D 207 VAL cc_start: 0.8639 (t) cc_final: 0.7830 (p) REVERT: D 227 ARG cc_start: 0.6905 (mmt90) cc_final: 0.6521 (mmt90) REVERT: D 233 LEU cc_start: 0.7682 (tp) cc_final: 0.7236 (tp) REVERT: D 267 LEU cc_start: 0.8075 (mm) cc_final: 0.7493 (mt) REVERT: D 294 SER cc_start: 0.7419 (t) cc_final: 0.6804 (p) REVERT: D 340 ILE cc_start: 0.8535 (pt) cc_final: 0.8055 (mm) REVERT: D 365 GLN cc_start: 0.7763 (tm-30) cc_final: 0.7300 (tm-30) REVERT: D 378 LYS cc_start: 0.8511 (tttt) cc_final: 0.8086 (mtpp) REVERT: D 396 ASP cc_start: 0.8169 (m-30) cc_final: 0.7944 (m-30) REVERT: D 405 ARG cc_start: 0.7790 (mpt90) cc_final: 0.7527 (mpt90) REVERT: D 428 VAL cc_start: 0.6348 (OUTLIER) cc_final: 0.5260 (p) REVERT: D 439 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6761 (mm-30) REVERT: D 441 LEU cc_start: 0.8828 (mt) cc_final: 0.8577 (mp) REVERT: D 464 GLU cc_start: 0.8121 (tp30) cc_final: 0.7720 (tp30) REVERT: E 5 ARG cc_start: 0.7288 (ptm-80) cc_final: 0.6938 (ptm-80) REVERT: E 112 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.7042 (m-30) REVERT: E 127 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7676 (mt-10) REVERT: E 201 GLU cc_start: 0.7798 (tp30) cc_final: 0.7294 (tp30) REVERT: E 202 MET cc_start: 0.7765 (mtt) cc_final: 0.7374 (ttt) REVERT: E 207 VAL cc_start: 0.7779 (t) cc_final: 0.6971 (m) REVERT: E 210 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7182 (ttpt) REVERT: E 231 THR cc_start: 0.8041 (m) cc_final: 0.7832 (t) REVERT: E 241 ASP cc_start: 0.7827 (t0) cc_final: 0.7613 (t0) REVERT: E 322 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: E 333 ARG cc_start: 0.7781 (ttm-80) cc_final: 0.7511 (ttm-80) REVERT: E 369 LYS cc_start: 0.8295 (mttm) cc_final: 0.8067 (mtmm) REVERT: E 378 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7926 (tmmm) REVERT: E 380 LEU cc_start: 0.8300 (tp) cc_final: 0.8075 (pp) REVERT: E 391 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.5523 (tm-30) REVERT: E 435 ARG cc_start: 0.6680 (ttp80) cc_final: 0.6358 (ttp80) REVERT: E 450 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7145 (pm20) REVERT: E 469 MET cc_start: 0.6162 (mmm) cc_final: 0.5786 (mmm) REVERT: F 15 ASP cc_start: 0.7483 (m-30) cc_final: 0.7191 (m-30) REVERT: F 22 HIS cc_start: 0.7387 (m-70) cc_final: 0.7112 (m-70) REVERT: F 37 ARG cc_start: 0.7056 (ttm110) cc_final: 0.6849 (ttm110) REVERT: F 38 ASN cc_start: 0.7913 (t0) cc_final: 0.7673 (t0) REVERT: F 60 ARG cc_start: 0.7939 (ttt180) cc_final: 0.7678 (ttm170) REVERT: F 202 MET cc_start: 0.7257 (mmp) cc_final: 0.7042 (mmp) REVERT: F 218 MET cc_start: 0.7206 (mtp) cc_final: 0.6957 (ptp) REVERT: F 227 ARG cc_start: 0.6645 (mmm160) cc_final: 0.6427 (mmt180) REVERT: F 278 GLN cc_start: 0.7924 (pm20) cc_final: 0.7546 (pm20) REVERT: F 285 MET cc_start: 0.7416 (ttp) cc_final: 0.6883 (ttp) REVERT: F 338 MET cc_start: 0.7442 (mtm) cc_final: 0.7221 (mtm) REVERT: F 354 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7032 (tp) REVERT: F 401 HIS cc_start: 0.7619 (t-90) cc_final: 0.7401 (t-90) REVERT: F 438 LYS cc_start: 0.8537 (tttt) cc_final: 0.8199 (tttt) REVERT: F 458 ARG cc_start: 0.7157 (ttp-110) cc_final: 0.6360 (mtp-110) REVERT: G 15 ASN cc_start: 0.8410 (m110) cc_final: 0.8067 (m-40) REVERT: G 37 ARG cc_start: 0.7768 (ttp80) cc_final: 0.7278 (ttp80) REVERT: G 48 TYR cc_start: 0.7946 (t80) cc_final: 0.7589 (t80) REVERT: G 70 MET cc_start: 0.8269 (mmp) cc_final: 0.7678 (mmp) REVERT: G 123 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6971 (ttm110) REVERT: G 146 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7330 (pp30) REVERT: G 148 SER cc_start: 0.8823 (m) cc_final: 0.8466 (p) REVERT: G 153 LYS cc_start: 0.8039 (tttm) cc_final: 0.7679 (tttm) REVERT: G 183 GLN cc_start: 0.7714 (pp30) cc_final: 0.7040 (pp30) REVERT: G 185 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7065 (mm-30) REVERT: G 188 GLU cc_start: 0.7708 (tt0) cc_final: 0.7393 (tt0) REVERT: G 194 LEU cc_start: 0.5830 (OUTLIER) cc_final: 0.5548 (tm) REVERT: G 222 GLN cc_start: 0.8230 (mt0) cc_final: 0.7924 (mt0) REVERT: G 239 GLU cc_start: 0.8259 (tt0) cc_final: 0.8057 (tt0) REVERT: G 267 ARG cc_start: 0.8341 (ttm-80) cc_final: 0.8066 (ttm-80) REVERT: G 269 ARG cc_start: 0.7897 (ttp80) cc_final: 0.7524 (ttp80) REVERT: G 279 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7143 (mm-30) outliers start: 164 outliers final: 109 residues processed: 1046 average time/residue: 0.1783 time to fit residues: 281.9500 Evaluate side-chains 1096 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 962 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 120 ARG Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 179 HIS Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain G residue 123 ARG Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 190 LYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 285 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 293 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 135 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 243 optimal weight: 0.9990 chunk 282 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 296 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN C 230 GLN C 433 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN E 375 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.143058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.124548 restraints weight = 39522.783| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 3.09 r_work: 0.3589 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24608 Z= 0.171 Angle : 0.677 18.614 33370 Z= 0.348 Chirality : 0.047 0.275 3840 Planarity : 0.006 0.088 4349 Dihedral : 5.983 87.847 3418 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.16 % Favored : 95.81 % Rotamer: Outliers : 6.06 % Allowed : 29.79 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 3104 helix: 0.69 (0.14), residues: 1290 sheet: 0.07 (0.23), residues: 483 loop : -0.93 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 283 TYR 0.028 0.002 TYR F 199 PHE 0.027 0.002 PHE D 185 HIS 0.010 0.001 HIS F 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (24608) covalent geometry : angle 0.67673 / 0.35 (33370) hydrogen bonds : bond 0.05408 / 3.70 ( 1143) hydrogen bonds : angle 5.15870 / 3.70 ( 3267) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1124 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 969 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 VAL cc_start: 0.7932 (OUTLIER) cc_final: 0.7599 (p) REVERT: A 60 MET cc_start: 0.6895 (mmt) cc_final: 0.6604 (mmp) REVERT: A 62 MET cc_start: 0.7345 (ptp) cc_final: 0.7030 (ptp) REVERT: A 67 GLU cc_start: 0.7530 (mm-30) cc_final: 0.6993 (mm-30) REVERT: A 87 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6740 (mm-30) REVERT: A 93 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7028 (ttm-80) REVERT: A 95 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6683 (tmm) REVERT: A 96 GLU cc_start: 0.6704 (pt0) cc_final: 0.5904 (pt0) REVERT: A 113 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7540 (mm-40) REVERT: A 139 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7661 (mtt-85) REVERT: A 154 ASP cc_start: 0.8275 (m-30) cc_final: 0.8036 (t0) REVERT: A 164 ARG cc_start: 0.7115 (mtm110) cc_final: 0.6738 (mtm110) REVERT: A 170 ASP cc_start: 0.6207 (t0) cc_final: 0.5968 (t0) REVERT: A 181 ASP cc_start: 0.7747 (m-30) cc_final: 0.7537 (m-30) REVERT: A 190 ASN cc_start: 0.8008 (m-40) cc_final: 0.7642 (m-40) REVERT: A 191 MET cc_start: 0.6779 (mmm) cc_final: 0.6271 (mmm) REVERT: A 193 SER cc_start: 0.7711 (m) cc_final: 0.7008 (t) REVERT: A 215 HIS cc_start: 0.7612 (OUTLIER) cc_final: 0.6556 (t-90) REVERT: A 245 MET cc_start: 0.7220 (mtt) cc_final: 0.6936 (mtt) REVERT: A 266 GLN cc_start: 0.7601 (tt0) cc_final: 0.7246 (tp40) REVERT: A 335 ILE cc_start: 0.8627 (mm) cc_final: 0.8213 (tt) REVERT: A 341 GLN cc_start: 0.7722 (pm20) cc_final: 0.7333 (pm20) REVERT: A 365 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7029 (mmt-90) REVERT: A 383 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6598 (tpt170) REVERT: A 391 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7070 (pt0) REVERT: A 420 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7807 (mm) REVERT: A 432 LYS cc_start: 0.7961 (mttt) cc_final: 0.7727 (mttt) REVERT: A 446 ASP cc_start: 0.7220 (m-30) cc_final: 0.6967 (m-30) REVERT: A 456 PHE cc_start: 0.8000 (t80) cc_final: 0.7741 (t80) REVERT: B 86 ASP cc_start: 0.7260 (m-30) cc_final: 0.7003 (m-30) REVERT: B 88 VAL cc_start: 0.8153 (t) cc_final: 0.7818 (p) REVERT: B 93 ARG cc_start: 0.7399 (mmm160) cc_final: 0.6801 (mmm-85) REVERT: B 96 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6793 (mt-10) REVERT: B 122 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6595 (mm-30) REVERT: B 136 VAL cc_start: 0.6806 (p) cc_final: 0.5617 (m) REVERT: B 171 ARG cc_start: 0.6820 (mtp-110) cc_final: 0.6596 (mtp85) REVERT: B 181 ASP cc_start: 0.7766 (t70) cc_final: 0.7444 (t70) REVERT: B 191 MET cc_start: 0.7605 (tpp) cc_final: 0.7264 (tpp) REVERT: B 305 SER cc_start: 0.7573 (m) cc_final: 0.7308 (m) REVERT: B 333 ASN cc_start: 0.8244 (t0) cc_final: 0.7925 (t0) REVERT: B 341 GLN cc_start: 0.7264 (pt0) cc_final: 0.6930 (pt0) REVERT: B 373 LYS cc_start: 0.7601 (ttmt) cc_final: 0.6993 (ttmt) REVERT: B 377 LYS cc_start: 0.8308 (mttp) cc_final: 0.7926 (mttp) REVERT: B 392 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7909 (tp) REVERT: B 432 LYS cc_start: 0.8696 (mttt) cc_final: 0.8243 (mttt) REVERT: B 436 ILE cc_start: 0.8155 (mm) cc_final: 0.7916 (tp) REVERT: B 458 LYS cc_start: 0.7182 (tmmt) cc_final: 0.6826 (mttp) REVERT: C 95 MET cc_start: 0.7075 (tpt) cc_final: 0.6662 (tpt) REVERT: C 161 ARG cc_start: 0.7478 (mtt180) cc_final: 0.6979 (mmt90) REVERT: C 202 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7073 (tt0) REVERT: C 206 ARG cc_start: 0.7862 (ttt180) cc_final: 0.7653 (tpp-160) REVERT: C 214 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8322 (ttpt) REVERT: C 272 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7230 (mt-10) REVERT: C 299 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7465 (mt-10) REVERT: C 353 VAL cc_start: 0.8386 (t) cc_final: 0.7951 (p) REVERT: C 361 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7912 (tp) REVERT: C 376 LYS cc_start: 0.7595 (mmmt) cc_final: 0.7289 (mmmm) REVERT: C 377 LYS cc_start: 0.8437 (tttp) cc_final: 0.8084 (tttp) REVERT: C 389 TYR cc_start: 0.7952 (t80) cc_final: 0.7622 (t80) REVERT: C 409 LYS cc_start: 0.8199 (tptt) cc_final: 0.7793 (mtpp) REVERT: C 435 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8097 (mm) REVERT: C 484 GLU cc_start: 0.7336 (tt0) cc_final: 0.6830 (tt0) REVERT: C 488 ASN cc_start: 0.7827 (m110) cc_final: 0.7494 (m110) REVERT: D 8 GLN cc_start: 0.7584 (tt0) cc_final: 0.6842 (tt0) REVERT: D 10 MET cc_start: 0.7544 (mtm) cc_final: 0.7234 (mtm) REVERT: D 17 LYS cc_start: 0.8031 (tmtt) cc_final: 0.7685 (tmtt) REVERT: D 35 LYS cc_start: 0.8086 (ttmt) cc_final: 0.7732 (ttmt) REVERT: D 120 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6665 (ptt-90) REVERT: D 154 ILE cc_start: 0.7858 (mm) cc_final: 0.7449 (mt) REVERT: D 157 PHE cc_start: 0.7350 (m-80) cc_final: 0.7016 (m-80) REVERT: D 202 MET cc_start: 0.7609 (mmt) cc_final: 0.7098 (mmt) REVERT: D 207 VAL cc_start: 0.8630 (t) cc_final: 0.7819 (p) REVERT: D 227 ARG cc_start: 0.6895 (mmt90) cc_final: 0.6674 (mmt90) REVERT: D 267 LEU cc_start: 0.8039 (mm) cc_final: 0.7453 (mt) REVERT: D 294 SER cc_start: 0.7375 (t) cc_final: 0.6781 (p) REVERT: D 365 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7232 (tm-30) REVERT: D 378 LYS cc_start: 0.8480 (tttt) cc_final: 0.8046 (mtpp) REVERT: D 396 ASP cc_start: 0.8178 (m-30) cc_final: 0.7948 (m-30) REVERT: D 405 ARG cc_start: 0.7733 (mpt90) cc_final: 0.7476 (mpt90) REVERT: D 428 VAL cc_start: 0.6311 (OUTLIER) cc_final: 0.5233 (p) REVERT: D 439 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6800 (mm-30) REVERT: D 441 LEU cc_start: 0.8821 (mt) cc_final: 0.8567 (mp) REVERT: D 464 GLU cc_start: 0.8089 (tp30) cc_final: 0.7689 (tp30) REVERT: E 5 ARG cc_start: 0.7268 (ptm-80) cc_final: 0.6937 (ptm-80) REVERT: E 112 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.7078 (m-30) REVERT: E 127 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7727 (mt-10) REVERT: E 201 GLU cc_start: 0.7756 (tp30) cc_final: 0.7164 (tp30) REVERT: E 202 MET cc_start: 0.7761 (mtt) cc_final: 0.7326 (ttt) REVERT: E 207 VAL cc_start: 0.7736 (t) cc_final: 0.6831 (m) REVERT: E 210 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.7087 (ttpt) REVERT: E 231 THR cc_start: 0.8037 (m) cc_final: 0.7831 (t) REVERT: E 322 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: E 330 ASN cc_start: 0.7212 (m-40) cc_final: 0.6942 (t0) REVERT: E 333 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7513 (ttm-80) REVERT: E 369 LYS cc_start: 0.8270 (mttm) cc_final: 0.8065 (mtmm) REVERT: E 380 LEU cc_start: 0.8303 (tp) cc_final: 0.8087 (tp) REVERT: E 391 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5518 (tm-30) REVERT: E 435 ARG cc_start: 0.6614 (ttp80) cc_final: 0.6259 (ttp80) REVERT: E 469 MET cc_start: 0.6092 (mmm) cc_final: 0.5649 (mmm) REVERT: F 15 ASP cc_start: 0.7459 (m-30) cc_final: 0.7152 (m-30) REVERT: F 22 HIS cc_start: 0.7349 (m-70) cc_final: 0.7073 (m-70) REVERT: F 37 ARG cc_start: 0.7051 (ttm110) cc_final: 0.6835 (ttm110) REVERT: F 38 ASN cc_start: 0.7877 (t0) cc_final: 0.7670 (t0) REVERT: F 60 ARG cc_start: 0.7927 (ttt180) cc_final: 0.7687 (ttm170) REVERT: F 202 MET cc_start: 0.7212 (mmp) cc_final: 0.7008 (mmp) REVERT: F 218 MET cc_start: 0.7145 (mtp) cc_final: 0.6800 (ptp) REVERT: F 278 GLN cc_start: 0.7943 (pm20) cc_final: 0.7543 (pm20) REVERT: F 285 MET cc_start: 0.7376 (ttp) cc_final: 0.6833 (ttp) REVERT: F 330 ASN cc_start: 0.6759 (m-40) cc_final: 0.6272 (m-40) REVERT: F 338 MET cc_start: 0.7414 (mtm) cc_final: 0.7192 (mtm) REVERT: F 438 LYS cc_start: 0.8518 (tttt) cc_final: 0.8112 (tttt) REVERT: F 458 ARG cc_start: 0.6845 (ttp-110) cc_final: 0.6381 (mtp-110) REVERT: G 15 ASN cc_start: 0.8397 (m110) cc_final: 0.8035 (m-40) REVERT: G 37 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7295 (ttp80) REVERT: G 48 TYR cc_start: 0.7989 (t80) cc_final: 0.7583 (t80) REVERT: G 70 MET cc_start: 0.8280 (mmp) cc_final: 0.7623 (mmp) REVERT: G 103 TYR cc_start: 0.8248 (t80) cc_final: 0.7740 (t80) REVERT: G 132 ARG cc_start: 0.8075 (mmp80) cc_final: 0.7274 (mmm-85) REVERT: G 146 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7228 (pp30) REVERT: G 148 SER cc_start: 0.8787 (m) cc_final: 0.8444 (p) REVERT: G 153 LYS cc_start: 0.8082 (tttm) cc_final: 0.7692 (tttm) REVERT: G 183 GLN cc_start: 0.7696 (pp30) cc_final: 0.7017 (pp30) REVERT: G 185 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7059 (mm-30) REVERT: G 188 GLU cc_start: 0.7730 (tt0) cc_final: 0.7429 (tt0) REVERT: G 194 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5581 (tm) REVERT: G 222 GLN cc_start: 0.8237 (mt0) cc_final: 0.7929 (mt0) REVERT: G 244 MET cc_start: 0.8128 (ttp) cc_final: 0.7852 (ttp) REVERT: G 267 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.8068 (ttm-80) REVERT: G 269 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7537 (ttp80) REVERT: G 279 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7176 (mm-30) outliers start: 155 outliers final: 103 residues processed: 1034 average time/residue: 0.1622 time to fit residues: 254.0334 Evaluate side-chains 1077 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 953 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 179 HIS Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 190 LYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 285 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 75 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 295 optimal weight: 9.9990 chunk 224 optimal weight: 0.9990 chunk 292 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 195 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 285 optimal weight: 9.9990 chunk 266 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN C 407 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN F 324 HIS ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 HIS ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.143874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.125337 restraints weight = 39542.301| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.10 r_work: 0.3605 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24608 Z= 0.151 Angle : 0.669 18.247 33370 Z= 0.343 Chirality : 0.047 0.283 3840 Planarity : 0.005 0.078 4349 Dihedral : 5.879 86.899 3418 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.03 % Favored : 95.94 % Rotamer: Outliers : 5.71 % Allowed : 30.45 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 3104 helix: 0.82 (0.14), residues: 1289 sheet: 0.09 (0.24), residues: 477 loop : -0.86 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 3 TYR 0.020 0.001 TYR E 238 PHE 0.024 0.002 PHE D 185 HIS 0.010 0.001 HIS F 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (24608) covalent geometry : angle 0.66867 / 0.34 (33370) hydrogen bonds : bond 0.05062 / 3.47 ( 1143) hydrogen bonds : angle 5.08474 / 3.66 ( 3267) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 951 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7585 (p) REVERT: A 60 MET cc_start: 0.6900 (mmt) cc_final: 0.6614 (mmp) REVERT: A 62 MET cc_start: 0.7273 (ptp) cc_final: 0.6972 (ptp) REVERT: A 67 GLU cc_start: 0.7507 (mm-30) cc_final: 0.6979 (mm-30) REVERT: A 87 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6764 (mm-30) REVERT: A 93 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7069 (ttm-80) REVERT: A 95 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6687 (tmm) REVERT: A 96 GLU cc_start: 0.6766 (pt0) cc_final: 0.6013 (pt0) REVERT: A 113 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7576 (mm-40) REVERT: A 125 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7194 (mm-30) REVERT: A 139 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7665 (mtt-85) REVERT: A 164 ARG cc_start: 0.7154 (mtm110) cc_final: 0.6786 (mtm110) REVERT: A 181 ASP cc_start: 0.7713 (m-30) cc_final: 0.7498 (m-30) REVERT: A 190 ASN cc_start: 0.7959 (m-40) cc_final: 0.7603 (m-40) REVERT: A 191 MET cc_start: 0.6735 (mmm) cc_final: 0.6232 (mmm) REVERT: A 193 SER cc_start: 0.7607 (m) cc_final: 0.6940 (t) REVERT: A 215 HIS cc_start: 0.7597 (OUTLIER) cc_final: 0.6602 (t-90) REVERT: A 245 MET cc_start: 0.7196 (mtt) cc_final: 0.6918 (mtt) REVERT: A 335 ILE cc_start: 0.8607 (mm) cc_final: 0.8207 (tt) REVERT: A 341 GLN cc_start: 0.7650 (pm20) cc_final: 0.7191 (pm20) REVERT: A 365 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6987 (mmt-90) REVERT: A 383 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6600 (tpt170) REVERT: A 391 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6978 (pt0) REVERT: A 420 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7830 (mm) REVERT: A 456 PHE cc_start: 0.8003 (t80) cc_final: 0.7748 (t80) REVERT: B 88 VAL cc_start: 0.8146 (t) cc_final: 0.7791 (p) REVERT: B 122 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6630 (mm-30) REVERT: B 136 VAL cc_start: 0.6795 (p) cc_final: 0.5593 (m) REVERT: B 171 ARG cc_start: 0.6808 (mtp-110) cc_final: 0.6591 (mtp85) REVERT: B 181 ASP cc_start: 0.7713 (t70) cc_final: 0.7395 (t70) REVERT: B 191 MET cc_start: 0.7564 (tpp) cc_final: 0.7212 (tpp) REVERT: B 305 SER cc_start: 0.7555 (m) cc_final: 0.7290 (m) REVERT: B 333 ASN cc_start: 0.8226 (t0) cc_final: 0.7928 (t0) REVERT: B 341 GLN cc_start: 0.7225 (pt0) cc_final: 0.6863 (pt0) REVERT: B 373 LYS cc_start: 0.7583 (ttmt) cc_final: 0.7025 (ttmt) REVERT: B 377 LYS cc_start: 0.8292 (mttp) cc_final: 0.7928 (mttp) REVERT: B 392 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7886 (tp) REVERT: B 432 LYS cc_start: 0.8678 (mttt) cc_final: 0.8221 (mttt) REVERT: B 436 ILE cc_start: 0.8112 (mm) cc_final: 0.7858 (tp) REVERT: B 458 LYS cc_start: 0.7169 (tmmt) cc_final: 0.6807 (mttp) REVERT: C 95 MET cc_start: 0.7037 (tpt) cc_final: 0.6613 (tpt) REVERT: C 202 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7018 (tt0) REVERT: C 206 ARG cc_start: 0.7833 (ttt180) cc_final: 0.7626 (tpp-160) REVERT: C 214 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8328 (ttpt) REVERT: C 272 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7303 (mt-10) REVERT: C 299 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7462 (mt-10) REVERT: C 353 VAL cc_start: 0.8371 (t) cc_final: 0.7927 (p) REVERT: C 361 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7947 (tp) REVERT: C 376 LYS cc_start: 0.7589 (mmmt) cc_final: 0.7280 (mmmm) REVERT: C 377 LYS cc_start: 0.8429 (tttp) cc_final: 0.8079 (tttp) REVERT: C 389 TYR cc_start: 0.7922 (t80) cc_final: 0.7597 (t80) REVERT: C 407 GLN cc_start: 0.8021 (pt0) cc_final: 0.7785 (pt0) REVERT: C 409 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7775 (mtpp) REVERT: C 435 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8068 (mm) REVERT: C 484 GLU cc_start: 0.7301 (tt0) cc_final: 0.6783 (tt0) REVERT: C 488 ASN cc_start: 0.7851 (m110) cc_final: 0.7524 (m110) REVERT: C 489 LYS cc_start: 0.8495 (tmtt) cc_final: 0.8285 (tttt) REVERT: D 8 GLN cc_start: 0.7598 (tt0) cc_final: 0.7297 (tt0) REVERT: D 17 LYS cc_start: 0.8012 (tmtt) cc_final: 0.7672 (tmtt) REVERT: D 35 LYS cc_start: 0.8051 (ttmt) cc_final: 0.7543 (ttmt) REVERT: D 120 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6696 (ptt-90) REVERT: D 154 ILE cc_start: 0.7825 (mm) cc_final: 0.7420 (mt) REVERT: D 157 PHE cc_start: 0.7307 (m-80) cc_final: 0.7031 (m-80) REVERT: D 202 MET cc_start: 0.7597 (mmt) cc_final: 0.7103 (mmt) REVERT: D 203 LYS cc_start: 0.7623 (ttmm) cc_final: 0.7130 (mttt) REVERT: D 207 VAL cc_start: 0.8575 (t) cc_final: 0.7752 (p) REVERT: D 220 GLU cc_start: 0.7430 (mp0) cc_final: 0.7025 (mp0) REVERT: D 267 LEU cc_start: 0.8027 (mm) cc_final: 0.7410 (mt) REVERT: D 294 SER cc_start: 0.7321 (t) cc_final: 0.6743 (p) REVERT: D 333 ARG cc_start: 0.7575 (ttm110) cc_final: 0.7342 (ttm110) REVERT: D 365 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7179 (tm-30) REVERT: D 378 LYS cc_start: 0.8449 (tttt) cc_final: 0.8030 (mtpp) REVERT: D 382 ASP cc_start: 0.8114 (p0) cc_final: 0.7717 (p0) REVERT: D 405 ARG cc_start: 0.7710 (mpt90) cc_final: 0.7458 (mpt90) REVERT: D 428 VAL cc_start: 0.6302 (OUTLIER) cc_final: 0.5228 (p) REVERT: D 439 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6760 (mm-30) REVERT: D 441 LEU cc_start: 0.8804 (mt) cc_final: 0.8549 (mp) REVERT: D 464 GLU cc_start: 0.8070 (tp30) cc_final: 0.7647 (tp30) REVERT: E 5 ARG cc_start: 0.7234 (ptm-80) cc_final: 0.6909 (ptm-80) REVERT: E 112 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.7037 (m-30) REVERT: E 127 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7663 (mt-10) REVERT: E 201 GLU cc_start: 0.7751 (tp30) cc_final: 0.7172 (tp30) REVERT: E 202 MET cc_start: 0.7757 (mtt) cc_final: 0.7320 (ttt) REVERT: E 207 VAL cc_start: 0.7687 (t) cc_final: 0.6778 (m) REVERT: E 210 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.7055 (ttpt) REVERT: E 231 THR cc_start: 0.8037 (m) cc_final: 0.7830 (t) REVERT: E 302 SER cc_start: 0.7709 (OUTLIER) cc_final: 0.7336 (p) REVERT: E 322 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: E 330 ASN cc_start: 0.7183 (m-40) cc_final: 0.6971 (t0) REVERT: E 333 ARG cc_start: 0.7837 (ttm-80) cc_final: 0.7518 (ttm-80) REVERT: E 352 ARG cc_start: 0.8038 (tmm-80) cc_final: 0.7707 (ttp-170) REVERT: E 380 LEU cc_start: 0.8288 (tp) cc_final: 0.8039 (pp) REVERT: E 391 GLU cc_start: 0.5919 (OUTLIER) cc_final: 0.5485 (tm-30) REVERT: E 435 ARG cc_start: 0.6593 (ttp80) cc_final: 0.6220 (ttp80) REVERT: E 458 ARG cc_start: 0.6849 (mtp-110) cc_final: 0.6387 (ptm-80) REVERT: E 465 LYS cc_start: 0.8575 (tttp) cc_final: 0.7868 (tttp) REVERT: E 469 MET cc_start: 0.6048 (mmm) cc_final: 0.5484 (mmm) REVERT: F 15 ASP cc_start: 0.7450 (m-30) cc_final: 0.7170 (m-30) REVERT: F 22 HIS cc_start: 0.7259 (m-70) cc_final: 0.7008 (m-70) REVERT: F 37 ARG cc_start: 0.7037 (ttm110) cc_final: 0.6829 (ttm110) REVERT: F 38 ASN cc_start: 0.7873 (t0) cc_final: 0.7644 (t0) REVERT: F 202 MET cc_start: 0.7170 (mmp) cc_final: 0.6673 (mmp) REVERT: F 218 MET cc_start: 0.7113 (mtp) cc_final: 0.6828 (ptp) REVERT: F 278 GLN cc_start: 0.7930 (pm20) cc_final: 0.7500 (pm20) REVERT: F 285 MET cc_start: 0.7395 (ttp) cc_final: 0.6828 (ttp) REVERT: F 330 ASN cc_start: 0.6736 (m-40) cc_final: 0.6294 (m-40) REVERT: F 338 MET cc_start: 0.7387 (mtm) cc_final: 0.7174 (mtm) REVERT: F 438 LYS cc_start: 0.8462 (tttt) cc_final: 0.8094 (tttt) REVERT: F 458 ARG cc_start: 0.6863 (ttp-110) cc_final: 0.6394 (mtp-110) REVERT: G 15 ASN cc_start: 0.8360 (m110) cc_final: 0.7944 (m-40) REVERT: G 37 ARG cc_start: 0.7693 (ttp80) cc_final: 0.7277 (ttp80) REVERT: G 48 TYR cc_start: 0.7965 (t80) cc_final: 0.7362 (t80) REVERT: G 49 MET cc_start: 0.7624 (mmt) cc_final: 0.6734 (mmt) REVERT: G 70 MET cc_start: 0.8268 (mmp) cc_final: 0.7624 (mmp) REVERT: G 132 ARG cc_start: 0.8086 (mmp80) cc_final: 0.7866 (mmp80) REVERT: G 134 MET cc_start: 0.6656 (mtt) cc_final: 0.6266 (mtt) REVERT: G 146 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7246 (pp30) REVERT: G 148 SER cc_start: 0.8787 (m) cc_final: 0.8445 (p) REVERT: G 153 LYS cc_start: 0.8001 (tttm) cc_final: 0.7705 (tttm) REVERT: G 183 GLN cc_start: 0.7662 (pp30) cc_final: 0.6939 (pp30) REVERT: G 185 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7053 (mm-30) REVERT: G 188 GLU cc_start: 0.7745 (tt0) cc_final: 0.7471 (tt0) REVERT: G 194 LEU cc_start: 0.5852 (OUTLIER) cc_final: 0.5568 (tm) REVERT: G 222 GLN cc_start: 0.8198 (mt0) cc_final: 0.7938 (mt0) REVERT: G 244 MET cc_start: 0.8098 (ttp) cc_final: 0.7759 (ttp) REVERT: G 269 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7524 (ttp80) REVERT: G 279 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7159 (mm-30) outliers start: 146 outliers final: 102 residues processed: 1014 average time/residue: 0.1540 time to fit residues: 238.0567 Evaluate side-chains 1072 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 947 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 120 ARG Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 179 HIS Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 190 LYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 267 ARG Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 274 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 122 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 301 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 chunk 253 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 264 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** F 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.139995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.121833 restraints weight = 39869.816| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 3.06 r_work: 0.3552 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 24608 Z= 0.307 Angle : 0.789 17.448 33370 Z= 0.416 Chirality : 0.052 0.296 3840 Planarity : 0.006 0.067 4349 Dihedral : 6.367 85.911 3418 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.86 % Favored : 94.10 % Rotamer: Outliers : 5.36 % Allowed : 30.88 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.15), residues: 3104 helix: 0.29 (0.14), residues: 1291 sheet: -0.13 (0.24), residues: 466 loop : -1.11 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 383 TYR 0.024 0.002 TYR E 238 PHE 0.034 0.003 PHE D 185 HIS 0.010 0.002 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.31 (24608) covalent geometry : angle 0.78880 / 0.42 (33370) hydrogen bonds : bond 0.06615 / 4.51 ( 1143) hydrogen bonds : angle 5.56130 / 3.98 ( 3267) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 962 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.6858 (mmt) cc_final: 0.6544 (mmp) REVERT: A 62 MET cc_start: 0.7346 (ptp) cc_final: 0.7040 (ptp) REVERT: A 67 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7132 (mm-30) REVERT: A 87 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6821 (mm-30) REVERT: A 93 ARG cc_start: 0.7852 (ttm-80) cc_final: 0.7338 (ttm-80) REVERT: A 95 MET cc_start: 0.7056 (mmm) cc_final: 0.6677 (tmm) REVERT: A 139 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7688 (mtt-85) REVERT: A 164 ARG cc_start: 0.7211 (mtm110) cc_final: 0.6778 (mtm110) REVERT: A 181 ASP cc_start: 0.7748 (m-30) cc_final: 0.7536 (m-30) REVERT: A 190 ASN cc_start: 0.7977 (m-40) cc_final: 0.7650 (m-40) REVERT: A 191 MET cc_start: 0.6861 (mmm) cc_final: 0.6332 (mmm) REVERT: A 193 SER cc_start: 0.7785 (m) cc_final: 0.7092 (t) REVERT: A 237 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7208 (tp) REVERT: A 245 MET cc_start: 0.7253 (mtt) cc_final: 0.6990 (mtt) REVERT: A 266 GLN cc_start: 0.7723 (tt0) cc_final: 0.7455 (tp40) REVERT: A 317 PRO cc_start: 0.8176 (Cg_endo) cc_final: 0.7860 (Cg_exo) REVERT: A 341 GLN cc_start: 0.7700 (pm20) cc_final: 0.7335 (pm20) REVERT: A 375 MET cc_start: 0.7408 (ttm) cc_final: 0.7012 (ttm) REVERT: A 383 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6725 (tpt170) REVERT: A 391 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7060 (pt0) REVERT: A 420 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7889 (mm) REVERT: A 456 PHE cc_start: 0.8032 (t80) cc_final: 0.7813 (t80) REVERT: B 76 LEU cc_start: 0.6544 (mp) cc_final: 0.6212 (mp) REVERT: B 86 ASP cc_start: 0.7417 (m-30) cc_final: 0.7084 (m-30) REVERT: B 88 VAL cc_start: 0.8128 (t) cc_final: 0.7784 (p) REVERT: B 122 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6657 (mm-30) REVERT: B 136 VAL cc_start: 0.6908 (p) cc_final: 0.5654 (m) REVERT: B 144 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7462 (tm-30) REVERT: B 171 ARG cc_start: 0.6878 (mtp-110) cc_final: 0.6619 (mtp85) REVERT: B 175 LYS cc_start: 0.7982 (mtmm) cc_final: 0.7604 (mtmm) REVERT: B 181 ASP cc_start: 0.7806 (t70) cc_final: 0.7515 (t70) REVERT: B 191 MET cc_start: 0.7653 (tpp) cc_final: 0.7258 (tpp) REVERT: B 272 GLU cc_start: 0.7969 (tt0) cc_final: 0.7356 (tt0) REVERT: B 305 SER cc_start: 0.7678 (m) cc_final: 0.7409 (m) REVERT: B 318 PHE cc_start: 0.7439 (m-80) cc_final: 0.7121 (m-80) REVERT: B 333 ASN cc_start: 0.8299 (t0) cc_final: 0.7991 (t0) REVERT: B 341 GLN cc_start: 0.7184 (pt0) cc_final: 0.6777 (pt0) REVERT: B 373 LYS cc_start: 0.7642 (ttmt) cc_final: 0.7094 (ttmt) REVERT: B 377 LYS cc_start: 0.8337 (mttp) cc_final: 0.7982 (mttp) REVERT: B 392 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8057 (tp) REVERT: B 432 LYS cc_start: 0.8692 (mttt) cc_final: 0.8243 (mttt) REVERT: B 458 LYS cc_start: 0.7257 (tmmt) cc_final: 0.6912 (mttp) REVERT: C 95 MET cc_start: 0.7201 (tpt) cc_final: 0.6715 (tpt) REVERT: C 191 MET cc_start: 0.7178 (tpp) cc_final: 0.6854 (tpp) REVERT: C 202 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7247 (tt0) REVERT: C 214 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8328 (ttpt) REVERT: C 272 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7385 (mt-10) REVERT: C 299 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7592 (mt-10) REVERT: C 353 VAL cc_start: 0.8510 (t) cc_final: 0.8093 (p) REVERT: C 361 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7946 (tp) REVERT: C 376 LYS cc_start: 0.7783 (mmmt) cc_final: 0.7475 (mmmm) REVERT: C 377 LYS cc_start: 0.8477 (tttp) cc_final: 0.8113 (tttp) REVERT: C 389 TYR cc_start: 0.8042 (t80) cc_final: 0.7342 (t80) REVERT: C 409 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7561 (tptt) REVERT: C 418 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7077 (mm-30) REVERT: C 433 GLN cc_start: 0.8191 (mt0) cc_final: 0.7875 (mt0) REVERT: C 435 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8137 (mm) REVERT: C 484 GLU cc_start: 0.7454 (tt0) cc_final: 0.6953 (tt0) REVERT: C 488 ASN cc_start: 0.7917 (m110) cc_final: 0.7586 (m110) REVERT: D 8 GLN cc_start: 0.7642 (tt0) cc_final: 0.6911 (tt0) REVERT: D 10 MET cc_start: 0.7579 (mtm) cc_final: 0.7232 (mtm) REVERT: D 17 LYS cc_start: 0.8057 (tmtt) cc_final: 0.7693 (tmtt) REVERT: D 35 LYS cc_start: 0.8032 (ttmt) cc_final: 0.7669 (ttmt) REVERT: D 120 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6697 (ptt-90) REVERT: D 153 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.6479 (mtmm) REVERT: D 154 ILE cc_start: 0.7867 (mm) cc_final: 0.7476 (mt) REVERT: D 157 PHE cc_start: 0.7418 (m-80) cc_final: 0.7048 (m-80) REVERT: D 174 ASN cc_start: 0.7838 (m-40) cc_final: 0.7481 (t0) REVERT: D 202 MET cc_start: 0.7627 (mmt) cc_final: 0.7166 (mmt) REVERT: D 203 LYS cc_start: 0.7639 (ttmm) cc_final: 0.7040 (mttp) REVERT: D 207 VAL cc_start: 0.8606 (t) cc_final: 0.7871 (p) REVERT: D 220 GLU cc_start: 0.7582 (mp0) cc_final: 0.7147 (mp0) REVERT: D 233 LEU cc_start: 0.7676 (tp) cc_final: 0.7279 (tp) REVERT: D 294 SER cc_start: 0.7335 (t) cc_final: 0.6733 (p) REVERT: D 365 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7414 (tm-30) REVERT: D 378 LYS cc_start: 0.8524 (tttt) cc_final: 0.8140 (mtpp) REVERT: D 382 ASP cc_start: 0.8088 (p0) cc_final: 0.7682 (p0) REVERT: D 439 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6859 (mm-30) REVERT: D 441 LEU cc_start: 0.8806 (mt) cc_final: 0.8549 (mp) REVERT: D 464 GLU cc_start: 0.8098 (tp30) cc_final: 0.7690 (tp30) REVERT: E 5 ARG cc_start: 0.7378 (ptm-80) cc_final: 0.7004 (ptm-80) REVERT: E 30 LEU cc_start: 0.7968 (mt) cc_final: 0.7702 (mm) REVERT: E 112 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.6995 (m-30) REVERT: E 199 TYR cc_start: 0.8278 (t80) cc_final: 0.8078 (t80) REVERT: E 201 GLU cc_start: 0.7731 (tp30) cc_final: 0.7215 (tp30) REVERT: E 202 MET cc_start: 0.7853 (mtt) cc_final: 0.7482 (ttt) REVERT: E 207 VAL cc_start: 0.7919 (t) cc_final: 0.7149 (m) REVERT: E 210 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7219 (ttpt) REVERT: E 333 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7511 (ttm-80) REVERT: E 380 LEU cc_start: 0.8316 (tp) cc_final: 0.8066 (pp) REVERT: E 391 GLU cc_start: 0.5895 (OUTLIER) cc_final: 0.5477 (tm-30) REVERT: E 435 ARG cc_start: 0.6643 (ttp80) cc_final: 0.6288 (ttp80) REVERT: E 458 ARG cc_start: 0.6989 (mtp-110) cc_final: 0.6407 (ptm-80) REVERT: E 465 LYS cc_start: 0.8599 (tttp) cc_final: 0.7894 (tttp) REVERT: E 469 MET cc_start: 0.6001 (mmm) cc_final: 0.5475 (mmm) REVERT: F 9 VAL cc_start: 0.8411 (t) cc_final: 0.8171 (p) REVERT: F 15 ASP cc_start: 0.7538 (m-30) cc_final: 0.7238 (m-30) REVERT: F 22 HIS cc_start: 0.7435 (m-70) cc_final: 0.7163 (m-70) REVERT: F 37 ARG cc_start: 0.7148 (ttm110) cc_final: 0.6934 (ttm110) REVERT: F 38 ASN cc_start: 0.7859 (t0) cc_final: 0.7583 (t0) REVERT: F 202 MET cc_start: 0.7361 (mmp) cc_final: 0.6876 (mmp) REVERT: F 278 GLN cc_start: 0.7979 (pm20) cc_final: 0.7653 (pm20) REVERT: F 285 MET cc_start: 0.7502 (ttp) cc_final: 0.6944 (ttp) REVERT: F 330 ASN cc_start: 0.6830 (m-40) cc_final: 0.6314 (m-40) REVERT: F 338 MET cc_start: 0.7437 (mtm) cc_final: 0.7225 (mtm) REVERT: F 389 MET cc_start: 0.7835 (mmm) cc_final: 0.7354 (mmm) REVERT: F 438 LYS cc_start: 0.8503 (tttt) cc_final: 0.8160 (tttt) REVERT: F 446 ASP cc_start: 0.7298 (p0) cc_final: 0.7069 (p0) REVERT: F 458 ARG cc_start: 0.7137 (ttp-110) cc_final: 0.6632 (mtp-110) REVERT: G 15 ASN cc_start: 0.8430 (m110) cc_final: 0.8054 (m-40) REVERT: G 37 ARG cc_start: 0.7839 (ttp80) cc_final: 0.7478 (ttp80) REVERT: G 48 TYR cc_start: 0.7963 (t80) cc_final: 0.7568 (t80) REVERT: G 70 MET cc_start: 0.8272 (mmp) cc_final: 0.7619 (mmp) REVERT: G 103 TYR cc_start: 0.8255 (t80) cc_final: 0.7594 (t80) REVERT: G 105 THR cc_start: 0.8733 (m) cc_final: 0.8445 (t) REVERT: G 132 ARG cc_start: 0.8056 (mmp80) cc_final: 0.7271 (mmm-85) REVERT: G 146 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7369 (pp30) REVERT: G 148 SER cc_start: 0.8832 (m) cc_final: 0.8568 (p) REVERT: G 152 ILE cc_start: 0.7815 (pp) cc_final: 0.7605 (mm) REVERT: G 153 LYS cc_start: 0.8078 (tttm) cc_final: 0.7821 (tttm) REVERT: G 178 TYR cc_start: 0.8224 (t80) cc_final: 0.8010 (t80) REVERT: G 183 GLN cc_start: 0.7811 (pp30) cc_final: 0.7160 (pp30) REVERT: G 185 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7047 (mm-30) REVERT: G 194 LEU cc_start: 0.5925 (OUTLIER) cc_final: 0.5635 (tm) REVERT: G 222 GLN cc_start: 0.8264 (mt0) cc_final: 0.7964 (mt0) REVERT: G 244 MET cc_start: 0.8181 (ttp) cc_final: 0.7896 (ttp) REVERT: G 267 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.8109 (ttm-80) REVERT: G 269 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7601 (ttp80) REVERT: G 279 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7153 (mm-30) outliers start: 137 outliers final: 103 residues processed: 1018 average time/residue: 0.1600 time to fit residues: 248.3938 Evaluate side-chains 1079 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 958 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 120 ARG Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 365 GLN Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 179 HIS Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 190 LYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 274 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 265 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 275 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 228 optimal weight: 3.9990 chunk 299 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN B 185 ASN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** F 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.141546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.123173 restraints weight = 39664.439| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.08 r_work: 0.3572 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 24608 Z= 0.227 Angle : 0.747 18.188 33370 Z= 0.387 Chirality : 0.050 0.309 3840 Planarity : 0.006 0.070 4349 Dihedral : 6.219 81.786 3418 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 5.08 % Allowed : 31.67 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.15), residues: 3104 helix: 0.39 (0.14), residues: 1295 sheet: -0.11 (0.23), residues: 480 loop : -1.10 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 3 TYR 0.022 0.002 TYR E 238 PHE 0.027 0.002 PHE D 185 HIS 0.009 0.001 HIS F 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.23 (24608) covalent geometry : angle 0.74728 / 0.39 (33370) hydrogen bonds : bond 0.05942 / 4.08 ( 1143) hydrogen bonds : angle 5.37489 / 3.85 ( 3267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6115.33 seconds wall clock time: 105 minutes 12.76 seconds (6312.76 seconds total)