Starting phenix.real_space_refine on Tue Sep 15 11:25:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6fkh_4271/09_2026/6fkh_4271.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fkh_4271/09_2026/6fkh_4271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6fkh_4271/09_2026/6fkh_4271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fkh_4271/09_2026/6fkh_4271.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6fkh_4271/09_2026/6fkh_4271.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6fkh_4271/09_2026/6fkh_4271.cif" model { file = "/net/cci-nas-00/data/ceres_data/6fkh_4271/09_2026/6fkh_4271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fkh_4271/09_2026/6fkh_4271.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 13 5.49 5 Mg 5 5.21 5 S 129 5.16 5 C 24906 2.51 5 N 6683 2.21 5 O 7495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39231 Number of models: 1 Model: "" Number of chains: 31 Chain: "a" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1741 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "C" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3851 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Chain: "D" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3627 Classifications: {'peptide': 479} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "E" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3818 Classifications: {'peptide': 497} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 478} Chain: "F" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Chain: "A" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3858 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 484} Chain: "B" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 453} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "g" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2497 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 308} Chain: "S" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "N" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "O" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "P" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Q" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "M" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "T" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "G" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "H" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "L" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "K" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "J" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "I" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "p" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1124 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "b" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1299 Classifications: {'peptide': 161} Link IDs: {'TRANS': 160} Chain: "d" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1383 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.71, per 1000 atoms: 0.20 Number of scatterers: 39231 At special positions: 0 Unit cell: (131.625, 141.102, 233.766, 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 129 16.00 P 13 15.00 Mg 5 11.99 O 7495 8.00 N 6683 7.00 C 24906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 246 " distance=2.70 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=28, symmetry=0 Number of additional bonds: simple=28, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 1.7 seconds 10294 Ramachandran restraints generated. 5147 Oldfield, 0 Emsley, 5147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9452 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 26 sheets defined 61.8% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'a' and resid 37 through 59 removed outlier: 4.035A pdb=" N ARG a 59 " --> pdb=" O ALA a 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 88 removed outlier: 4.135A pdb=" N PHE a 72 " --> pdb=" O GLY a 68 " (cutoff:3.500A) Processing helix chain 'a' and resid 94 through 115 removed outlier: 3.573A pdb=" N ILE a 105 " --> pdb=" O MET a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 133 through 156 removed outlier: 4.073A pdb=" N THR a 137 " --> pdb=" O ASP a 133 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS a 156 " --> pdb=" O GLY a 152 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 170 No H-bonds generated for 'chain 'a' and resid 168 through 170' Processing helix chain 'a' and resid 171 through 208 removed outlier: 3.751A pdb=" N PHE a 180 " --> pdb=" O ILE a 176 " (cutoff:3.500A) Proline residue: a 183 - end of helix removed outlier: 4.053A pdb=" N LEU a 190 " --> pdb=" O LEU a 186 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU a 207 " --> pdb=" O VAL a 203 " (cutoff:3.500A) Processing helix chain 'a' and resid 213 through 244 removed outlier: 3.516A pdb=" N GLY a 225 " --> pdb=" O LEU a 221 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE a 226 " --> pdb=" O PHE a 222 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA a 228 " --> pdb=" O SER a 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 19 Processing helix chain 'C' and resid 101 through 105 removed outlier: 3.872A pdb=" N TYR C 104 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 105 " --> pdb=" O GLU C 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 101 through 105' Processing helix chain 'C' and resid 151 through 158 removed outlier: 3.721A pdb=" N MET C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.745A pdb=" N GLN C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 217 through 220 Processing helix chain 'C' and resid 232 through 252 Proline residue: C 240 - end of helix removed outlier: 3.609A pdb=" N PHE C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 removed outlier: 3.707A pdb=" N ALA C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 289 through 301 removed outlier: 4.535A pdb=" N TYR C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 326 Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.632A pdb=" N ALA C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 393 removed outlier: 3.598A pdb=" N VAL C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 403 removed outlier: 4.097A pdb=" N GLN C 398 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA C 400 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER C 401 " --> pdb=" O GLN C 398 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 403 " --> pdb=" O ALA C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 422 removed outlier: 3.675A pdb=" N ARG C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS C 422 " --> pdb=" O ARG C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 443 removed outlier: 3.664A pdb=" N ASN C 443 " --> pdb=" O TYR C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 469 removed outlier: 4.087A pdb=" N ARG C 455 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS C 456 " --> pdb=" O ASP C 452 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 459 " --> pdb=" O ARG C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 480 removed outlier: 4.373A pdb=" N GLN C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C 474 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 504 Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 177 through 193 removed outlier: 3.745A pdb=" N ALA D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 219 removed outlier: 3.610A pdb=" N LYS D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.531A pdb=" N ARG D 246 " --> pdb=" O PRO D 242 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 242 through 248' Processing helix chain 'D' and resid 248 through 263 removed outlier: 3.945A pdb=" N PHE D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 290 removed outlier: 3.667A pdb=" N PHE D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 298 removed outlier: 3.765A pdb=" N TYR D 298 " --> pdb=" O ALA D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 311 removed outlier: 3.522A pdb=" N LEU D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 333 Processing helix chain 'D' and resid 336 through 346 removed outlier: 4.142A pdb=" N HIS D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 removed outlier: 3.842A pdb=" N ALA D 357 " --> pdb=" O SER D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 381 through 413 removed outlier: 4.700A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N ASP D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU D 412 " --> pdb=" O LEU D 408 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 413 " --> pdb=" O GLY D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 432 removed outlier: 3.747A pdb=" N LEU D 419 " --> pdb=" O GLU D 415 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 421 " --> pdb=" O ASP D 417 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER D 432 " --> pdb=" O GLU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 450 through 463 removed outlier: 3.575A pdb=" N LEU D 460 " --> pdb=" O ARG D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 474 Processing helix chain 'D' and resid 479 through 496 removed outlier: 3.551A pdb=" N ALA D 483 " --> pdb=" O ASN D 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 25 removed outlier: 3.722A pdb=" N GLU E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 105 removed outlier: 3.690A pdb=" N TYR E 104 " --> pdb=" O SER E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 158 Processing helix chain 'E' and resid 175 through 186 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 232 through 252 Proline residue: E 240 - end of helix removed outlier: 3.855A pdb=" N PHE E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 283 through 287 Processing helix chain 'E' and resid 288 through 289 No H-bonds generated for 'chain 'E' and resid 288 through 289' Processing helix chain 'E' and resid 290 through 300 removed outlier: 3.623A pdb=" N LEU E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 337 removed outlier: 3.502A pdb=" N SER E 337 " --> pdb=" O THR E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 Processing helix chain 'E' and resid 373 through 395 removed outlier: 4.052A pdb=" N LYS E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU E 383 " --> pdb=" O VAL E 379 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU E 385 " --> pdb=" O GLY E 381 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU E 392 " --> pdb=" O ALA E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 404 through 422 removed outlier: 3.898A pdb=" N GLN E 410 " --> pdb=" O ALA E 406 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG E 416 " --> pdb=" O ALA E 412 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU E 421 " --> pdb=" O LEU E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 443 Processing helix chain 'E' and resid 450 through 468 removed outlier: 4.633A pdb=" N ARG E 455 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LYS E 456 " --> pdb=" O ASP E 452 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL E 459 " --> pdb=" O ARG E 455 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 460 " --> pdb=" O LYS E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 479 removed outlier: 3.570A pdb=" N GLU E 474 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 503 removed outlier: 3.803A pdb=" N ALA E 493 " --> pdb=" O LEU E 489 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU E 503 " --> pdb=" O GLU E 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 107 Processing helix chain 'F' and resid 138 through 142 removed outlier: 3.743A pdb=" N LEU F 142 " --> pdb=" O PHE F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 160 removed outlier: 3.520A pdb=" N ALA F 160 " --> pdb=" O VAL F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 193 removed outlier: 4.457A pdb=" N LYS F 191 " --> pdb=" O ASN F 187 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 219 Processing helix chain 'F' and resid 226 through 230 Processing helix chain 'F' and resid 242 through 264 removed outlier: 4.048A pdb=" N ARG F 248 " --> pdb=" O GLY F 244 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU F 251 " --> pdb=" O MET F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 290 removed outlier: 3.718A pdb=" N PHE F 278 " --> pdb=" O ASN F 274 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 312 removed outlier: 3.867A pdb=" N ARG F 312 " --> pdb=" O SER F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 333 Processing helix chain 'F' and resid 336 through 346 removed outlier: 3.541A pdb=" N THR F 342 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N HIS F 345 " --> pdb=" O THR F 341 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU F 346 " --> pdb=" O THR F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 360 Processing helix chain 'F' and resid 376 through 408 removed outlier: 7.564A pdb=" N GLU F 382 " --> pdb=" O ARG F 378 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N GLU F 383 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N HIS F 384 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG F 390 " --> pdb=" O GLU F 386 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE F 407 " --> pdb=" O ASP F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 413 removed outlier: 3.949A pdb=" N GLU F 412 " --> pdb=" O GLY F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 432 removed outlier: 3.657A pdb=" N SER F 432 " --> pdb=" O GLU F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 443 Processing helix chain 'F' and resid 450 through 464 Processing helix chain 'F' and resid 470 through 474 Processing helix chain 'F' and resid 479 through 493 removed outlier: 3.639A pdb=" N ALA F 483 " --> pdb=" O ASN F 479 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN F 489 " --> pdb=" O ALA F 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 18 removed outlier: 4.304A pdb=" N ARG A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 17 " --> pdb=" O ILE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 4.063A pdb=" N TYR A 104 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 105 " --> pdb=" O GLU A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 105' Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.696A pdb=" N MET A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 252 Proline residue: A 240 - end of helix removed outlier: 3.544A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.645A pdb=" N ALA A 286 " --> pdb=" O GLY A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 289 No H-bonds generated for 'chain 'A' and resid 288 through 289' Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.540A pdb=" N HIS A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 326 Processing helix chain 'A' and resid 329 through 339 removed outlier: 3.598A pdb=" N SER A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.742A pdb=" N ALA A 352 " --> pdb=" O ASP A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.878A pdb=" N ALA A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 372 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 382 through 395 removed outlier: 3.603A pdb=" N LEU A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.937A pdb=" N GLN A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 443 removed outlier: 3.543A pdb=" N THR A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 468 removed outlier: 3.883A pdb=" N ARG A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 479 removed outlier: 4.131A pdb=" N GLN A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 504 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 177 through 193 Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 248 through 263 Processing helix chain 'B' and resid 274 through 287 removed outlier: 3.947A pdb=" N PHE B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 282 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 298 removed outlier: 3.800A pdb=" N TYR B 298 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 313 removed outlier: 3.513A pdb=" N GLY B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 333 Processing helix chain 'B' and resid 336 through 346 removed outlier: 3.726A pdb=" N THR B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N HIS B 345 " --> pdb=" O THR B 341 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 381 through 409 removed outlier: 3.601A pdb=" N LYS B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 413 Processing helix chain 'B' and resid 414 through 432 removed outlier: 3.980A pdb=" N SER B 432 " --> pdb=" O GLU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.522A pdb=" N ILE B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 474 Processing helix chain 'B' and resid 479 through 496 Processing helix chain 'e' and resid 88 through 106 Processing helix chain 'e' and resid 108 through 130 removed outlier: 3.900A pdb=" N ILE e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR e 124 " --> pdb=" O ARG e 120 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG e 125 " --> pdb=" O ARG e 121 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL e 126 " --> pdb=" O ALA e 122 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU e 127 " --> pdb=" O ARG e 123 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA e 128 " --> pdb=" O THR e 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 82 removed outlier: 3.611A pdb=" N GLY g 82 " --> pdb=" O ALA g 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 82 through 101 removed outlier: 3.666A pdb=" N GLN g 101 " --> pdb=" O ASN g 97 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 152 removed outlier: 3.526A pdb=" N ARG g 144 " --> pdb=" O LYS g 140 " (cutoff:3.500A) Processing helix chain 'g' and resid 161 through 171 removed outlier: 3.589A pdb=" N ARG g 170 " --> pdb=" O THR g 166 " (cutoff:3.500A) Processing helix chain 'g' and resid 187 through 204 removed outlier: 3.615A pdb=" N ALA g 193 " --> pdb=" O LYS g 189 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE g 194 " --> pdb=" O GLU g 190 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER g 204 " --> pdb=" O SER g 200 " (cutoff:3.500A) Processing helix chain 'g' and resid 287 through 362 Proline residue: g 297 - end of helix Processing helix chain 'S' and resid 4 through 21 removed outlier: 3.867A pdb=" N VAL S 17 " --> pdb=" O ALA S 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER S 21 " --> pdb=" O VAL S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 42 removed outlier: 3.761A pdb=" N GLY S 29 " --> pdb=" O GLY S 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY S 38 " --> pdb=" O GLN S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 76 removed outlier: 3.605A pdb=" N GLY S 51 " --> pdb=" O GLY S 47 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR S 52 " --> pdb=" O LYS S 48 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU S 63 " --> pdb=" O PHE S 59 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR S 64 " --> pdb=" O MET S 60 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 21 removed outlier: 3.866A pdb=" N VAL N 17 " --> pdb=" O ALA N 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER N 21 " --> pdb=" O VAL N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 42 removed outlier: 3.760A pdb=" N GLY N 29 " --> pdb=" O GLY N 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY N 38 " --> pdb=" O GLN N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 76 removed outlier: 3.604A pdb=" N GLY N 51 " --> pdb=" O GLY N 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR N 52 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU N 63 " --> pdb=" O PHE N 59 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 21 removed outlier: 3.867A pdb=" N VAL O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER O 21 " --> pdb=" O VAL O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 42 removed outlier: 3.760A pdb=" N GLY O 29 " --> pdb=" O GLY O 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY O 38 " --> pdb=" O GLN O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 76 removed outlier: 3.604A pdb=" N GLY O 51 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR O 52 " --> pdb=" O LYS O 48 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU O 63 " --> pdb=" O PHE O 59 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 21 removed outlier: 3.866A pdb=" N VAL P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER P 21 " --> pdb=" O VAL P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 42 removed outlier: 3.760A pdb=" N GLY P 29 " --> pdb=" O GLY P 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY P 38 " --> pdb=" O GLN P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 76 removed outlier: 3.603A pdb=" N GLY P 51 " --> pdb=" O GLY P 47 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR P 52 " --> pdb=" O LYS P 48 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU P 63 " --> pdb=" O PHE P 59 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY P 67 " --> pdb=" O LEU P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 21 removed outlier: 3.867A pdb=" N VAL Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER Q 21 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 42 removed outlier: 3.760A pdb=" N GLY Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY Q 38 " --> pdb=" O GLN Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 76 removed outlier: 3.604A pdb=" N GLY Q 51 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR Q 52 " --> pdb=" O LYS Q 48 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU Q 63 " --> pdb=" O PHE Q 59 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR Q 64 " --> pdb=" O MET Q 60 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY Q 67 " --> pdb=" O LEU Q 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 21 removed outlier: 3.866A pdb=" N VAL R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER R 21 " --> pdb=" O VAL R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 42 removed outlier: 3.761A pdb=" N GLY R 29 " --> pdb=" O GLY R 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY R 38 " --> pdb=" O GLN R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 76 removed outlier: 3.604A pdb=" N GLY R 51 " --> pdb=" O GLY R 47 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR R 52 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU R 63 " --> pdb=" O PHE R 59 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR R 64 " --> pdb=" O MET R 60 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 21 removed outlier: 3.867A pdb=" N VAL M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 42 removed outlier: 3.760A pdb=" N GLY M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY M 38 " --> pdb=" O GLN M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 76 removed outlier: 3.604A pdb=" N GLY M 51 " --> pdb=" O GLY M 47 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR M 52 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU M 63 " --> pdb=" O PHE M 59 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR M 64 " --> pdb=" O MET M 60 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY M 67 " --> pdb=" O LEU M 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 21 removed outlier: 3.866A pdb=" N VAL T 17 " --> pdb=" O ALA T 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER T 21 " --> pdb=" O VAL T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 21 through 42 removed outlier: 3.760A pdb=" N GLY T 29 " --> pdb=" O GLY T 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY T 38 " --> pdb=" O GLN T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 76 removed outlier: 3.603A pdb=" N GLY T 51 " --> pdb=" O GLY T 47 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR T 52 " --> pdb=" O LYS T 48 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU T 63 " --> pdb=" O PHE T 59 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR T 64 " --> pdb=" O MET T 60 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 21 removed outlier: 3.866A pdb=" N VAL G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER G 21 " --> pdb=" O VAL G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 42 removed outlier: 3.760A pdb=" N GLY G 29 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY G 38 " --> pdb=" O GLN G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 76 removed outlier: 3.603A pdb=" N GLY G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR G 52 " --> pdb=" O LYS G 48 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU G 63 " --> pdb=" O PHE G 59 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR G 64 " --> pdb=" O MET G 60 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 21 removed outlier: 3.866A pdb=" N VAL H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 42 removed outlier: 3.760A pdb=" N GLY H 29 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY H 38 " --> pdb=" O GLN H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 76 removed outlier: 3.605A pdb=" N GLY H 51 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR H 52 " --> pdb=" O LYS H 48 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU H 63 " --> pdb=" O PHE H 59 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR H 64 " --> pdb=" O MET H 60 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY H 67 " --> pdb=" O LEU H 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 21 removed outlier: 3.866A pdb=" N VAL L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER L 21 " --> pdb=" O VAL L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 42 removed outlier: 3.760A pdb=" N GLY L 29 " --> pdb=" O GLY L 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY L 38 " --> pdb=" O GLN L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 76 removed outlier: 3.604A pdb=" N GLY L 51 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR L 52 " --> pdb=" O LYS L 48 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU L 63 " --> pdb=" O PHE L 59 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR L 64 " --> pdb=" O MET L 60 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 21 removed outlier: 3.867A pdb=" N VAL K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER K 21 " --> pdb=" O VAL K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 42 removed outlier: 3.759A pdb=" N GLY K 29 " --> pdb=" O GLY K 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY K 38 " --> pdb=" O GLN K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 76 removed outlier: 3.603A pdb=" N GLY K 51 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR K 52 " --> pdb=" O LYS K 48 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU K 63 " --> pdb=" O PHE K 59 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR K 64 " --> pdb=" O MET K 60 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 21 removed outlier: 3.866A pdb=" N VAL J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER J 21 " --> pdb=" O VAL J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 42 removed outlier: 3.761A pdb=" N GLY J 29 " --> pdb=" O GLY J 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY J 38 " --> pdb=" O GLN J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 76 removed outlier: 3.604A pdb=" N GLY J 51 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR J 52 " --> pdb=" O LYS J 48 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU J 63 " --> pdb=" O PHE J 59 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR J 64 " --> pdb=" O MET J 60 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 21 removed outlier: 3.867A pdb=" N VAL I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER I 21 " --> pdb=" O VAL I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 42 removed outlier: 3.761A pdb=" N GLY I 29 " --> pdb=" O GLY I 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY I 38 " --> pdb=" O GLN I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 76 removed outlier: 3.604A pdb=" N GLY I 51 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR I 52 " --> pdb=" O LYS I 48 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU I 63 " --> pdb=" O PHE I 59 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR I 64 " --> pdb=" O MET I 60 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY I 67 " --> pdb=" O LEU I 63 " (cutoff:3.500A) Processing helix chain 'p' and resid 88 through 108 Processing helix chain 'p' and resid 108 through 202 Processing helix chain 'p' and resid 203 through 219 removed outlier: 3.551A pdb=" N ILE p 207 " --> pdb=" O LEU p 203 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE p 214 " --> pdb=" O LEU p 210 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL p 215 " --> pdb=" O SER p 211 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS p 216 " --> pdb=" O ASP p 212 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS p 217 " --> pdb=" O ASP p 213 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU p 219 " --> pdb=" O VAL p 215 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 159 removed outlier: 3.593A pdb=" N VAL b 36 " --> pdb=" O ILE b 32 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL b 37 " --> pdb=" O ASN b 33 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN b 66 " --> pdb=" O ASN b 62 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL b 97 " --> pdb=" O ASP b 93 " (cutoff:3.500A) Processing helix chain 'b' and resid 163 through 182 Processing helix chain 'd' and resid 73 through 90 Processing helix chain 'd' and resid 91 through 107 removed outlier: 3.535A pdb=" N ASP d 98 " --> pdb=" O ALA d 94 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG d 104 " --> pdb=" O GLU d 100 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE d 105 " --> pdb=" O LYS d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 117 Processing helix chain 'd' and resid 121 through 137 Processing helix chain 'd' and resid 139 through 152 Processing helix chain 'd' and resid 153 through 156 removed outlier: 4.089A pdb=" N ASN d 156 " --> pdb=" O GLU d 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 153 through 156' Processing helix chain 'd' and resid 157 through 174 removed outlier: 3.761A pdb=" N GLU d 166 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP d 167 " --> pdb=" O ASN d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 203 removed outlier: 3.526A pdb=" N LEU d 191 " --> pdb=" O GLU d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 237 through 249 removed outlier: 3.934A pdb=" N LEU d 248 " --> pdb=" O ILE d 244 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU d 249 " --> pdb=" O ALA d 245 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'a' and resid 121 through 122 Processing sheet with id=AA3, first strand: chain 'C' and resid 61 through 67 removed outlier: 6.537A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 65 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN D 19 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU D 90 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG D 75 " --> pdb=" O GLN D 66 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU D 68 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG D 73 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP D 32 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.702A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 108 through 109 removed outlier: 6.462A pdb=" N CYS C 194 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL C 225 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TYR C 196 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLU C 227 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA C 198 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE C 193 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE C 260 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL C 195 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP C 262 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL C 197 " --> pdb=" O ASP C 262 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY C 170 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU C 167 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU C 345 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 169 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AA7, first strand: chain 'D' and resid 110 through 111 removed outlier: 5.848A pdb=" N PHE D 111 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLN D 238 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE D 272 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE D 168 " --> pdb=" O GLN D 325 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LYS D 167 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR D 350 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLY D 169 " --> pdb=" O THR D 350 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 148 through 149 removed outlier: 4.265A pdb=" N TYR D 162 " --> pdb=" O PHE D 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 61 through 67 removed outlier: 6.730A pdb=" N ARG E 41 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL E 35 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE E 39 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU E 67 " --> pdb=" O ASN E 71 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY E 73 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE E 61 " --> pdb=" O MET E 77 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR F 94 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N ILE F 48 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ALA F 96 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN F 45 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL F 61 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 97 through 100 removed outlier: 3.691A pdb=" N GLU E 126 " --> pdb=" O VAL E 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 108 through 109 removed outlier: 4.010A pdb=" N GLY E 200 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU E 167 " --> pdb=" O ILE E 343 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU E 345 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE E 169 " --> pdb=" O LEU E 345 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE E 344 " --> pdb=" O ASN E 359 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AB4, first strand: chain 'F' and resid 110 through 111 removed outlier: 6.403A pdb=" N PHE F 111 " --> pdb=" O TYR F 236 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE F 168 " --> pdb=" O GLN F 325 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL F 327 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU F 170 " --> pdb=" O VAL F 327 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 148 through 149 removed outlier: 4.139A pdb=" N TYR F 162 " --> pdb=" O PHE F 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'd' and resid 206 through 213 removed outlier: 5.725A pdb=" N GLU d 176 " --> pdb=" O ARG d 208 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS d 210 " --> pdb=" O GLU d 176 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ALA d 178 " --> pdb=" O LYS d 210 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL d 212 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL d 180 " --> pdb=" O VAL d 212 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE d 221 " --> pdb=" O MET d 235 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU d 232 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A 27 " --> pdb=" O LEU d 232 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN A 28 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.908A pdb=" N GLU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.173A pdb=" N ILE A 193 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE A 260 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 195 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ASP A 262 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A 197 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 319 through 321 removed outlier: 6.230A pdb=" N ILE A 168 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 20 through 27 removed outlier: 6.385A pdb=" N ASP B 32 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE B 26 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B 30 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 77 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL B 65 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLU B 90 " --> pdb=" O LYS B 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 99 through 101 Processing sheet with id=AC3, first strand: chain 'B' and resid 110 through 111 removed outlier: 7.043A pdb=" N SER B 197 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N VAL B 235 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE B 199 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLY B 237 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLY B 201 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL B 268 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE B 324 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU B 270 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA B 326 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE B 272 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TYR B 328 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE B 168 " --> pdb=" O GLN B 325 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL B 327 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU B 170 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS B 167 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N THR B 350 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY B 169 " --> pdb=" O THR B 350 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'e' and resid 13 through 15 removed outlier: 5.956A pdb=" N ASN e 4 " --> pdb=" O ILE e 74 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE e 76 " --> pdb=" O ASN e 4 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS e 6 " --> pdb=" O ILE e 76 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL e 78 " --> pdb=" O CYS e 6 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LEU e 8 " --> pdb=" O VAL e 78 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU e 73 " --> pdb=" O GLY e 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'e' and resid 31 through 33 removed outlier: 3.624A pdb=" N ILE e 22 " --> pdb=" O VAL e 33 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU e 62 " --> pdb=" O GLY e 47 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU e 53 " --> pdb=" O GLN e 56 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'g' and resid 176 through 180 removed outlier: 11.112A pdb=" N TYR g 155 " --> pdb=" O VAL g 176 " (cutoff:3.500A) removed outlier: 10.523A pdb=" N ARG g 178 " --> pdb=" O TYR g 155 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE g 157 " --> pdb=" O ARG g 178 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE g 180 " --> pdb=" O ILE g 157 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N SER g 159 " --> pdb=" O PHE g 180 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA g 119 " --> pdb=" O GLU g 211 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU g 213 " --> pdb=" O ALA g 119 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N MET g 121 " --> pdb=" O LEU g 213 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 239 through 240 Processing sheet with id=AC8, first strand: chain 'g' and resid 251 through 256 removed outlier: 4.180A pdb=" N ASP g 252 " --> pdb=" O ILE g 271 " (cutoff:3.500A) 2443 hydrogen bonds defined for protein. 7173 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: 9.11 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.23: 2220 1.23 - 1.48: 20510 1.48 - 1.74: 16801 1.74 - 1.99: 246 1.99 - 2.25: 1 Bond restraints: 39778 Sorted by residual: bond pdb=" C GLN b 77 " pdb=" N LEU b 78 " ideal model delta sigma weight residual 1.335 2.248 -0.913 1.25e-02 6.40e+03 5.34e+03 bond pdb=" C GLY C 30 " pdb=" N THR C 31 " ideal model delta sigma weight residual 1.330 1.731 -0.401 1.39e-02 5.18e+03 8.34e+02 bond pdb=" C PHE D 276 " pdb=" N ARG D 277 " ideal model delta sigma weight residual 1.335 0.970 0.365 1.31e-02 5.83e+03 7.75e+02 bond pdb=" C GLY E 30 " pdb=" N THR E 31 " ideal model delta sigma weight residual 1.331 1.635 -0.304 1.38e-02 5.25e+03 4.86e+02 bond pdb=" C GLY A 30 " pdb=" N THR A 31 " ideal model delta sigma weight residual 1.331 1.579 -0.248 1.55e-02 4.16e+03 2.56e+02 ... (remaining 39773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.53: 53815 7.53 - 15.06: 122 15.06 - 22.59: 1 22.59 - 30.11: 2 30.11 - 37.64: 3 Bond angle restraints: 53943 Sorted by residual: angle pdb=" O GLY C 30 " pdb=" C GLY C 30 " pdb=" N THR C 31 " ideal model delta sigma weight residual 123.49 98.52 24.97 8.00e-01 1.56e+00 9.74e+02 angle pdb=" O GLY E 30 " pdb=" C GLY E 30 " pdb=" N THR E 31 " ideal model delta sigma weight residual 123.29 154.73 -31.44 1.06e+00 8.90e-01 8.80e+02 angle pdb=" C GLY E 30 " pdb=" N THR E 31 " pdb=" CA THR E 31 " ideal model delta sigma weight residual 122.74 85.10 37.64 1.54e+00 4.22e-01 5.97e+02 angle pdb=" CA GLY C 30 " pdb=" C GLY C 30 " pdb=" N THR C 31 " ideal model delta sigma weight residual 115.49 138.77 -23.28 1.03e+00 9.43e-01 5.11e+02 angle pdb=" CA GLY E 30 " pdb=" C GLY E 30 " pdb=" N THR E 31 " ideal model delta sigma weight residual 115.24 81.12 34.12 1.59e+00 3.96e-01 4.60e+02 ... (remaining 53938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.83: 23473 26.83 - 53.67: 586 53.67 - 80.50: 57 80.50 - 107.34: 5 107.34 - 134.17: 4 Dihedral angle restraints: 24125 sinusoidal: 9370 harmonic: 14755 Sorted by residual: dihedral pdb=" CA ASP C 262 " pdb=" C ASP C 262 " pdb=" N ASP C 263 " pdb=" CA ASP C 263 " ideal model delta harmonic sigma weight residual -180.00 -49.94 -130.06 0 5.00e+00 4.00e-02 6.77e+02 dihedral pdb=" CA ASP A 262 " pdb=" C ASP A 262 " pdb=" N ASP A 263 " pdb=" CA ASP A 263 " ideal model delta harmonic sigma weight residual -180.00 -51.19 -128.81 0 5.00e+00 4.00e-02 6.64e+02 dihedral pdb=" CA ASP E 262 " pdb=" C ASP E 262 " pdb=" N ASP E 263 " pdb=" CA ASP E 263 " ideal model delta harmonic sigma weight residual 0.00 -44.86 44.86 0 5.00e+00 4.00e-02 8.05e+01 ... (remaining 24122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 5868 0.146 - 0.292: 498 0.292 - 0.438: 69 0.438 - 0.584: 6 0.584 - 0.730: 15 Chirality restraints: 6456 Sorted by residual: chirality pdb=" CB VAL T 81 " pdb=" CA VAL T 81 " pdb=" CG1 VAL T 81 " pdb=" CG2 VAL T 81 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CB VAL M 81 " pdb=" CA VAL M 81 " pdb=" CG1 VAL M 81 " pdb=" CG2 VAL M 81 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CB VAL S 81 " pdb=" CA VAL S 81 " pdb=" CG1 VAL S 81 " pdb=" CG2 VAL S 81 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.32e+01 ... (remaining 6453 not shown) Planarity restraints: 6961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU b 181 " 0.067 2.00e-02 2.50e+03 1.24e-01 1.55e+02 pdb=" C GLU b 181 " -0.215 2.00e-02 2.50e+03 pdb=" O GLU b 181 " 0.080 2.00e-02 2.50e+03 pdb=" N ILE b 182 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 77 " -0.045 2.00e-02 2.50e+03 8.90e-02 7.92e+01 pdb=" C ALA Q 77 " 0.154 2.00e-02 2.50e+03 pdb=" O ALA Q 77 " -0.058 2.00e-02 2.50e+03 pdb=" N ASN Q 78 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA M 77 " -0.045 2.00e-02 2.50e+03 8.89e-02 7.91e+01 pdb=" C ALA M 77 " 0.154 2.00e-02 2.50e+03 pdb=" O ALA M 77 " -0.058 2.00e-02 2.50e+03 pdb=" N ASN M 78 " -0.052 2.00e-02 2.50e+03 ... (remaining 6958 not shown) Histogram of nonbonded interaction distances: 0.34 - 1.25: 92 1.25 - 2.17: 522 2.17 - 3.08: 30803 3.08 - 3.99: 106673 3.99 - 4.90: 203002 Warning: very small nonbonded interaction distances. Nonbonded interactions: 341092 Sorted by model distance: nonbonded pdb=" CB ALA a 54 " pdb=" CD1 TYR p 108 " model vdw 0.343 3.760 nonbonded pdb=" CA GLN a 121 " pdb=" C ASP b 25 " model vdw 0.416 2.960 nonbonded pdb=" CG1 VAL p 147 " pdb=" CB LEU b 85 " model vdw 0.438 3.860 nonbonded pdb=" CD GLN a 121 " pdb=" OD1 ASP b 25 " model vdw 0.482 3.270 nonbonded pdb=" CA ARG A 14 " pdb=" OD1 ASP p 213 " model vdw 0.484 3.470 ... (remaining 341087 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 7 through 503) selection = (chain 'C' and resid 7 through 503) selection = (chain 'E' and resid 7 through 503) } ncs_group { reference = (chain 'B' and resid 18 through 494) selection = (chain 'D' and resid 18 through 494) selection = (chain 'F' and resid 18 through 494) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 34.730 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 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 : 0.019 0.913 39807 Z= 1.349 Angle : 1.465 50.475 53945 Z= 0.970 Chirality : 0.094 0.730 6456 Planarity : 0.009 0.124 6961 Dihedral : 11.908 134.172 14670 Min Nonbonded Distance : 0.343 Molprobity Statistics. All-atom Clashscore : 62.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.89 % Favored : 96.04 % Rotamer: Outliers : 0.15 % Allowed : 5.46 % Favored : 94.40 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.12), residues: 5147 helix: 0.85 (0.10), residues: 2777 sheet: -1.33 (0.21), residues: 564 loop : -1.11 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 246 TYR 0.034 0.003 TYR E 287 PHE 0.067 0.003 PHE B 171 TRP 0.045 0.005 TRP a 110 HIS 0.018 0.003 HIS E 295 Details of bonding type rmsd/Z covalent geometry : bond 0.01522 / 0.89 (39778) covalent geometry : angle 1.44531 / 0.96 (53943) SS BOND : bond 0.66581 / 35.04 ( 1) SS BOND : angle 39.83056 / 21.47 ( 2) hydrogen bonds : bond 0.24698 / 16.39 ( 2443) hydrogen bonds : angle 8.82739 / 6.26 ( 7173) Misc. bond : bond 0.37801 / 25.11 ( 28) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10294 Ramachandran restraints generated. 5147 Oldfield, 0 Emsley, 5147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10294 Ramachandran restraints generated. 5147 Oldfield, 0 Emsley, 5147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1816 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1810 time to evaluate : 1.415 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: 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: 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: 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 169 PRO cc_start: 0.0563 (Cg_exo) cc_final: 0.0327 (Cg_endo) REVERT: C 9 ILE cc_start: 0.8047 (tt) cc_final: 0.7691 (tt) REVERT: C 71 ASN cc_start: 0.8103 (p0) cc_final: 0.7896 (p0) REVERT: C 105 LEU cc_start: 0.8946 (mt) cc_final: 0.8615 (mp) REVERT: C 166 GLU cc_start: 0.9195 (tp30) cc_final: 0.8923 (tp30) REVERT: C 184 ILE cc_start: 0.9247 (mt) cc_final: 0.8924 (mm) REVERT: C 190 GLN cc_start: 0.7617 (mp10) cc_final: 0.7222 (mm-40) REVERT: C 258 LEU cc_start: 0.9205 (tp) cc_final: 0.8906 (tp) REVERT: C 274 MET cc_start: 0.8986 (mtm) cc_final: 0.8720 (mtm) REVERT: C 285 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7880 (tt0) REVERT: C 287 TYR cc_start: 0.8970 (m-80) cc_final: 0.8258 (m-10) REVERT: C 290 ASP cc_start: 0.8295 (m-30) cc_final: 0.7859 (t0) REVERT: C 365 SER cc_start: 0.9031 (t) cc_final: 0.8514 (m) REVERT: C 409 ASN cc_start: 0.7964 (m-40) cc_final: 0.7284 (m-40) REVERT: C 417 LEU cc_start: 0.9086 (mt) cc_final: 0.8691 (mm) REVERT: C 447 ASP cc_start: 0.7686 (m-30) cc_final: 0.7268 (p0) REVERT: C 451 LEU cc_start: 0.8289 (mt) cc_final: 0.7893 (mt) REVERT: C 480 LYS cc_start: 0.8589 (mttt) cc_final: 0.8243 (ptmt) REVERT: C 498 MET cc_start: 0.8080 (ttm) cc_final: 0.7272 (tpt) REVERT: D 193 HIS cc_start: 0.7194 (m-70) cc_final: 0.6855 (m90) REVERT: D 198 VAL cc_start: 0.8777 (t) cc_final: 0.8571 (m) REVERT: D 306 MET cc_start: 0.9160 (tpp) cc_final: 0.8721 (tpp) REVERT: D 333 ASP cc_start: 0.8399 (t0) cc_final: 0.7904 (t0) REVERT: D 454 THR cc_start: 0.8837 (m) cc_final: 0.8136 (m) REVERT: D 458 PHE cc_start: 0.7387 (m-80) cc_final: 0.6794 (m-80) REVERT: D 462 LEU cc_start: 0.8968 (mt) cc_final: 0.8570 (tt) REVERT: E 53 LEU cc_start: 0.9133 (mt) cc_final: 0.8810 (tt) REVERT: E 74 VAL cc_start: 0.8774 (t) cc_final: 0.8512 (p) REVERT: E 147 LEU cc_start: 0.8196 (tt) cc_final: 0.7789 (tt) REVERT: E 237 TYR cc_start: 0.8861 (t80) cc_final: 0.8142 (t80) REVERT: E 251 MET cc_start: 0.8746 (ttm) cc_final: 0.7721 (ttt) REVERT: E 290 ASP cc_start: 0.9027 (m-30) cc_final: 0.8757 (t0) REVERT: E 292 PHE cc_start: 0.9173 (t80) cc_final: 0.8862 (t80) REVERT: E 298 LEU cc_start: 0.9293 (tp) cc_final: 0.9080 (tt) REVERT: E 438 ILE cc_start: 0.8999 (mm) cc_final: 0.8753 (mm) REVERT: E 445 TYR cc_start: 0.6112 (m-80) cc_final: 0.5719 (m-80) REVERT: E 456 LYS cc_start: 0.8579 (tttt) cc_final: 0.8349 (mmmt) REVERT: F 27 ILE cc_start: 0.9252 (mt) cc_final: 0.8991 (mp) REVERT: F 86 THR cc_start: 0.8707 (m) cc_final: 0.8327 (m) REVERT: F 158 LEU cc_start: 0.9617 (tp) cc_final: 0.9326 (tp) REVERT: F 196 VAL cc_start: 0.8488 (t) cc_final: 0.8051 (p) REVERT: F 239 MET cc_start: 0.8276 (mtt) cc_final: 0.7872 (mtt) REVERT: F 264 ASN cc_start: 0.8350 (m-40) cc_final: 0.7776 (t0) REVERT: F 311 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7900 (tp30) REVERT: F 369 ASP cc_start: 0.8081 (t0) cc_final: 0.7706 (t0) REVERT: F 442 THR cc_start: 0.8440 (p) cc_final: 0.8190 (t) REVERT: A 35 VAL cc_start: 0.8642 (t) cc_final: 0.7929 (p) REVERT: A 140 ARG cc_start: 0.8789 (mtt180) cc_final: 0.8393 (mtt-85) REVERT: A 154 ILE cc_start: 0.9381 (mp) cc_final: 0.9170 (mp) REVERT: A 155 ASP cc_start: 0.7085 (m-30) cc_final: 0.6688 (t0) REVERT: A 195 VAL cc_start: 0.9285 (t) cc_final: 0.9041 (t) REVERT: A 231 SER cc_start: 0.9531 (p) cc_final: 0.9073 (p) REVERT: A 264 LEU cc_start: 0.9440 (mt) cc_final: 0.9122 (mt) REVERT: A 266 LYS cc_start: 0.8669 (mttp) cc_final: 0.8336 (mmmm) REVERT: A 267 GLN cc_start: 0.8834 (tt0) cc_final: 0.8595 (tt0) REVERT: A 274 MET cc_start: 0.8454 (mtp) cc_final: 0.8244 (mmp) REVERT: A 340 ASP cc_start: 0.7744 (m-30) cc_final: 0.7540 (m-30) REVERT: A 344 PHE cc_start: 0.8146 (m-80) cc_final: 0.7939 (m-80) REVERT: A 502 LEU cc_start: 0.8262 (mt) cc_final: 0.7977 (tp) REVERT: B 44 TYR cc_start: 0.8689 (m-10) cc_final: 0.8391 (m-80) REVERT: B 79 MET cc_start: 0.9043 (mmm) cc_final: 0.8174 (mmm) REVERT: B 80 SER cc_start: 0.9288 (m) cc_final: 0.8881 (p) REVERT: B 239 MET cc_start: 0.8640 (mtt) cc_final: 0.8091 (mtt) REVERT: B 299 GLN cc_start: 0.9094 (pm20) cc_final: 0.8570 (pt0) REVERT: B 311 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7920 (mm-30) REVERT: B 370 SER cc_start: 0.9359 (m) cc_final: 0.8805 (p) REVERT: B 390 ARG cc_start: 0.8597 (ttm170) cc_final: 0.7766 (ttp80) REVERT: B 423 ARG cc_start: 0.8986 (mtt180) cc_final: 0.8551 (ttm110) REVERT: B 476 LEU cc_start: 0.8928 (mt) cc_final: 0.7800 (mt) REVERT: e 22 ILE cc_start: 0.8293 (pt) cc_final: 0.8083 (pt) REVERT: e 40 THR cc_start: 0.5406 (m) cc_final: 0.5120 (p) REVERT: e 111 GLN cc_start: 0.8684 (tt0) cc_final: 0.8396 (mp10) REVERT: g 135 ASN cc_start: 0.8498 (m-40) cc_final: 0.8139 (t0) REVERT: g 211 GLU cc_start: 0.7833 (pt0) cc_final: 0.7598 (pt0) REVERT: g 260 LYS cc_start: 0.7507 (tttt) cc_final: 0.7209 (pttm) REVERT: g 285 GLU cc_start: 0.8336 (tp30) cc_final: 0.7492 (tm-30) REVERT: g 287 ASP cc_start: 0.8327 (t70) cc_final: 0.7708 (m-30) REVERT: g 304 ILE cc_start: 0.8448 (mt) cc_final: 0.8223 (mm) REVERT: S 28 GLN cc_start: 0.6056 (mt0) cc_final: 0.5836 (tt0) REVERT: S 60 MET cc_start: 0.5830 (mtm) cc_final: 0.5156 (mmm) REVERT: N 34 GLN cc_start: 0.7649 (tt0) cc_final: 0.6797 (tt0) REVERT: Q 34 GLN cc_start: 0.7175 (tt0) cc_final: 0.6752 (tt0) REVERT: Q 60 MET cc_start: 0.4439 (mtm) cc_final: 0.3850 (mtp) REVERT: G 34 GLN cc_start: 0.5396 (tt0) cc_final: 0.4787 (tt0) REVERT: L 50 ARG cc_start: 0.7142 (ttt180) cc_final: 0.6806 (mtp180) REVERT: K 68 LEU cc_start: 0.6245 (tp) cc_final: 0.5753 (tp) REVERT: K 70 VAL cc_start: 0.7275 (t) cc_final: 0.7074 (p) REVERT: K 79 PRO cc_start: 0.2309 (Cg_endo) cc_final: 0.1882 (Cg_exo) REVERT: J 28 GLN cc_start: 0.7706 (mt0) cc_final: 0.6244 (mt0) REVERT: J 52 THR cc_start: 0.7391 (m) cc_final: 0.7180 (p) REVERT: I 46 GLU cc_start: 0.2182 (tt0) cc_final: 0.1734 (tm-30) REVERT: p 191 SER cc_start: 0.7520 (p) cc_final: 0.7188 (t) REVERT: d 92 LEU cc_start: 0.8374 (mt) cc_final: 0.7883 (mt) REVERT: d 138 LEU cc_start: 0.7302 (mt) cc_final: 0.6908 (mt) REVERT: d 145 PHE cc_start: 0.7788 (t80) cc_final: 0.7499 (t80) REVERT: d 151 ASP cc_start: 0.8161 (t0) cc_final: 0.7912 (m-30) REVERT: d 244 ILE cc_start: 0.7942 (mt) cc_final: 0.7564 (mt) outliers start: 6 outliers final: 1 residues processed: 1812 average time/residue: 0.2501 time to fit residues: 725.6516 Evaluate side-chains 914 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 913 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 494 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0970 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 25 HIS ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 175 ASN ** a 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 398 GLN C 415 GLN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 188 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN E 148 GLN E 187 GLN E 214 GLN ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 GLN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 ASN F 72 ASN F 112 ASN F 141 GLN F 193 HIS F 210 ASN F 345 HIS F 376 GLN ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN A 398 GLN A 423 GLN A 443 ASN B 210 ASN B 238 GLN B 310 GLN B 325 GLN B 472 GLN e 93 GLN g 76 GLN g 81 ASN g 301 ASN ** g 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 309 GLN g 346 GLN S 28 GLN ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN O 42 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 143 GLN ** p 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 133 GLN b 139 GLN d 124 ASN d 141 HIS d 147 ASN ** d 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.140290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.113008 restraints weight = 98313.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.112188 restraints weight = 83895.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.112682 restraints weight = 60264.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.113124 restraints weight = 46781.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.113285 restraints weight = 42916.442| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.585 39807 Z= 0.314 Angle : 0.965 37.199 53945 Z= 0.497 Chirality : 0.058 1.551 6456 Planarity : 0.007 0.212 6961 Dihedral : 6.791 127.307 5589 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.80 % Favored : 97.05 % Rotamer: Outliers : 0.80 % Allowed : 4.94 % Favored : 94.25 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.02 (0.11), residues: 5149 helix: 0.82 (0.09), residues: 2913 sheet: -0.91 (0.21), residues: 572 loop : -0.93 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG p 152 TYR 0.042 0.002 TYR a 74 PHE 0.046 0.003 PHE F 474 TRP 0.026 0.004 TRP e 57 HIS 0.013 0.002 HIS d 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00711 / 0.31 (39778) covalent geometry : angle 0.96480 / 0.50 (53943) SS BOND : bond 0.03381 / 1.78 ( 1) SS BOND : angle 3.59349 / 1.99 ( 2) hydrogen bonds : bond 0.06628 / 4.56 ( 2443) hydrogen bonds : angle 5.85204 / 4.12 ( 7173) Misc. bond : bond 0.01745 / 1.14 ( 28) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1294 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 1261 time to evaluate : 1.444 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 142 LEU cc_start: 0.8327 (pp) cc_final: 0.7920 (tt) REVERT: C 49 MET cc_start: 0.7501 (ptm) cc_final: 0.7263 (ptm) REVERT: C 71 ASN cc_start: 0.8287 (p0) cc_final: 0.8002 (p0) REVERT: C 95 ILE cc_start: 0.9141 (pt) cc_final: 0.8900 (pt) REVERT: C 130 ILE cc_start: 0.8797 (mt) cc_final: 0.8589 (mt) REVERT: C 190 GLN cc_start: 0.7407 (mp10) cc_final: 0.7125 (mm-40) REVERT: C 194 CYS cc_start: 0.8429 (m) cc_final: 0.8182 (m) REVERT: C 264 LEU cc_start: 0.9299 (mt) cc_final: 0.9076 (mt) REVERT: C 287 TYR cc_start: 0.8877 (m-80) cc_final: 0.8089 (m-80) REVERT: C 326 ASP cc_start: 0.7644 (t0) cc_final: 0.7344 (p0) REVERT: C 365 SER cc_start: 0.8406 (t) cc_final: 0.8018 (m) REVERT: C 384 LYS cc_start: 0.8842 (mttt) cc_final: 0.7750 (tptm) REVERT: C 405 LYS cc_start: 0.8228 (tptt) cc_final: 0.7866 (tptp) REVERT: C 498 MET cc_start: 0.7957 (ttm) cc_final: 0.7124 (tpt) REVERT: D 280 GLN cc_start: 0.8526 (pp30) cc_final: 0.8212 (pp30) REVERT: D 306 MET cc_start: 0.8880 (tpp) cc_final: 0.8663 (tpp) REVERT: D 333 ASP cc_start: 0.8734 (t0) cc_final: 0.8191 (t0) REVERT: D 431 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8984 (mm) REVERT: D 462 LEU cc_start: 0.8816 (mt) cc_final: 0.8343 (tp) REVERT: D 476 LEU cc_start: 0.8915 (mt) cc_final: 0.8138 (pp) REVERT: D 481 ASP cc_start: 0.8592 (m-30) cc_final: 0.8391 (p0) REVERT: E 191 ASN cc_start: 0.8261 (m-40) cc_final: 0.7885 (p0) REVERT: E 201 GLN cc_start: 0.6807 (mt0) cc_final: 0.6279 (mt0) REVERT: E 258 LEU cc_start: 0.9206 (tp) cc_final: 0.8971 (tp) REVERT: E 262 ASP cc_start: 0.8821 (t0) cc_final: 0.8201 (t0) REVERT: E 292 PHE cc_start: 0.8914 (t80) cc_final: 0.8665 (t80) REVERT: E 298 LEU cc_start: 0.9182 (tp) cc_final: 0.8968 (tt) REVERT: E 342 GLN cc_start: 0.8396 (pm20) cc_final: 0.7762 (pp30) REVERT: E 408 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8206 (tm-30) REVERT: E 445 TYR cc_start: 0.5956 (m-80) cc_final: 0.4982 (m-10) REVERT: E 456 LYS cc_start: 0.8679 (tttt) cc_final: 0.8219 (mmmt) REVERT: E 497 GLN cc_start: 0.6417 (tp40) cc_final: 0.5776 (tp40) REVERT: F 106 THR cc_start: 0.8558 (p) cc_final: 0.8348 (p) REVERT: F 158 LEU cc_start: 0.9601 (tp) cc_final: 0.9184 (tp) REVERT: F 184 GLU cc_start: 0.8331 (tp30) cc_final: 0.8055 (tp30) REVERT: F 216 MET cc_start: 0.8041 (mmm) cc_final: 0.7792 (mpp) REVERT: F 246 ARG cc_start: 0.9364 (mtm180) cc_final: 0.9143 (mtm180) REVERT: F 247 MET cc_start: 0.8905 (mtm) cc_final: 0.8626 (mtp) REVERT: F 314 THR cc_start: 0.8371 (p) cc_final: 0.8135 (p) REVERT: F 374 MET cc_start: 0.8266 (mmm) cc_final: 0.7924 (mmt) REVERT: F 379 ILE cc_start: 0.8818 (mt) cc_final: 0.8548 (mt) REVERT: F 442 THR cc_start: 0.8453 (p) cc_final: 0.8127 (t) REVERT: A 140 ARG cc_start: 0.8609 (mtt180) cc_final: 0.8101 (mtt90) REVERT: A 157 MET cc_start: 0.8753 (mpp) cc_final: 0.7679 (mpp) REVERT: A 194 CYS cc_start: 0.8324 (m) cc_final: 0.7859 (m) REVERT: A 195 VAL cc_start: 0.9488 (t) cc_final: 0.9229 (t) REVERT: A 231 SER cc_start: 0.9118 (p) cc_final: 0.8596 (t) REVERT: A 258 LEU cc_start: 0.8685 (tp) cc_final: 0.8381 (tt) REVERT: A 267 GLN cc_start: 0.8799 (tt0) cc_final: 0.8546 (tt0) REVERT: A 274 MET cc_start: 0.8369 (mtp) cc_final: 0.8168 (mtm) REVERT: A 290 ASP cc_start: 0.7039 (p0) cc_final: 0.6626 (p0) REVERT: A 340 ASP cc_start: 0.7615 (m-30) cc_final: 0.7304 (m-30) REVERT: A 344 PHE cc_start: 0.8079 (m-80) cc_final: 0.7743 (m-80) REVERT: A 382 LYS cc_start: 0.8455 (mttt) cc_final: 0.7998 (pttm) REVERT: A 436 MET cc_start: 0.7742 (ppp) cc_final: 0.6915 (tmm) REVERT: A 502 LEU cc_start: 0.8393 (mt) cc_final: 0.7886 (tp) REVERT: B 27 ILE cc_start: 0.9429 (mp) cc_final: 0.8935 (tt) REVERT: B 176 VAL cc_start: 0.9320 (m) cc_final: 0.9020 (t) REVERT: B 274 ASN cc_start: 0.8878 (t0) cc_final: 0.8184 (m-40) REVERT: B 298 TYR cc_start: 0.8356 (m-80) cc_final: 0.8114 (m-80) REVERT: B 299 GLN cc_start: 0.8880 (pm20) cc_final: 0.8238 (pt0) REVERT: B 329 VAL cc_start: 0.8984 (t) cc_final: 0.8757 (t) REVERT: B 370 SER cc_start: 0.9182 (m) cc_final: 0.8515 (p) REVERT: B 405 ILE cc_start: 0.9298 (pt) cc_final: 0.9008 (mt) REVERT: B 435 PHE cc_start: 0.7993 (m-80) cc_final: 0.7385 (m-80) REVERT: B 442 THR cc_start: 0.7347 (p) cc_final: 0.6753 (p) REVERT: B 476 LEU cc_start: 0.8670 (mt) cc_final: 0.7705 (mt) REVERT: B 492 MET cc_start: 0.8205 (mtm) cc_final: 0.7960 (ptp) REVERT: e 3 LEU cc_start: 0.7059 (pp) cc_final: 0.6758 (tp) REVERT: g 50 ARG cc_start: 0.8310 (tpt-90) cc_final: 0.7972 (tpt-90) REVERT: g 136 MET cc_start: 0.7968 (tpp) cc_final: 0.7541 (tpp) REVERT: g 192 GLN cc_start: 0.7729 (tp40) cc_final: 0.7411 (tp40) REVERT: g 248 ASP cc_start: 0.8037 (p0) cc_final: 0.7620 (p0) REVERT: g 290 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7644 (tm-30) REVERT: S 28 GLN cc_start: 0.7153 (mt0) cc_final: 0.6153 (mt0) REVERT: S 60 MET cc_start: 0.5951 (mtm) cc_final: 0.5537 (mmm) REVERT: S 75 LEU cc_start: 0.7735 (tp) cc_final: 0.7442 (tp) REVERT: P 41 ARG cc_start: 0.7333 (ttp80) cc_final: 0.7127 (ptm-80) REVERT: P 57 LEU cc_start: 0.5032 (mt) cc_final: 0.3888 (mt) REVERT: T 37 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7379 (mt-10) REVERT: G 19 LEU cc_start: 0.8026 (mt) cc_final: 0.7753 (tp) REVERT: K 34 GLN cc_start: 0.6435 (mt0) cc_final: 0.6083 (mt0) REVERT: K 37 GLU cc_start: 0.8034 (pp20) cc_final: 0.7692 (pp20) REVERT: J 28 GLN cc_start: 0.7106 (mt0) cc_final: 0.5909 (tt0) REVERT: J 34 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8000 (mm110) REVERT: I 50 ARG cc_start: 0.7930 (ttp80) cc_final: 0.6490 (ttm170) REVERT: p 83 LEU cc_start: 0.1673 (pp) cc_final: 0.0143 (pp) REVERT: p 102 PHE cc_start: 0.3405 (m-10) cc_final: 0.2998 (m-80) REVERT: p 165 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8175 (tt0) REVERT: b 66 ASN cc_start: 0.5245 (OUTLIER) cc_final: 0.4980 (t0) REVERT: d 74 THR cc_start: 0.8122 (p) cc_final: 0.7857 (p) REVERT: d 88 VAL cc_start: 0.8290 (t) cc_final: 0.8043 (p) REVERT: d 141 HIS cc_start: 0.6674 (p-80) cc_final: 0.6366 (p90) REVERT: d 155 ILE cc_start: 0.8746 (tt) cc_final: 0.8386 (mp) REVERT: d 242 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7920 (mt-10) REVERT: d 247 GLN cc_start: 0.6630 (OUTLIER) cc_final: 0.6198 (tt0) outliers start: 33 outliers final: 13 residues processed: 1287 average time/residue: 0.2217 time to fit residues: 474.1457 Evaluate side-chains 819 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 803 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 316 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 201 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 413 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 502 optimal weight: 1.9990 chunk 444 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 25 HIS ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 227 GLN C 70 ASN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN D 66 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN D 193 HIS D 238 GLN D 280 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 GLN F 66 GLN F 210 ASN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 HIS A 28 ASN A 208 GLN A 351 ASN B 25 GLN B 133 HIS B 210 ASN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 GLN O 42 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 143 GLN p 195 GLN ** p 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 139 GLN b 146 GLN d 147 ASN ** d 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 247 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.137443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.110550 restraints weight = 97196.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.109322 restraints weight = 81880.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.110218 restraints weight = 62562.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.110462 restraints weight = 51504.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.110665 restraints weight = 42442.054| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.539 39807 Z= 0.244 Angle : 0.854 44.231 53945 Z= 0.430 Chirality : 0.051 0.689 6456 Planarity : 0.005 0.087 6961 Dihedral : 6.349 116.937 5589 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.85 % Rotamer: Outliers : 0.49 % Allowed : 4.43 % Favored : 95.08 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.37 (0.11), residues: 5149 helix: 1.08 (0.09), residues: 2886 sheet: -0.88 (0.20), residues: 616 loop : -0.66 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG A 5 TYR 0.035 0.002 TYR p 109 PHE 0.041 0.003 PHE a 72 TRP 0.010 0.002 TRP e 15 HIS 0.007 0.001 HIS a 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 (39778) covalent geometry : angle 0.85148 / 0.43 (53943) SS BOND : bond 0.03062 / 1.61 ( 1) SS BOND : angle 10.41499 / 6.00 ( 2) hydrogen bonds : bond 0.05396 / 3.74 ( 2443) hydrogen bonds : angle 5.37570 / 3.80 ( 7173) Misc. bond : bond 0.01705 / 1.11 ( 28) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1110 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 1090 time to evaluate : 1.331 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: 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: C 71 ASN cc_start: 0.8369 (p0) cc_final: 0.8099 (p0) REVERT: C 95 ILE cc_start: 0.9089 (pt) cc_final: 0.8885 (pt) REVERT: C 287 TYR cc_start: 0.8716 (m-80) cc_final: 0.8442 (m-80) REVERT: C 365 SER cc_start: 0.8318 (t) cc_final: 0.7928 (m) REVERT: C 384 LYS cc_start: 0.8878 (mttt) cc_final: 0.8293 (tptm) REVERT: C 498 MET cc_start: 0.8047 (ttm) cc_final: 0.7386 (tpt) REVERT: D 40 MET cc_start: 0.7580 (tpp) cc_final: 0.7220 (tpt) REVERT: D 142 LEU cc_start: 0.8718 (mt) cc_final: 0.8174 (pp) REVERT: D 151 THR cc_start: 0.9241 (p) cc_final: 0.8232 (p) REVERT: D 157 ASP cc_start: 0.8256 (m-30) cc_final: 0.7153 (p0) REVERT: D 280 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8466 (tp40) REVERT: D 333 ASP cc_start: 0.8738 (t0) cc_final: 0.8296 (t0) REVERT: D 428 GLU cc_start: 0.7906 (pt0) cc_final: 0.7650 (pt0) REVERT: D 462 LEU cc_start: 0.8880 (mt) cc_final: 0.8451 (tp) REVERT: D 481 ASP cc_start: 0.8580 (m-30) cc_final: 0.8365 (p0) REVERT: D 492 MET cc_start: 0.8419 (tmm) cc_final: 0.8163 (tmm) REVERT: E 22 ARG cc_start: 0.6581 (mpp80) cc_final: 0.5887 (mpp80) REVERT: E 191 ASN cc_start: 0.8198 (m-40) cc_final: 0.7857 (p0) REVERT: E 201 GLN cc_start: 0.6953 (mt0) cc_final: 0.6249 (mt0) REVERT: E 258 LEU cc_start: 0.9254 (tp) cc_final: 0.8967 (tp) REVERT: E 262 ASP cc_start: 0.8615 (t0) cc_final: 0.8063 (t0) REVERT: E 298 LEU cc_start: 0.9179 (tp) cc_final: 0.8934 (tp) REVERT: E 336 ILE cc_start: 0.9157 (mm) cc_final: 0.8919 (mm) REVERT: E 342 GLN cc_start: 0.8320 (pm20) cc_final: 0.7716 (pt0) REVERT: E 436 MET cc_start: 0.7143 (ppp) cc_final: 0.6828 (ppp) REVERT: E 456 LYS cc_start: 0.8667 (tttt) cc_final: 0.8282 (mmmt) REVERT: F 39 LYS cc_start: 0.7978 (mmtm) cc_final: 0.7746 (mmtp) REVERT: F 158 LEU cc_start: 0.9529 (tp) cc_final: 0.9208 (tp) REVERT: F 258 GLU cc_start: 0.7799 (pt0) cc_final: 0.7557 (pt0) REVERT: F 314 THR cc_start: 0.8231 (p) cc_final: 0.7874 (p) REVERT: F 374 MET cc_start: 0.8541 (mmm) cc_final: 0.7875 (mmt) REVERT: F 379 ILE cc_start: 0.8934 (mt) cc_final: 0.8216 (mt) REVERT: F 442 THR cc_start: 0.8541 (p) cc_final: 0.8231 (t) REVERT: A 13 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.3866 (mm) REVERT: A 143 VAL cc_start: 0.8402 (t) cc_final: 0.8180 (p) REVERT: A 157 MET cc_start: 0.8716 (mpp) cc_final: 0.7748 (mpp) REVERT: A 251 MET cc_start: 0.6977 (tmm) cc_final: 0.6689 (tmm) REVERT: A 290 ASP cc_start: 0.7266 (p0) cc_final: 0.6757 (p0) REVERT: A 296 SER cc_start: 0.9432 (p) cc_final: 0.9083 (t) REVERT: A 327 VAL cc_start: 0.9323 (m) cc_final: 0.9007 (p) REVERT: A 340 ASP cc_start: 0.7523 (m-30) cc_final: 0.7248 (m-30) REVERT: A 433 GLU cc_start: 0.7624 (pt0) cc_final: 0.7143 (pt0) REVERT: A 436 MET cc_start: 0.7739 (ppp) cc_final: 0.6966 (tmm) REVERT: A 502 LEU cc_start: 0.8105 (mt) cc_final: 0.7781 (tp) REVERT: B 27 ILE cc_start: 0.9383 (mp) cc_final: 0.8950 (tt) REVERT: B 80 SER cc_start: 0.9064 (p) cc_final: 0.8863 (m) REVERT: B 274 ASN cc_start: 0.8962 (t0) cc_final: 0.8113 (m-40) REVERT: B 299 GLN cc_start: 0.8761 (pm20) cc_final: 0.8449 (pt0) REVERT: B 370 SER cc_start: 0.9397 (m) cc_final: 0.8753 (p) REVERT: B 405 ILE cc_start: 0.9264 (pt) cc_final: 0.8972 (mt) REVERT: B 435 PHE cc_start: 0.8014 (m-80) cc_final: 0.7252 (m-80) REVERT: B 476 LEU cc_start: 0.8643 (mt) cc_final: 0.7716 (mt) REVERT: B 492 MET cc_start: 0.8171 (mtm) cc_final: 0.7823 (ptp) REVERT: e 3 LEU cc_start: 0.7014 (pp) cc_final: 0.6626 (mp) REVERT: e 94 GLN cc_start: 0.9220 (tt0) cc_final: 0.8542 (mt0) REVERT: e 119 LEU cc_start: 0.8510 (tt) cc_final: 0.8208 (tp) REVERT: g 85 PHE cc_start: 0.8189 (t80) cc_final: 0.7594 (t80) REVERT: g 136 MET cc_start: 0.7585 (tpp) cc_final: 0.7363 (tpp) REVERT: g 201 LEU cc_start: 0.8760 (tt) cc_final: 0.8071 (tt) REVERT: g 207 VAL cc_start: 0.6557 (t) cc_final: 0.6320 (t) REVERT: g 248 ASP cc_start: 0.7837 (p0) cc_final: 0.7559 (p0) REVERT: g 287 ASP cc_start: 0.7244 (t0) cc_final: 0.6850 (m-30) REVERT: g 290 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7667 (tm-30) REVERT: S 34 GLN cc_start: 0.5949 (tt0) cc_final: 0.5563 (tt0) REVERT: S 54 LEU cc_start: 0.7217 (mm) cc_final: 0.7008 (mm) REVERT: S 60 MET cc_start: 0.6633 (mtm) cc_final: 0.5927 (mmt) REVERT: S 63 LEU cc_start: 0.6231 (mt) cc_final: 0.5825 (mt) REVERT: O 61 GLU cc_start: 0.7309 (tp30) cc_final: 0.6875 (tp30) REVERT: O 68 LEU cc_start: 0.6285 (tp) cc_final: 0.5865 (tp) REVERT: P 24 PRO cc_start: 0.8671 (Cg_exo) cc_final: 0.8298 (Cg_endo) REVERT: P 61 GLU cc_start: 0.7342 (pp20) cc_final: 0.6863 (mm-30) REVERT: H 37 GLU cc_start: 0.7233 (pp20) cc_final: 0.7002 (pp20) REVERT: H 49 ILE cc_start: 0.8519 (mt) cc_final: 0.8309 (mt) REVERT: L 34 GLN cc_start: 0.8448 (mt0) cc_final: 0.7925 (mt0) REVERT: K 37 GLU cc_start: 0.7913 (pp20) cc_final: 0.7637 (pp20) REVERT: K 60 MET cc_start: 0.5590 (mtp) cc_final: 0.4672 (tpp) REVERT: J 28 GLN cc_start: 0.6947 (mt0) cc_final: 0.6220 (tt0) REVERT: J 42 GLN cc_start: 0.8322 (mp10) cc_final: 0.7920 (mp10) REVERT: I 50 ARG cc_start: 0.7924 (ttp80) cc_final: 0.6462 (ttp-110) REVERT: I 59 PHE cc_start: 0.6947 (m-10) cc_final: 0.6662 (t80) REVERT: p 83 LEU cc_start: 0.0995 (pp) cc_final: -0.1931 (pp) REVERT: p 84 PHE cc_start: 0.2724 (m-80) cc_final: 0.2131 (m-80) REVERT: p 102 PHE cc_start: 0.3357 (m-10) cc_final: 0.2788 (m-80) REVERT: b 59 ARG cc_start: 0.7824 (mtm110) cc_final: 0.7432 (ttp80) REVERT: b 60 ILE cc_start: 0.5640 (tt) cc_final: 0.5382 (mm) REVERT: b 146 GLN cc_start: 0.8418 (tp-100) cc_final: 0.7913 (tm-30) REVERT: b 147 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8386 (mm110) REVERT: d 88 VAL cc_start: 0.8307 (t) cc_final: 0.8023 (m) REVERT: d 141 HIS cc_start: 0.6591 (p-80) cc_final: 0.6388 (p90) REVERT: d 155 ILE cc_start: 0.8684 (tt) cc_final: 0.8386 (mp) outliers start: 20 outliers final: 7 residues processed: 1105 average time/residue: 0.2307 time to fit residues: 424.9088 Evaluate side-chains 754 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 745 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 395 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 502 optimal weight: 10.0000 chunk 398 optimal weight: 6.9990 chunk 277 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 10 optimal weight: 50.0000 chunk 290 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN C 398 GLN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN D 280 GLN D 310 GLN F 210 ASN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN B 310 GLN g 76 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 143 GLN ** p 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 ASN ** d 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 206 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.132936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.107276 restraints weight = 99355.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.105517 restraints weight = 113518.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.106265 restraints weight = 89534.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.106582 restraints weight = 72134.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.107065 restraints weight = 58106.876| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.536 39807 Z= 0.270 Angle : 0.858 44.059 53945 Z= 0.434 Chirality : 0.050 0.708 6456 Planarity : 0.007 0.313 6961 Dihedral : 6.478 142.631 5589 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.03 % Favored : 96.85 % Rotamer: Outliers : 0.19 % Allowed : 4.21 % Favored : 95.59 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.49 % Twisted General : 0.12 % 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: 0.41 (0.12), residues: 5149 helix: 1.11 (0.09), residues: 2893 sheet: -0.75 (0.20), residues: 634 loop : -0.68 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG E 418 TYR 0.036 0.002 TYR C 237 PHE 0.063 0.003 PHE b 145 TRP 0.015 0.002 TRP e 15 HIS 0.006 0.001 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.27 (39778) covalent geometry : angle 0.85595 / 0.43 (53943) SS BOND : bond 0.01449 / 0.76 ( 1) SS BOND : angle 9.10943 / 5.22 ( 2) hydrogen bonds : bond 0.05265 / 3.62 ( 2443) hydrogen bonds : angle 5.28857 / 3.75 ( 7173) Misc. bond : bond 0.01734 / 1.14 ( 28) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 957 time to evaluate : 1.216 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 84 LYS cc_start: 0.8101 (tttt) cc_final: 0.7711 (mtpp) REVERT: a 101 MET cc_start: 0.6641 (mpp) cc_final: 0.6303 (mpp) REVERT: C 71 ASN cc_start: 0.8610 (p0) cc_final: 0.8305 (p0) REVERT: C 95 ILE cc_start: 0.9068 (pt) cc_final: 0.8862 (pt) REVERT: C 251 MET cc_start: 0.8436 (ptt) cc_final: 0.8068 (ptt) REVERT: C 298 LEU cc_start: 0.9005 (tt) cc_final: 0.8766 (tt) REVERT: C 384 LYS cc_start: 0.8980 (mttt) cc_final: 0.8262 (tptm) REVERT: C 498 MET cc_start: 0.7894 (ttm) cc_final: 0.7185 (tpt) REVERT: D 142 LEU cc_start: 0.8853 (mt) cc_final: 0.8094 (pp) REVERT: D 239 MET cc_start: 0.7977 (mmm) cc_final: 0.7580 (mmm) REVERT: D 333 ASP cc_start: 0.8715 (t0) cc_final: 0.8350 (t70) REVERT: D 428 GLU cc_start: 0.7967 (pt0) cc_final: 0.7661 (pt0) REVERT: D 481 ASP cc_start: 0.8614 (m-30) cc_final: 0.8352 (p0) REVERT: E 191 ASN cc_start: 0.8222 (m-40) cc_final: 0.7989 (p0) REVERT: E 201 GLN cc_start: 0.7037 (mt0) cc_final: 0.6368 (mt0) REVERT: E 251 MET cc_start: 0.8244 (ttp) cc_final: 0.7508 (ttt) REVERT: E 258 LEU cc_start: 0.9254 (tp) cc_final: 0.8937 (tp) REVERT: E 262 ASP cc_start: 0.8861 (t0) cc_final: 0.8293 (t0) REVERT: E 340 ASP cc_start: 0.8276 (m-30) cc_final: 0.7840 (m-30) REVERT: E 342 GLN cc_start: 0.8441 (pm20) cc_final: 0.7760 (pt0) REVERT: E 408 GLN cc_start: 0.8368 (tm-30) cc_final: 0.8104 (tm-30) REVERT: E 436 MET cc_start: 0.7347 (ppp) cc_final: 0.7066 (ppp) REVERT: E 456 LYS cc_start: 0.8615 (tttt) cc_final: 0.8244 (mmmt) REVERT: F 92 ILE cc_start: 0.8646 (mt) cc_final: 0.8363 (mt) REVERT: F 113 VAL cc_start: 0.8777 (p) cc_final: 0.8539 (m) REVERT: F 158 LEU cc_start: 0.9606 (tp) cc_final: 0.9268 (tp) REVERT: F 254 LEU cc_start: 0.9382 (tp) cc_final: 0.8638 (tp) REVERT: F 292 MET cc_start: 0.8895 (mtt) cc_final: 0.8634 (mtt) REVERT: F 314 THR cc_start: 0.8347 (p) cc_final: 0.7984 (p) REVERT: F 379 ILE cc_start: 0.8935 (mt) cc_final: 0.8713 (mt) REVERT: F 442 THR cc_start: 0.8702 (p) cc_final: 0.8358 (t) REVERT: A 52 GLU cc_start: 0.8440 (tt0) cc_final: 0.8072 (tt0) REVERT: A 157 MET cc_start: 0.8894 (mpp) cc_final: 0.7853 (mpp) REVERT: A 251 MET cc_start: 0.7256 (tmm) cc_final: 0.6860 (tmm) REVERT: A 290 ASP cc_start: 0.7703 (p0) cc_final: 0.7048 (p0) REVERT: A 435 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8157 (p) REVERT: A 436 MET cc_start: 0.7950 (ppp) cc_final: 0.7295 (tmm) REVERT: A 502 LEU cc_start: 0.8169 (mt) cc_final: 0.7642 (tp) REVERT: B 27 ILE cc_start: 0.9459 (mp) cc_final: 0.8813 (tt) REVERT: B 299 GLN cc_start: 0.9051 (pm20) cc_final: 0.8306 (pt0) REVERT: B 333 ASP cc_start: 0.8998 (t0) cc_final: 0.8666 (t70) REVERT: B 335 THR cc_start: 0.8583 (p) cc_final: 0.8318 (p) REVERT: B 370 SER cc_start: 0.9587 (m) cc_final: 0.9070 (p) REVERT: B 423 ARG cc_start: 0.8932 (mtt180) cc_final: 0.8427 (ttm110) REVERT: B 435 PHE cc_start: 0.8333 (m-80) cc_final: 0.7551 (m-80) REVERT: B 476 LEU cc_start: 0.8656 (mt) cc_final: 0.8053 (mt) REVERT: B 492 MET cc_start: 0.8127 (mtm) cc_final: 0.7887 (ptp) REVERT: e 3 LEU cc_start: 0.6822 (pp) cc_final: 0.6346 (mp) REVERT: e 123 ARG cc_start: 0.7341 (ptm160) cc_final: 0.6584 (ptm160) REVERT: g 85 PHE cc_start: 0.8386 (t80) cc_final: 0.7883 (t80) REVERT: g 136 MET cc_start: 0.7696 (tpp) cc_final: 0.7483 (tpp) REVERT: g 173 GLU cc_start: 0.7071 (pp20) cc_final: 0.6851 (tm-30) REVERT: g 192 GLN cc_start: 0.8023 (tp40) cc_final: 0.7746 (tp40) REVERT: g 211 GLU cc_start: 0.6904 (pt0) cc_final: 0.6528 (pt0) REVERT: S 54 LEU cc_start: 0.7541 (mm) cc_final: 0.7191 (mm) REVERT: S 61 GLU cc_start: 0.5221 (mm-30) cc_final: 0.4889 (mm-30) REVERT: S 63 LEU cc_start: 0.6656 (mt) cc_final: 0.6352 (mt) REVERT: M 59 PHE cc_start: 0.5959 (m-80) cc_final: 0.5714 (m-80) REVERT: M 60 MET cc_start: 0.8138 (ttt) cc_final: 0.7916 (ttm) REVERT: T 60 MET cc_start: 0.5819 (mmm) cc_final: 0.5468 (mmm) REVERT: T 65 ILE cc_start: 0.6080 (tp) cc_final: 0.5770 (tp) REVERT: T 70 VAL cc_start: 0.4763 (m) cc_final: 0.4523 (m) REVERT: K 37 GLU cc_start: 0.8005 (pp20) cc_final: 0.7594 (pp20) REVERT: K 60 MET cc_start: 0.6176 (mtp) cc_final: 0.5153 (tpp) REVERT: J 28 GLN cc_start: 0.7563 (mt0) cc_final: 0.6230 (tt0) REVERT: I 50 ARG cc_start: 0.7967 (ttp80) cc_final: 0.6521 (ttm170) REVERT: I 55 LEU cc_start: 0.8312 (tp) cc_final: 0.7907 (tp) REVERT: I 59 PHE cc_start: 0.7082 (m-10) cc_final: 0.6549 (m-80) REVERT: p 83 LEU cc_start: 0.1829 (pp) cc_final: -0.0390 (pp) REVERT: p 94 MET cc_start: 0.0415 (ptt) cc_final: 0.0183 (ptm) REVERT: p 102 PHE cc_start: 0.3433 (m-10) cc_final: 0.2970 (m-80) REVERT: b 59 ARG cc_start: 0.7911 (mtm110) cc_final: 0.7575 (ttp80) REVERT: b 90 MET cc_start: 0.7374 (ppp) cc_final: 0.7158 (ppp) REVERT: d 74 THR cc_start: 0.8046 (p) cc_final: 0.7835 (p) REVERT: d 155 ILE cc_start: 0.8844 (tt) cc_final: 0.8568 (mp) REVERT: d 188 ASN cc_start: 0.6772 (m-40) cc_final: 0.6426 (m-40) outliers start: 8 outliers final: 2 residues processed: 962 average time/residue: 0.2273 time to fit residues: 367.2732 Evaluate side-chains 668 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 665 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 99 optimal weight: 7.9990 chunk 363 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 274 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 282 optimal weight: 0.0570 chunk 256 optimal weight: 10.0000 chunk 334 optimal weight: 0.7980 chunk 148 optimal weight: 0.1980 chunk 392 optimal weight: 7.9990 chunk 275 optimal weight: 7.9990 overall best weight: 2.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 25 HIS ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN F 210 ASN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 93 GLN g 134 ASN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 GLN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 HIS d 147 ASN ** d 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.133356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.107582 restraints weight = 99448.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.106207 restraints weight = 105063.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.106493 restraints weight = 82417.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.106822 restraints weight = 71902.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.107117 restraints weight = 57610.507| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.542 39807 Z= 0.239 Angle : 0.817 45.882 53945 Z= 0.409 Chirality : 0.049 0.536 6456 Planarity : 0.006 0.143 6961 Dihedral : 6.017 114.827 5589 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.89 % Favored : 96.99 % Rotamer: Outliers : 0.12 % Allowed : 3.31 % Favored : 96.57 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.49 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.12), residues: 5149 helix: 1.14 (0.10), residues: 2896 sheet: -0.76 (0.20), residues: 616 loop : -0.63 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 5 TYR 0.029 0.002 TYR a 74 PHE 0.034 0.002 PHE b 145 TRP 0.012 0.001 TRP a 110 HIS 0.007 0.001 HIS a 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 (39778) covalent geometry : angle 0.81514 / 0.41 (53943) SS BOND : bond 0.00587 / 0.31 ( 1) SS BOND : angle 9.36722 / 5.39 ( 2) hydrogen bonds : bond 0.05013 / 3.46 ( 2443) hydrogen bonds : angle 5.14049 / 3.65 ( 7173) Misc. bond : bond 0.01809 / 1.24 ( 28) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 946 time to evaluate : 1.550 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: 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 187 SER cc_start: 0.7601 (p) cc_final: 0.7289 (t) REVERT: C 251 MET cc_start: 0.8276 (ptt) cc_final: 0.7920 (ptt) REVERT: C 418 ARG cc_start: 0.7928 (ttm110) cc_final: 0.7587 (ttm110) REVERT: C 498 MET cc_start: 0.7747 (ttm) cc_final: 0.6947 (tpt) REVERT: D 142 LEU cc_start: 0.8736 (mt) cc_final: 0.8056 (pp) REVERT: D 239 MET cc_start: 0.7865 (mmm) cc_final: 0.7644 (mmm) REVERT: D 280 GLN cc_start: 0.8805 (pp30) cc_final: 0.8084 (pp30) REVERT: D 333 ASP cc_start: 0.8858 (t0) cc_final: 0.8495 (t70) REVERT: D 481 ASP cc_start: 0.8552 (m-30) cc_final: 0.8309 (p0) REVERT: D 492 MET cc_start: 0.8311 (tmm) cc_final: 0.8014 (tmm) REVERT: E 201 GLN cc_start: 0.6920 (mt0) cc_final: 0.6275 (mt0) REVERT: E 251 MET cc_start: 0.8200 (ttp) cc_final: 0.7448 (ttt) REVERT: E 258 LEU cc_start: 0.9240 (tp) cc_final: 0.8942 (tp) REVERT: E 262 ASP cc_start: 0.8828 (t0) cc_final: 0.8398 (t0) REVERT: E 340 ASP cc_start: 0.8231 (m-30) cc_final: 0.7784 (m-30) REVERT: E 342 GLN cc_start: 0.8417 (pm20) cc_final: 0.7799 (pt0) REVERT: E 376 MET cc_start: 0.6900 (mmt) cc_final: 0.6123 (mmt) REVERT: E 436 MET cc_start: 0.7423 (ppp) cc_final: 0.6984 (ppp) REVERT: F 39 LYS cc_start: 0.8060 (mmtm) cc_final: 0.7793 (mmtp) REVERT: F 92 ILE cc_start: 0.8553 (mt) cc_final: 0.8271 (mt) REVERT: F 113 VAL cc_start: 0.8767 (p) cc_final: 0.8535 (m) REVERT: F 158 LEU cc_start: 0.9576 (tp) cc_final: 0.9269 (tp) REVERT: F 184 GLU cc_start: 0.8395 (tp30) cc_final: 0.8192 (tp30) REVERT: F 241 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7661 (mm-30) REVERT: F 247 MET cc_start: 0.9004 (mmm) cc_final: 0.8602 (mmm) REVERT: F 254 LEU cc_start: 0.9364 (tp) cc_final: 0.8719 (tp) REVERT: F 292 MET cc_start: 0.8977 (mtt) cc_final: 0.8697 (mtt) REVERT: F 314 THR cc_start: 0.8310 (p) cc_final: 0.7975 (p) REVERT: F 442 THR cc_start: 0.8660 (p) cc_final: 0.8290 (t) REVERT: F 462 LEU cc_start: 0.8583 (pp) cc_final: 0.8363 (tt) REVERT: A 157 MET cc_start: 0.8704 (mpp) cc_final: 0.8134 (mpp) REVERT: A 251 MET cc_start: 0.7428 (tmm) cc_final: 0.6954 (tmm) REVERT: A 290 ASP cc_start: 0.7453 (p0) cc_final: 0.6902 (p0) REVERT: A 340 ASP cc_start: 0.7280 (m-30) cc_final: 0.7070 (m-30) REVERT: A 402 ASP cc_start: 0.7688 (t0) cc_final: 0.7486 (t0) REVERT: A 436 MET cc_start: 0.7073 (ppp) cc_final: 0.6835 (tmm) REVERT: A 437 THR cc_start: 0.9145 (m) cc_final: 0.8824 (p) REVERT: B 213 TYR cc_start: 0.7758 (t80) cc_final: 0.7535 (t80) REVERT: B 239 MET cc_start: 0.8355 (mtm) cc_final: 0.8106 (mtm) REVERT: B 299 GLN cc_start: 0.8875 (pm20) cc_final: 0.8245 (pt0) REVERT: B 333 ASP cc_start: 0.8903 (t0) cc_final: 0.8563 (t70) REVERT: B 335 THR cc_start: 0.8468 (p) cc_final: 0.8208 (p) REVERT: B 370 SER cc_start: 0.9606 (m) cc_final: 0.9085 (p) REVERT: B 423 ARG cc_start: 0.8979 (mtt180) cc_final: 0.8278 (ttm110) REVERT: B 435 PHE cc_start: 0.8273 (m-80) cc_final: 0.7394 (m-80) REVERT: B 462 LEU cc_start: 0.8273 (tp) cc_final: 0.7993 (tp) REVERT: B 476 LEU cc_start: 0.8629 (mt) cc_final: 0.8136 (mt) REVERT: e 112 LYS cc_start: 0.7980 (mmtp) cc_final: 0.7472 (pttp) REVERT: g 136 MET cc_start: 0.7638 (tpp) cc_final: 0.7425 (tpp) REVERT: g 192 GLN cc_start: 0.8167 (tp40) cc_final: 0.7741 (tp40) REVERT: g 211 GLU cc_start: 0.6905 (pt0) cc_final: 0.6636 (pt0) REVERT: S 54 LEU cc_start: 0.7380 (mm) cc_final: 0.7176 (mm) REVERT: S 60 MET cc_start: 0.6948 (mtt) cc_final: 0.6282 (mtp) REVERT: S 61 GLU cc_start: 0.5563 (mm-30) cc_final: 0.5286 (mm-30) REVERT: S 63 LEU cc_start: 0.6852 (mt) cc_final: 0.6563 (mt) REVERT: O 60 MET cc_start: 0.6421 (tpp) cc_final: 0.6129 (tpp) REVERT: P 61 GLU cc_start: 0.7987 (pp20) cc_final: 0.7643 (tm-30) REVERT: M 59 PHE cc_start: 0.5906 (m-80) cc_final: 0.5530 (m-80) REVERT: T 37 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8134 (mt-10) REVERT: G 34 GLN cc_start: 0.6070 (tt0) cc_final: 0.5847 (tt0) REVERT: G 54 LEU cc_start: 0.5195 (mt) cc_final: 0.4892 (pp) REVERT: K 37 GLU cc_start: 0.7879 (pp20) cc_final: 0.7587 (pp20) REVERT: K 68 LEU cc_start: 0.6757 (tp) cc_final: 0.6539 (tp) REVERT: J 28 GLN cc_start: 0.7575 (mt0) cc_final: 0.6122 (tt0) REVERT: I 50 ARG cc_start: 0.7933 (ttp80) cc_final: 0.6563 (ttm170) REVERT: p 97 PHE cc_start: 0.4992 (t80) cc_final: 0.4643 (t80) REVERT: p 102 PHE cc_start: 0.3368 (m-10) cc_final: 0.3111 (m-80) REVERT: p 203 LEU cc_start: 0.1279 (OUTLIER) cc_final: 0.0596 (mm) REVERT: b 59 ARG cc_start: 0.8024 (mtm110) cc_final: 0.7620 (ttp80) REVERT: b 91 ASP cc_start: 0.6116 (t0) cc_final: 0.5886 (t0) REVERT: b 120 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8679 (pt0) REVERT: b 146 GLN cc_start: 0.8422 (tp-100) cc_final: 0.8108 (tp-100) REVERT: b 179 MET cc_start: 0.7686 (ttp) cc_final: 0.7465 (ttp) REVERT: d 155 ILE cc_start: 0.8857 (tt) cc_final: 0.8608 (mp) REVERT: d 188 ASN cc_start: 0.7027 (m-40) cc_final: 0.6790 (m-40) outliers start: 5 outliers final: 1 residues processed: 951 average time/residue: 0.2286 time to fit residues: 364.5520 Evaluate side-chains 678 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 675 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 256 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 442 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 497 optimal weight: 20.0000 chunk 175 optimal weight: 10.0000 chunk 478 optimal weight: 6.9990 chunk 303 optimal weight: 9.9990 chunk 248 optimal weight: 0.7980 chunk 176 optimal weight: 0.0770 chunk 240 optimal weight: 3.9990 overall best weight: 3.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 25 HIS a 29 GLN ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 ASN F 210 ASN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 GLN B 210 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN g 97 ASN g 228 HIS ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 77 GLN d 141 HIS d 147 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.130595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.104010 restraints weight = 100599.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.102094 restraints weight = 83099.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.102379 restraints weight = 70880.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102637 restraints weight = 60077.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.102851 restraints weight = 54651.660| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.6890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.530 39807 Z= 0.268 Angle : 0.841 45.600 53945 Z= 0.424 Chirality : 0.050 0.661 6456 Planarity : 0.006 0.244 6961 Dihedral : 6.426 166.823 5589 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.52 % Favored : 96.37 % Rotamer: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.81 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.49 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.12), residues: 5149 helix: 1.06 (0.09), residues: 2892 sheet: -0.78 (0.20), residues: 613 loop : -0.61 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG A 16 TYR 0.027 0.002 TYR G 66 PHE 0.032 0.002 PHE a 72 TRP 0.018 0.002 TRP a 110 HIS 0.007 0.001 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.26 (39778) covalent geometry : angle 0.83909 / 0.42 (53943) SS BOND : bond 0.01251 / 0.66 ( 1) SS BOND : angle 9.24692 / 5.33 ( 2) hydrogen bonds : bond 0.05008 / 3.46 ( 2443) hydrogen bonds : angle 5.18344 / 3.68 ( 7173) Misc. bond : bond 0.01861 / 1.25 ( 28) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 894 time to evaluate : 1.263 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 187 SER cc_start: 0.7852 (p) cc_final: 0.7591 (t) REVERT: C 251 MET cc_start: 0.8518 (ptt) cc_final: 0.7914 (ptt) REVERT: C 436 MET cc_start: 0.7267 (tmm) cc_final: 0.6965 (tmm) REVERT: C 498 MET cc_start: 0.7841 (ttm) cc_final: 0.6880 (tpt) REVERT: D 280 GLN cc_start: 0.8936 (pp30) cc_final: 0.8060 (pp30) REVERT: D 333 ASP cc_start: 0.8638 (t0) cc_final: 0.8282 (t70) REVERT: D 428 GLU cc_start: 0.7907 (pp20) cc_final: 0.7641 (pp20) REVERT: D 481 ASP cc_start: 0.8656 (m-30) cc_final: 0.8349 (p0) REVERT: E 258 LEU cc_start: 0.9316 (tp) cc_final: 0.9058 (tp) REVERT: E 342 GLN cc_start: 0.8581 (pm20) cc_final: 0.7993 (pp30) REVERT: E 376 MET cc_start: 0.7130 (mmt) cc_final: 0.6456 (mmt) REVERT: E 436 MET cc_start: 0.8032 (ppp) cc_final: 0.7623 (ppp) REVERT: F 32 ASP cc_start: 0.7923 (m-30) cc_final: 0.7492 (m-30) REVERT: F 59 MET cc_start: 0.6362 (tpp) cc_final: 0.5691 (tmm) REVERT: F 113 VAL cc_start: 0.8881 (p) cc_final: 0.8629 (m) REVERT: F 158 LEU cc_start: 0.9610 (tp) cc_final: 0.9316 (tp) REVERT: F 184 GLU cc_start: 0.8364 (tp30) cc_final: 0.8087 (tp30) REVERT: F 204 GLU cc_start: 0.5886 (tm-30) cc_final: 0.5357 (tm-30) REVERT: F 208 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7655 (tm-30) REVERT: F 212 LEU cc_start: 0.9034 (tp) cc_final: 0.7727 (tp) REVERT: F 216 MET cc_start: 0.7996 (mpp) cc_final: 0.7540 (mpp) REVERT: F 241 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7721 (mm-30) REVERT: F 379 ILE cc_start: 0.9108 (mt) cc_final: 0.8884 (mm) REVERT: F 442 THR cc_start: 0.8533 (p) cc_final: 0.8149 (t) REVERT: F 462 LEU cc_start: 0.8552 (pp) cc_final: 0.8273 (tt) REVERT: A 157 MET cc_start: 0.8749 (mpp) cc_final: 0.8156 (mpp) REVERT: A 251 MET cc_start: 0.7692 (tmm) cc_final: 0.7450 (tmm) REVERT: A 290 ASP cc_start: 0.7653 (p0) cc_final: 0.7053 (p0) REVERT: A 402 ASP cc_start: 0.7653 (t0) cc_final: 0.7400 (t0) REVERT: A 464 TYR cc_start: 0.7337 (t80) cc_final: 0.6785 (t80) REVERT: B 239 MET cc_start: 0.8295 (mtm) cc_final: 0.8067 (mtm) REVERT: B 299 GLN cc_start: 0.8803 (pm20) cc_final: 0.8250 (pm20) REVERT: B 370 SER cc_start: 0.9590 (m) cc_final: 0.9071 (p) REVERT: B 374 MET cc_start: 0.6683 (tpt) cc_final: 0.6471 (tpt) REVERT: B 423 ARG cc_start: 0.9082 (mtt180) cc_final: 0.8581 (ttm110) REVERT: B 435 PHE cc_start: 0.8399 (m-80) cc_final: 0.7545 (m-80) REVERT: B 462 LEU cc_start: 0.8521 (tp) cc_final: 0.8304 (tt) REVERT: B 476 LEU cc_start: 0.8627 (mt) cc_final: 0.8077 (mt) REVERT: e 3 LEU cc_start: 0.7135 (pp) cc_final: 0.6702 (mp) REVERT: g 136 MET cc_start: 0.7711 (tpp) cc_final: 0.7485 (tpp) REVERT: g 173 GLU cc_start: 0.7137 (pp20) cc_final: 0.6902 (tm-30) REVERT: g 192 GLN cc_start: 0.8261 (tp40) cc_final: 0.7935 (tp40) REVERT: g 315 GLU cc_start: 0.8902 (tt0) cc_final: 0.8599 (tm-30) REVERT: g 316 LEU cc_start: 0.8895 (mt) cc_final: 0.8589 (mt) REVERT: S 54 LEU cc_start: 0.7542 (mm) cc_final: 0.7118 (mm) REVERT: S 60 MET cc_start: 0.6556 (mtt) cc_final: 0.5906 (mtp) REVERT: S 61 GLU cc_start: 0.5784 (mm-30) cc_final: 0.5442 (mm-30) REVERT: O 60 MET cc_start: 0.6400 (tpp) cc_final: 0.6055 (tpp) REVERT: P 54 LEU cc_start: 0.6037 (mp) cc_final: 0.5808 (mp) REVERT: P 61 GLU cc_start: 0.8008 (pp20) cc_final: 0.7686 (tm-30) REVERT: T 37 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7909 (mt-10) REVERT: G 34 GLN cc_start: 0.6322 (tt0) cc_final: 0.5578 (tt0) REVERT: H 46 GLU cc_start: 0.4874 (pm20) cc_final: 0.4523 (pm20) REVERT: K 37 GLU cc_start: 0.8048 (pp20) cc_final: 0.7781 (pp20) REVERT: K 68 LEU cc_start: 0.6448 (tp) cc_final: 0.5840 (tp) REVERT: J 28 GLN cc_start: 0.7554 (mt0) cc_final: 0.7320 (mt0) REVERT: I 50 ARG cc_start: 0.7904 (ttp80) cc_final: 0.6520 (ttp-110) REVERT: p 102 PHE cc_start: 0.3625 (m-10) cc_final: 0.3170 (m-80) REVERT: b 59 ARG cc_start: 0.8146 (mtm110) cc_final: 0.7911 (ttp80) REVERT: b 146 GLN cc_start: 0.8555 (tp-100) cc_final: 0.8269 (tp-100) REVERT: d 72 ASP cc_start: 0.7868 (t0) cc_final: 0.7280 (t0) REVERT: d 242 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8215 (pt0) outliers start: 5 outliers final: 2 residues processed: 898 average time/residue: 0.2296 time to fit residues: 346.1783 Evaluate side-chains 631 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 629 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 229 optimal weight: 0.0010 chunk 270 optimal weight: 2.9990 chunk 453 optimal weight: 6.9990 chunk 203 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 475 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 228 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 252 optimal weight: 3.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 25 HIS a 34 GLN ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 ASN F 210 ASN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 GLN B 210 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN g 97 ASN g 228 HIS ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 GLN H 34 GLN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN I 28 GLN ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 HIS d 147 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.130561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.104244 restraints weight = 99980.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.102354 restraints weight = 82190.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.102838 restraints weight = 73847.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.102848 restraints weight = 65685.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.103361 restraints weight = 55603.805| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.7176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.525 39807 Z= 0.257 Angle : 0.841 44.805 53945 Z= 0.426 Chirality : 0.051 0.763 6456 Planarity : 0.006 0.172 6961 Dihedral : 6.410 173.694 5589 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.65 % Favored : 96.25 % Rotamer: Outliers : 0.05 % Allowed : 1.97 % Favored : 97.98 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.49 % Twisted General : 0.12 % 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: 0.40 (0.12), residues: 5149 helix: 1.07 (0.10), residues: 2890 sheet: -0.79 (0.20), residues: 598 loop : -0.61 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG p 119 TYR 0.022 0.002 TYR C 237 PHE 0.042 0.002 PHE b 145 TRP 0.019 0.002 TRP a 110 HIS 0.008 0.001 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.25 (39778) covalent geometry : angle 0.83827 / 0.42 (53943) SS BOND : bond 0.03483 / 1.83 ( 1) SS BOND : angle 11.10574 / 6.38 ( 2) hydrogen bonds : bond 0.05017 / 3.48 ( 2443) hydrogen bonds : angle 5.14095 / 3.65 ( 7173) Misc. bond : bond 0.01894 / 1.28 ( 28) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 889 time to evaluate : 1.523 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: 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 187 SER cc_start: 0.7730 (p) cc_final: 0.7374 (t) REVERT: a 222 PHE cc_start: 0.8410 (t80) cc_final: 0.8084 (t80) REVERT: C 183 THR cc_start: 0.9216 (m) cc_final: 0.8950 (m) REVERT: C 436 MET cc_start: 0.7301 (tmm) cc_final: 0.6950 (tmm) REVERT: C 498 MET cc_start: 0.7720 (ttm) cc_final: 0.6812 (tpt) REVERT: D 118 VAL cc_start: 0.8829 (t) cc_final: 0.8539 (p) REVERT: D 183 MET cc_start: 0.8984 (mmm) cc_final: 0.8596 (mmt) REVERT: D 280 GLN cc_start: 0.8806 (pp30) cc_final: 0.7911 (pp30) REVERT: D 333 ASP cc_start: 0.8629 (t0) cc_final: 0.8281 (t70) REVERT: D 428 GLU cc_start: 0.7866 (pp20) cc_final: 0.7639 (pp20) REVERT: D 481 ASP cc_start: 0.8600 (m-30) cc_final: 0.8329 (p0) REVERT: E 258 LEU cc_start: 0.9267 (tp) cc_final: 0.8989 (tp) REVERT: E 262 ASP cc_start: 0.8927 (t0) cc_final: 0.8621 (t0) REVERT: E 340 ASP cc_start: 0.8645 (m-30) cc_final: 0.8311 (m-30) REVERT: E 342 GLN cc_start: 0.8529 (pm20) cc_final: 0.7950 (pp30) REVERT: E 369 SER cc_start: 0.7325 (p) cc_final: 0.7018 (t) REVERT: E 376 MET cc_start: 0.7005 (mmt) cc_final: 0.6350 (mmt) REVERT: E 436 MET cc_start: 0.7508 (ppp) cc_final: 0.7165 (ppp) REVERT: F 32 ASP cc_start: 0.7849 (m-30) cc_final: 0.7613 (m-30) REVERT: F 59 MET cc_start: 0.6472 (tpp) cc_final: 0.5751 (tmm) REVERT: F 113 VAL cc_start: 0.8911 (p) cc_final: 0.8693 (m) REVERT: F 158 LEU cc_start: 0.9611 (tp) cc_final: 0.9354 (tp) REVERT: F 184 GLU cc_start: 0.8337 (tp30) cc_final: 0.8092 (tp30) REVERT: F 204 GLU cc_start: 0.5712 (tm-30) cc_final: 0.5491 (tm-30) REVERT: F 212 LEU cc_start: 0.8960 (tp) cc_final: 0.7746 (tp) REVERT: F 216 MET cc_start: 0.7990 (mpp) cc_final: 0.7554 (mpp) REVERT: F 247 MET cc_start: 0.9059 (mmm) cc_final: 0.8789 (mmm) REVERT: F 254 LEU cc_start: 0.9191 (tp) cc_final: 0.8895 (tp) REVERT: F 258 GLU cc_start: 0.7161 (pt0) cc_final: 0.6631 (pt0) REVERT: F 379 ILE cc_start: 0.9216 (mt) cc_final: 0.8887 (mm) REVERT: F 442 THR cc_start: 0.8551 (p) cc_final: 0.8237 (t) REVERT: F 462 LEU cc_start: 0.8554 (pp) cc_final: 0.8344 (tt) REVERT: A 157 MET cc_start: 0.8671 (mpp) cc_final: 0.8063 (mpp) REVERT: A 251 MET cc_start: 0.7659 (tmm) cc_final: 0.7107 (tmm) REVERT: A 290 ASP cc_start: 0.7534 (p0) cc_final: 0.7144 (p0) REVERT: A 436 MET cc_start: 0.8057 (ppp) cc_final: 0.7056 (tmm) REVERT: A 464 TYR cc_start: 0.7142 (t80) cc_final: 0.6556 (t80) REVERT: B 239 MET cc_start: 0.8232 (mtm) cc_final: 0.7918 (mtm) REVERT: B 370 SER cc_start: 0.9596 (m) cc_final: 0.9040 (p) REVERT: B 423 ARG cc_start: 0.9061 (mtt180) cc_final: 0.8653 (ttm110) REVERT: B 435 PHE cc_start: 0.8323 (m-80) cc_final: 0.7487 (m-80) REVERT: B 462 LEU cc_start: 0.8657 (tp) cc_final: 0.8170 (tp) REVERT: B 476 LEU cc_start: 0.8563 (mt) cc_final: 0.8050 (mt) REVERT: e 3 LEU cc_start: 0.7008 (pp) cc_final: 0.6579 (mp) REVERT: e 112 LYS cc_start: 0.8175 (mmtp) cc_final: 0.7496 (pttm) REVERT: e 123 ARG cc_start: 0.8069 (ptm160) cc_final: 0.7061 (ptm-80) REVERT: g 173 GLU cc_start: 0.7190 (pp20) cc_final: 0.6911 (tm-30) REVERT: g 192 GLN cc_start: 0.8245 (tp40) cc_final: 0.7896 (tp40) REVERT: g 248 ASP cc_start: 0.7576 (p0) cc_final: 0.7314 (p0) REVERT: g 315 GLU cc_start: 0.8921 (tt0) cc_final: 0.8715 (tm-30) REVERT: S 34 GLN cc_start: 0.7180 (tt0) cc_final: 0.6659 (tt0) REVERT: S 54 LEU cc_start: 0.7555 (mm) cc_final: 0.7116 (mm) REVERT: S 60 MET cc_start: 0.7083 (mtt) cc_final: 0.6312 (mtp) REVERT: O 60 MET cc_start: 0.6397 (tpp) cc_final: 0.6045 (tpp) REVERT: P 24 PRO cc_start: 0.8927 (Cg_exo) cc_final: 0.8654 (Cg_endo) REVERT: P 54 LEU cc_start: 0.6029 (mp) cc_final: 0.5817 (mp) REVERT: P 61 GLU cc_start: 0.8042 (pp20) cc_final: 0.7433 (tm-30) REVERT: T 37 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8034 (mt-10) REVERT: G 34 GLN cc_start: 0.6479 (tt0) cc_final: 0.6069 (tt0) REVERT: L 63 LEU cc_start: 0.6982 (tt) cc_final: 0.6648 (mp) REVERT: L 75 LEU cc_start: 0.4656 (tp) cc_final: 0.4173 (tp) REVERT: K 37 GLU cc_start: 0.8008 (pp20) cc_final: 0.7771 (pp20) REVERT: J 28 GLN cc_start: 0.6813 (mt0) cc_final: 0.5863 (tt0) REVERT: I 50 ARG cc_start: 0.7982 (ttp80) cc_final: 0.6685 (ttm170) REVERT: I 60 MET cc_start: 0.3773 (mmm) cc_final: 0.3274 (mtp) REVERT: I 63 LEU cc_start: 0.5374 (mp) cc_final: 0.5126 (mp) REVERT: p 102 PHE cc_start: 0.3749 (m-10) cc_final: 0.3278 (m-80) REVERT: b 120 GLN cc_start: 0.8992 (pm20) cc_final: 0.8623 (pm20) REVERT: b 138 ASN cc_start: 0.7267 (t0) cc_final: 0.6880 (t0) REVERT: d 164 GLU cc_start: 0.8495 (tp30) cc_final: 0.8270 (tp30) REVERT: d 242 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8200 (pt0) outliers start: 2 outliers final: 0 residues processed: 890 average time/residue: 0.2287 time to fit residues: 340.4982 Evaluate side-chains 638 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 638 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 107 optimal weight: 10.0000 chunk 287 optimal weight: 0.7980 chunk 371 optimal weight: 30.0000 chunk 186 optimal weight: 10.0000 chunk 478 optimal weight: 8.9990 chunk 344 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 423 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 320 optimal weight: 0.8980 chunk 303 optimal weight: 7.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 25 HIS ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN A 173 GLN A 269 GLN B 210 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN ** g 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 143 GLN ** p 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.130344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.105422 restraints weight = 100297.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.105436 restraints weight = 106122.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.106310 restraints weight = 72163.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105708 restraints weight = 55630.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.105828 restraints weight = 53905.857| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.7409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.523 39807 Z= 0.254 Angle : 0.837 44.814 53945 Z= 0.423 Chirality : 0.052 0.864 6456 Planarity : 0.006 0.138 6961 Dihedral : 6.352 169.926 5589 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.85 % Favored : 96.06 % Rotamer: Outliers : 0.05 % Allowed : 1.51 % Favored : 98.44 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.49 % Twisted General : 0.08 % 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: 0.38 (0.12), residues: 5149 helix: 1.07 (0.10), residues: 2895 sheet: -0.82 (0.20), residues: 598 loop : -0.64 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG g 171 TYR 0.052 0.002 TYR G 66 PHE 0.034 0.002 PHE B 343 TRP 0.019 0.002 TRP a 110 HIS 0.009 0.001 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.25 (39778) covalent geometry : angle 0.83515 / 0.42 (53943) SS BOND : bond 0.01029 / 0.54 ( 1) SS BOND : angle 9.97545 / 5.73 ( 2) hydrogen bonds : bond 0.04963 / 3.44 ( 2443) hydrogen bonds : angle 5.15765 / 3.66 ( 7173) Misc. bond : bond 0.01806 / 1.22 ( 28) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 864 time to evaluate : 1.583 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 187 SER cc_start: 0.7335 (p) cc_final: 0.6994 (t) REVERT: a 222 PHE cc_start: 0.8221 (t80) cc_final: 0.7985 (t80) REVERT: C 52 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7468 (mm-30) REVERT: C 82 MET cc_start: 0.7485 (tpp) cc_final: 0.7114 (tpp) REVERT: C 184 ILE cc_start: 0.8959 (mm) cc_final: 0.8601 (mm) REVERT: C 436 MET cc_start: 0.7223 (tmm) cc_final: 0.6971 (tmm) REVERT: C 498 MET cc_start: 0.7454 (ttm) cc_final: 0.6711 (tpt) REVERT: D 280 GLN cc_start: 0.8852 (pp30) cc_final: 0.7830 (pp30) REVERT: D 333 ASP cc_start: 0.8563 (t0) cc_final: 0.8214 (t70) REVERT: E 251 MET cc_start: 0.7946 (ttp) cc_final: 0.7253 (ttt) REVERT: E 262 ASP cc_start: 0.8892 (t0) cc_final: 0.8636 (t0) REVERT: E 293 TYR cc_start: 0.9084 (t80) cc_final: 0.8821 (t80) REVERT: E 340 ASP cc_start: 0.8460 (m-30) cc_final: 0.8096 (m-30) REVERT: E 342 GLN cc_start: 0.8501 (pm20) cc_final: 0.8050 (pp30) REVERT: E 376 MET cc_start: 0.6568 (mmt) cc_final: 0.5950 (mmt) REVERT: E 436 MET cc_start: 0.7153 (ppp) cc_final: 0.6838 (ppp) REVERT: F 32 ASP cc_start: 0.7942 (m-30) cc_final: 0.7700 (m-30) REVERT: F 59 MET cc_start: 0.6157 (tpp) cc_final: 0.5763 (tmm) REVERT: F 158 LEU cc_start: 0.9591 (tp) cc_final: 0.9360 (tp) REVERT: F 171 PHE cc_start: 0.9136 (m-80) cc_final: 0.8461 (m-10) REVERT: F 212 LEU cc_start: 0.8966 (tp) cc_final: 0.7675 (tp) REVERT: F 216 MET cc_start: 0.7719 (mpp) cc_final: 0.7476 (mpp) REVERT: F 247 MET cc_start: 0.9031 (mmm) cc_final: 0.8716 (mmm) REVERT: F 254 LEU cc_start: 0.9171 (tp) cc_final: 0.8711 (tp) REVERT: F 258 GLU cc_start: 0.7137 (pt0) cc_final: 0.6437 (pt0) REVERT: F 379 ILE cc_start: 0.9193 (mt) cc_final: 0.8837 (mm) REVERT: F 462 LEU cc_start: 0.8547 (pp) cc_final: 0.8268 (tt) REVERT: A 157 MET cc_start: 0.8469 (mpp) cc_final: 0.7923 (mpp) REVERT: A 251 MET cc_start: 0.7614 (tmm) cc_final: 0.7067 (tmm) REVERT: A 290 ASP cc_start: 0.7557 (p0) cc_final: 0.6936 (p0) REVERT: A 436 MET cc_start: 0.7787 (ppp) cc_final: 0.6878 (tmm) REVERT: A 464 TYR cc_start: 0.7096 (t80) cc_final: 0.6550 (t80) REVERT: B 204 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6075 (tp30) REVERT: B 239 MET cc_start: 0.8161 (mtm) cc_final: 0.7897 (mtm) REVERT: B 241 GLU cc_start: 0.8526 (mp0) cc_final: 0.8219 (mt-10) REVERT: B 273 ASP cc_start: 0.7823 (t0) cc_final: 0.7606 (t0) REVERT: B 370 SER cc_start: 0.9589 (m) cc_final: 0.9042 (p) REVERT: B 423 ARG cc_start: 0.9033 (mtt180) cc_final: 0.8385 (ttm110) REVERT: B 435 PHE cc_start: 0.8263 (m-80) cc_final: 0.7431 (m-80) REVERT: B 462 LEU cc_start: 0.8566 (tp) cc_final: 0.8258 (tp) REVERT: B 474 PHE cc_start: 0.8030 (m-80) cc_final: 0.7716 (m-80) REVERT: B 476 LEU cc_start: 0.8458 (mt) cc_final: 0.7961 (mt) REVERT: e 3 LEU cc_start: 0.6843 (pp) cc_final: 0.6561 (mp) REVERT: e 112 LYS cc_start: 0.7896 (mmtp) cc_final: 0.7428 (pttt) REVERT: e 123 ARG cc_start: 0.7322 (ptm160) cc_final: 0.6466 (ptm-80) REVERT: e 127 GLU cc_start: 0.7373 (pt0) cc_final: 0.6673 (pt0) REVERT: g 173 GLU cc_start: 0.7111 (pp20) cc_final: 0.6834 (pp20) REVERT: g 192 GLN cc_start: 0.8203 (tp40) cc_final: 0.7836 (tp40) REVERT: g 315 GLU cc_start: 0.8793 (tt0) cc_final: 0.8523 (tm-30) REVERT: S 36 VAL cc_start: 0.6899 (t) cc_final: 0.6698 (t) REVERT: S 59 PHE cc_start: 0.5428 (m-10) cc_final: 0.5209 (m-10) REVERT: S 60 MET cc_start: 0.7154 (mtt) cc_final: 0.6504 (mtt) REVERT: S 63 LEU cc_start: 0.7529 (mt) cc_final: 0.7278 (mm) REVERT: O 60 MET cc_start: 0.6456 (tpp) cc_final: 0.6221 (tpp) REVERT: P 24 PRO cc_start: 0.8772 (Cg_exo) cc_final: 0.8519 (Cg_endo) REVERT: P 61 GLU cc_start: 0.8135 (pp20) cc_final: 0.7563 (tm-30) REVERT: Q 37 GLU cc_start: 0.6669 (tp30) cc_final: 0.5142 (tp30) REVERT: G 34 GLN cc_start: 0.6372 (tt0) cc_final: 0.6143 (tt0) REVERT: G 37 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6631 (mt-10) REVERT: L 75 LEU cc_start: 0.4980 (tp) cc_final: 0.4751 (tp) REVERT: K 37 GLU cc_start: 0.8021 (pp20) cc_final: 0.7779 (pp20) REVERT: I 50 ARG cc_start: 0.7831 (ttp80) cc_final: 0.6618 (ttm110) REVERT: I 60 MET cc_start: 0.4154 (mmm) cc_final: 0.3759 (mtp) REVERT: I 74 LEU cc_start: 0.6146 (mt) cc_final: 0.5705 (mt) REVERT: p 83 LEU cc_start: 0.1651 (pp) cc_final: 0.0150 (pp) REVERT: p 102 PHE cc_start: 0.3624 (m-10) cc_final: 0.3263 (m-80) REVERT: b 182 ILE cc_start: 0.8088 (pt) cc_final: 0.7849 (pt) REVERT: d 72 ASP cc_start: 0.7827 (t0) cc_final: 0.7259 (t0) REVERT: d 84 ASP cc_start: 0.7665 (t0) cc_final: 0.7459 (t0) REVERT: d 242 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8016 (pt0) REVERT: d 243 GLU cc_start: 0.8274 (pp20) cc_final: 0.8005 (pp20) outliers start: 2 outliers final: 0 residues processed: 865 average time/residue: 0.2306 time to fit residues: 337.2517 Evaluate side-chains 623 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 623 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 423 optimal weight: 8.9990 chunk 303 optimal weight: 7.9990 chunk 240 optimal weight: 10.0000 chunk 421 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 410 optimal weight: 8.9990 chunk 401 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 390 optimal weight: 6.9990 chunk 225 optimal weight: 7.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 25 HIS ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN A 410 GLN B 25 GLN B 72 ASN B 210 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN B 325 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN H 34 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 30 ASN d 147 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.125819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.100090 restraints weight = 101694.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.097928 restraints weight = 96793.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098187 restraints weight = 85644.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.098440 restraints weight = 70060.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.098639 restraints weight = 61757.326| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.7744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.523 39807 Z= 0.342 Angle : 0.970 42.502 53945 Z= 0.492 Chirality : 0.057 1.179 6456 Planarity : 0.007 0.245 6961 Dihedral : 6.561 151.665 5589 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.72 % Favored : 95.18 % Rotamer: Outliers : 0.02 % Allowed : 1.10 % Favored : 98.88 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.49 % Twisted General : 0.14 % 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: -0.01 (0.11), residues: 5149 helix: 0.76 (0.09), residues: 2831 sheet: -1.03 (0.20), residues: 618 loop : -0.74 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG A 16 TYR 0.042 0.003 TYR H 66 PHE 0.041 0.003 PHE B 343 TRP 0.037 0.003 TRP a 110 HIS 0.009 0.001 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00769 / 0.34 (39778) covalent geometry : angle 0.96836 / 0.49 (53943) SS BOND : bond 0.00723 / 0.38 ( 1) SS BOND : angle 9.74343 / 5.60 ( 2) hydrogen bonds : bond 0.05450 / 3.76 ( 2443) hydrogen bonds : angle 5.47226 / 3.90 ( 7173) Misc. bond : bond 0.01868 / 1.23 ( 28) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 808 time to evaluate : 1.510 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: a 187 SER cc_start: 0.7772 (p) cc_final: 0.7439 (t) REVERT: a 222 PHE cc_start: 0.8410 (t80) cc_final: 0.8143 (t80) REVERT: C 184 ILE cc_start: 0.8975 (mm) cc_final: 0.8607 (mm) REVERT: C 436 MET cc_start: 0.7546 (tmm) cc_final: 0.7273 (tmm) REVERT: C 498 MET cc_start: 0.7756 (ttm) cc_final: 0.6838 (tpt) REVERT: D 118 VAL cc_start: 0.8857 (t) cc_final: 0.8648 (p) REVERT: D 235 VAL cc_start: 0.9094 (t) cc_final: 0.8821 (p) REVERT: D 239 MET cc_start: 0.8546 (mmm) cc_final: 0.8323 (mmm) REVERT: D 280 GLN cc_start: 0.9038 (pp30) cc_final: 0.8303 (pp30) REVERT: D 333 ASP cc_start: 0.8633 (t0) cc_final: 0.8389 (t70) REVERT: E 184 ILE cc_start: 0.9514 (mm) cc_final: 0.9293 (mm) REVERT: E 251 MET cc_start: 0.8399 (ttp) cc_final: 0.7526 (ttp) REVERT: E 262 ASP cc_start: 0.9110 (t0) cc_final: 0.8710 (t0) REVERT: E 273 GLN cc_start: 0.9253 (tt0) cc_final: 0.8775 (tt0) REVERT: E 340 ASP cc_start: 0.8446 (m-30) cc_final: 0.8135 (m-30) REVERT: E 342 GLN cc_start: 0.8686 (pm20) cc_final: 0.8130 (pp30) REVERT: E 436 MET cc_start: 0.7263 (ppp) cc_final: 0.6805 (ppp) REVERT: F 32 ASP cc_start: 0.8035 (m-30) cc_final: 0.7655 (m-30) REVERT: F 59 MET cc_start: 0.6633 (tpp) cc_final: 0.6089 (tmm) REVERT: F 79 MET cc_start: 0.9029 (mmt) cc_final: 0.8815 (mmt) REVERT: F 208 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7844 (tm-30) REVERT: F 212 LEU cc_start: 0.8843 (tp) cc_final: 0.7549 (tp) REVERT: F 216 MET cc_start: 0.7966 (mpp) cc_final: 0.7470 (mpp) REVERT: F 247 MET cc_start: 0.9145 (mmm) cc_final: 0.8658 (mmm) REVERT: F 379 ILE cc_start: 0.9326 (mt) cc_final: 0.8977 (mm) REVERT: F 477 VAL cc_start: 0.9529 (m) cc_final: 0.9259 (p) REVERT: F 490 LEU cc_start: 0.8837 (mt) cc_final: 0.8517 (tt) REVERT: A 25 LYS cc_start: 0.8548 (tppt) cc_final: 0.8337 (tppt) REVERT: A 157 MET cc_start: 0.8750 (mpp) cc_final: 0.8117 (mpp) REVERT: A 251 MET cc_start: 0.7814 (tmm) cc_final: 0.7119 (tmm) REVERT: A 290 ASP cc_start: 0.7674 (p0) cc_final: 0.7261 (p0) REVERT: A 436 MET cc_start: 0.8080 (ppp) cc_final: 0.7262 (tmm) REVERT: B 204 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6135 (tp30) REVERT: B 239 MET cc_start: 0.8227 (mtm) cc_final: 0.7876 (mtm) REVERT: B 370 SER cc_start: 0.9569 (m) cc_final: 0.9033 (p) REVERT: B 423 ARG cc_start: 0.9101 (mtt180) cc_final: 0.8429 (ttm110) REVERT: B 435 PHE cc_start: 0.8424 (m-80) cc_final: 0.7617 (m-80) REVERT: B 476 LEU cc_start: 0.8463 (mt) cc_final: 0.7934 (mt) REVERT: e 3 LEU cc_start: 0.7210 (pp) cc_final: 0.6545 (mp) REVERT: e 112 LYS cc_start: 0.8273 (mmtp) cc_final: 0.7642 (pttp) REVERT: g 136 MET cc_start: 0.8038 (tpp) cc_final: 0.7800 (tpp) REVERT: g 192 GLN cc_start: 0.8443 (tp40) cc_final: 0.8205 (tp40) REVERT: g 315 GLU cc_start: 0.8872 (tt0) cc_final: 0.8501 (tm-30) REVERT: g 316 LEU cc_start: 0.8970 (mt) cc_final: 0.8585 (tp) REVERT: S 34 GLN cc_start: 0.7197 (tt0) cc_final: 0.6750 (tt0) REVERT: S 60 MET cc_start: 0.6234 (mtt) cc_final: 0.5757 (mtt) REVERT: S 63 LEU cc_start: 0.7838 (mt) cc_final: 0.7578 (mm) REVERT: O 60 MET cc_start: 0.6457 (tpp) cc_final: 0.6126 (tpp) REVERT: P 24 PRO cc_start: 0.8915 (Cg_exo) cc_final: 0.8640 (Cg_endo) REVERT: P 54 LEU cc_start: 0.5972 (mp) cc_final: 0.5751 (mp) REVERT: P 61 GLU cc_start: 0.8169 (pp20) cc_final: 0.7818 (tm-30) REVERT: T 37 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7835 (mt-10) REVERT: G 34 GLN cc_start: 0.6172 (tt0) cc_final: 0.5928 (tt0) REVERT: G 60 MET cc_start: 0.6199 (mmm) cc_final: 0.5578 (mmm) REVERT: K 60 MET cc_start: 0.6161 (ttp) cc_final: 0.5327 (tpp) REVERT: I 50 ARG cc_start: 0.8071 (ttp80) cc_final: 0.6725 (ttm110) REVERT: I 60 MET cc_start: 0.3925 (mmm) cc_final: 0.3666 (mtp) REVERT: I 74 LEU cc_start: 0.6476 (mt) cc_final: 0.5963 (mt) REVERT: p 102 PHE cc_start: 0.3958 (m-10) cc_final: 0.3560 (m-80) REVERT: b 131 PHE cc_start: 0.7477 (t80) cc_final: 0.7114 (t80) REVERT: b 179 MET cc_start: 0.8277 (mtp) cc_final: 0.7820 (tpt) REVERT: d 72 ASP cc_start: 0.8138 (t0) cc_final: 0.7598 (t0) outliers start: 1 outliers final: 0 residues processed: 808 average time/residue: 0.2238 time to fit residues: 308.9122 Evaluate side-chains 579 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 579 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 3 optimal weight: 7.9990 chunk 329 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 422 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 237 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 279 optimal weight: 0.7980 chunk 335 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 25 HIS a 34 GLN ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 HIS C 148 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS D 188 ASN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 ASN F 120 ASN F 210 ASN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 GLN B 210 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN ** g 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 346 GLN S 34 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.128378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.102702 restraints weight = 100027.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.100639 restraints weight = 103983.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.101443 restraints weight = 80950.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.101601 restraints weight = 68939.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.101860 restraints weight = 58328.801| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.7911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.518 39807 Z= 0.259 Angle : 0.902 43.191 53945 Z= 0.458 Chirality : 0.053 0.860 6456 Planarity : 0.007 0.299 6961 Dihedral : 6.076 120.184 5589 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.14 % Favored : 95.77 % Rotamer: Outliers : 0.07 % Allowed : 0.56 % Favored : 99.37 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.49 % Twisted General : 0.10 % 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: 0.10 (0.12), residues: 5149 helix: 0.87 (0.10), residues: 2829 sheet: -1.02 (0.20), residues: 603 loop : -0.73 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.001 ARG E 418 TYR 0.046 0.002 TYR a 74 PHE 0.039 0.002 PHE B 343 TRP 0.029 0.002 TRP a 110 HIS 0.009 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.25 (39778) covalent geometry : angle 0.89970 / 0.46 (53943) SS BOND : bond 0.00938 / 0.49 ( 1) SS BOND : angle 10.00754 / 5.68 ( 2) hydrogen bonds : bond 0.05212 / 3.59 ( 2443) hydrogen bonds : angle 5.30330 / 3.77 ( 7173) Misc. bond : bond 0.01859 / 1.23 ( 28) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 807 time to evaluate : 1.552 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: C 52 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7597 (mm-30) REVERT: C 184 ILE cc_start: 0.8874 (mm) cc_final: 0.8536 (mm) REVERT: C 287 TYR cc_start: 0.8568 (m-80) cc_final: 0.8274 (m-80) REVERT: C 436 MET cc_start: 0.7319 (tmm) cc_final: 0.7063 (tmm) REVERT: C 498 MET cc_start: 0.7653 (ttm) cc_final: 0.6797 (tpt) REVERT: D 235 VAL cc_start: 0.8993 (t) cc_final: 0.8724 (p) REVERT: D 280 GLN cc_start: 0.8875 (pp30) cc_final: 0.7809 (pp30) REVERT: D 333 ASP cc_start: 0.8635 (t0) cc_final: 0.8338 (t70) REVERT: E 262 ASP cc_start: 0.8934 (t0) cc_final: 0.8690 (t0) REVERT: E 273 GLN cc_start: 0.9052 (tt0) cc_final: 0.8662 (tt0) REVERT: E 293 TYR cc_start: 0.9123 (t80) cc_final: 0.8763 (t80) REVERT: E 340 ASP cc_start: 0.8409 (m-30) cc_final: 0.8083 (m-30) REVERT: E 342 GLN cc_start: 0.8581 (pm20) cc_final: 0.8062 (pp30) REVERT: E 436 MET cc_start: 0.7390 (ppp) cc_final: 0.7041 (ppp) REVERT: F 32 ASP cc_start: 0.7866 (m-30) cc_final: 0.7470 (m-30) REVERT: F 59 MET cc_start: 0.6231 (tpp) cc_final: 0.5846 (tmm) REVERT: F 212 LEU cc_start: 0.8809 (tp) cc_final: 0.7648 (tp) REVERT: F 216 MET cc_start: 0.7687 (mpp) cc_final: 0.7398 (mpp) REVERT: F 254 LEU cc_start: 0.9158 (tp) cc_final: 0.8632 (tp) REVERT: F 258 GLU cc_start: 0.7214 (pt0) cc_final: 0.6397 (pt0) REVERT: F 379 ILE cc_start: 0.9253 (mt) cc_final: 0.8935 (mm) REVERT: F 462 LEU cc_start: 0.8673 (pp) cc_final: 0.8392 (tt) REVERT: F 477 VAL cc_start: 0.9451 (m) cc_final: 0.9214 (p) REVERT: F 490 LEU cc_start: 0.8746 (mt) cc_final: 0.8495 (tt) REVERT: A 157 MET cc_start: 0.8527 (mpp) cc_final: 0.7989 (mpp) REVERT: A 251 MET cc_start: 0.7612 (tmm) cc_final: 0.7005 (tmm) REVERT: A 290 ASP cc_start: 0.7393 (p0) cc_final: 0.6841 (p0) REVERT: A 436 MET cc_start: 0.7766 (ppp) cc_final: 0.7088 (ppp) REVERT: B 40 MET cc_start: 0.8179 (tpp) cc_final: 0.7820 (tpp) REVERT: B 239 MET cc_start: 0.8244 (mtm) cc_final: 0.7958 (mtm) REVERT: B 241 GLU cc_start: 0.8571 (mp0) cc_final: 0.8119 (mt-10) REVERT: B 370 SER cc_start: 0.9539 (m) cc_final: 0.8947 (p) REVERT: B 423 ARG cc_start: 0.9038 (mtt180) cc_final: 0.8395 (ttm110) REVERT: B 435 PHE cc_start: 0.8214 (m-80) cc_final: 0.7399 (m-80) REVERT: B 474 PHE cc_start: 0.7919 (m-80) cc_final: 0.7551 (m-80) REVERT: B 476 LEU cc_start: 0.8266 (mt) cc_final: 0.7829 (mt) REVERT: e 111 GLN cc_start: 0.8179 (pm20) cc_final: 0.7601 (mt0) REVERT: e 112 LYS cc_start: 0.8061 (mmtp) cc_final: 0.7455 (pttp) REVERT: e 121 ARG cc_start: 0.7011 (ttp80) cc_final: 0.6805 (ttp80) REVERT: g 192 GLN cc_start: 0.8310 (tp40) cc_final: 0.8047 (tp40) REVERT: g 315 GLU cc_start: 0.8816 (tt0) cc_final: 0.8465 (tm-30) REVERT: S 60 MET cc_start: 0.6899 (mtt) cc_final: 0.6472 (mtt) REVERT: S 63 LEU cc_start: 0.7808 (mt) cc_final: 0.7497 (mm) REVERT: O 60 MET cc_start: 0.6466 (tpp) cc_final: 0.6019 (tpp) REVERT: P 24 PRO cc_start: 0.8841 (Cg_exo) cc_final: 0.8540 (Cg_endo) REVERT: P 54 LEU cc_start: 0.6036 (mp) cc_final: 0.5732 (mp) REVERT: T 65 ILE cc_start: 0.6309 (tp) cc_final: 0.5995 (tp) REVERT: G 60 MET cc_start: 0.6341 (mmm) cc_final: 0.5647 (mtp) REVERT: H 24 PRO cc_start: 0.6568 (Cg_exo) cc_final: 0.6088 (Cg_endo) REVERT: K 59 PHE cc_start: 0.6170 (m-80) cc_final: 0.5803 (m-10) REVERT: J 41 ARG cc_start: 0.7117 (mtt180) cc_final: 0.6743 (mtt90) REVERT: I 50 ARG cc_start: 0.8013 (ttp80) cc_final: 0.6695 (ttm110) REVERT: I 60 MET cc_start: 0.3954 (mmm) cc_final: 0.3646 (mtp) REVERT: I 74 LEU cc_start: 0.6738 (mt) cc_final: 0.6318 (mt) REVERT: p 102 PHE cc_start: 0.3901 (m-10) cc_final: 0.3523 (m-80) REVERT: b 90 MET cc_start: 0.7384 (ppp) cc_final: 0.7106 (ppp) REVERT: b 179 MET cc_start: 0.7808 (mtp) cc_final: 0.7604 (tpt) REVERT: b 182 ILE cc_start: 0.8269 (pt) cc_final: 0.7979 (pt) REVERT: d 72 ASP cc_start: 0.8040 (t0) cc_final: 0.7811 (t0) REVERT: d 84 ASP cc_start: 0.7820 (t0) cc_final: 0.7526 (t0) outliers start: 3 outliers final: 0 residues processed: 809 average time/residue: 0.2247 time to fit residues: 310.2386 Evaluate side-chains 606 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 606 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 65 optimal weight: 2.9990 chunk 459 optimal weight: 5.9990 chunk 501 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 402 optimal weight: 0.7980 chunk 321 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 293 optimal weight: 0.8980 chunk 135 optimal weight: 8.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 25 HIS a 34 GLN ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 ASN F 210 ASN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN B 210 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN ** g 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 143 GLN ** p 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.129922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.105259 restraints weight = 100819.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103104 restraints weight = 82639.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.103017 restraints weight = 69808.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103204 restraints weight = 68396.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103481 restraints weight = 55934.088| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.8062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.516 39807 Z= 0.242 Angle : 0.875 39.835 53945 Z= 0.443 Chirality : 0.054 1.356 6456 Planarity : 0.007 0.262 6961 Dihedral : 5.935 119.212 5589 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.16 % Favored : 95.75 % Rotamer: Outliers : 0.07 % Allowed : 0.41 % Favored : 99.51 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.49 % Twisted General : 0.08 % 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 (0.12), residues: 5149 helix: 0.95 (0.10), residues: 2830 sheet: -0.87 (0.21), residues: 591 loop : -0.74 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.001 ARG E 418 TYR 0.046 0.002 TYR a 74 PHE 0.039 0.002 PHE B 343 TRP 0.026 0.002 TRP a 110 HIS 0.010 0.001 HIS e 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.24 (39778) covalent geometry : angle 0.87205 / 0.44 (53943) SS BOND : bond 0.01112 / 0.59 ( 1) SS BOND : angle 10.97748 / 6.26 ( 2) hydrogen bonds : bond 0.05146 / 3.57 ( 2443) hydrogen bonds : angle 5.23569 / 3.72 ( 7173) Misc. bond : bond 0.01853 / 1.23 ( 28) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8323.76 seconds wall clock time: 144 minutes 6.97 seconds (8646.97 seconds total)