Starting phenix.real_space_refine on Thu Feb 5 11:54:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kcv_62262/02_2026/9kcv_62262.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kcv_62262/02_2026/9kcv_62262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kcv_62262/02_2026/9kcv_62262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kcv_62262/02_2026/9kcv_62262.map" model { file = "/net/cci-nas-00/data/ceres_data/9kcv_62262/02_2026/9kcv_62262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kcv_62262/02_2026/9kcv_62262.cif" } resolution = 3.6 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= 0.001 sd= 0.038 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 10916 2.51 5 N 2792 2.21 5 O 2944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16748 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4187 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 19, 'TRANS': 500} Chain: "B" Number of atoms: 4187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4187 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 19, 'TRANS': 500} Chain: "C" Number of atoms: 4187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4187 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 19, 'TRANS': 500} Chain: "D" Number of atoms: 4187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4187 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 19, 'TRANS': 500} Time building chain proxies: 3.23, per 1000 atoms: 0.19 Number of scatterers: 16748 At special positions: 0 Unit cell: (112.32, 139.36, 116.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2944 8.00 N 2792 7.00 C 10916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 281 " distance=2.03 Simple disulfide: pdb=" SG CYS A 262 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 267 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 281 " distance=2.03 Simple disulfide: pdb=" SG CYS B 262 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 267 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 281 " distance=2.03 Simple disulfide: pdb=" SG CYS C 262 " - pdb=" SG CYS C 302 " distance=2.03 Simple disulfide: pdb=" SG CYS C 267 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 281 " distance=2.04 Simple disulfide: pdb=" SG CYS D 262 " - pdb=" SG CYS D 302 " distance=2.03 Simple disulfide: pdb=" SG CYS D 267 " - pdb=" SG CYS D 274 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 504.2 milliseconds 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 12 sheets defined 67.7% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 64 through 85 Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 103 through 129 Processing helix chain 'A' and resid 149 through 160 Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 171 through 179 removed outlier: 3.795A pdb=" N ILE A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.752A pdb=" N ASN A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.716A pdb=" N ASN A 194 " --> pdb=" O ASN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 221 removed outlier: 4.378A pdb=" N ILE A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 4.400A pdb=" N PHE A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 229 through 270 removed outlier: 4.336A pdb=" N ASN A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 284 removed outlier: 3.959A pdb=" N PHE A 279 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N CYS A 281 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ASN A 282 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 284 " --> pdb=" O CYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 326 through 344 Processing helix chain 'A' and resid 354 through 388 Processing helix chain 'A' and resid 388 through 407 removed outlier: 3.806A pdb=" N MET A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 429 removed outlier: 4.569A pdb=" N SER A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 440 removed outlier: 3.762A pdb=" N GLY A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 454 through 459 Processing helix chain 'A' and resid 460 through 465 removed outlier: 4.009A pdb=" N ALA A 465 " --> pdb=" O PRO A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 478 removed outlier: 3.772A pdb=" N LEU A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 473 " --> pdb=" O ARG A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 541 removed outlier: 3.768A pdb=" N LEU A 536 " --> pdb=" O GLY A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 577 removed outlier: 3.512A pdb=" N LEU A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 85 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 103 through 130 Processing helix chain 'B' and resid 149 through 160 removed outlier: 3.621A pdb=" N ILE B 153 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 168 removed outlier: 3.656A pdb=" N ALA B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 179 removed outlier: 3.667A pdb=" N ILE B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 removed outlier: 3.740A pdb=" N ASN B 194 " --> pdb=" O ASN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 221 removed outlier: 4.357A pdb=" N ILE B 201 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Proline residue: B 206 - end of helix removed outlier: 4.205A pdb=" N PHE B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Proline residue: B 213 - end of helix Processing helix chain 'B' and resid 229 through 270 removed outlier: 3.753A pdb=" N ASN B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 274 removed outlier: 3.883A pdb=" N CYS B 274 " --> pdb=" O GLU B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 274' Processing helix chain 'B' and resid 276 through 284 removed outlier: 3.864A pdb=" N PHE B 279 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N CYS B 281 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ASN B 282 " --> pdb=" O PHE B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 314 through 320 removed outlier: 3.713A pdb=" N VAL B 318 " --> pdb=" O TYR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 344 Processing helix chain 'B' and resid 354 through 388 Processing helix chain 'B' and resid 388 through 407 removed outlier: 3.754A pdb=" N GLU B 392 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 429 removed outlier: 3.801A pdb=" N SER B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 440 removed outlier: 3.769A pdb=" N GLY B 439 " --> pdb=" O SER B 435 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 453 Processing helix chain 'B' and resid 454 through 459 removed outlier: 3.515A pdb=" N ARG B 459 " --> pdb=" O GLU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 476 removed outlier: 3.800A pdb=" N LEU B 471 " --> pdb=" O ASP B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 541 removed outlier: 3.909A pdb=" N LEU B 536 " --> pdb=" O GLY B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 577 removed outlier: 3.549A pdb=" N GLN B 577 " --> pdb=" O PHE B 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 85 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 103 through 130 Processing helix chain 'C' and resid 149 through 160 Processing helix chain 'C' and resid 161 through 167 Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.574A pdb=" N LYS C 193 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN C 194 " --> pdb=" O ASN C 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 190 through 194' Processing helix chain 'C' and resid 198 through 221 removed outlier: 4.000A pdb=" N LEU C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Proline residue: C 206 - end of helix removed outlier: 4.583A pdb=" N PHE C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Proline residue: C 213 - end of helix Processing helix chain 'C' and resid 229 through 270 removed outlier: 4.307A pdb=" N ASN C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 284 removed outlier: 3.533A pdb=" N MET C 283 " --> pdb=" O ASP C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 Processing helix chain 'C' and resid 297 through 302 removed outlier: 3.589A pdb=" N CYS C 302 " --> pdb=" O VAL C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 321 through 325 removed outlier: 3.619A pdb=" N THR C 324 " --> pdb=" O LYS C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 344 Processing helix chain 'C' and resid 354 through 388 Processing helix chain 'C' and resid 388 through 408 removed outlier: 3.766A pdb=" N GLU C 392 " --> pdb=" O VAL C 388 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 429 removed outlier: 3.914A pdb=" N GLN C 415 " --> pdb=" O GLN C 411 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 439 removed outlier: 3.789A pdb=" N GLY C 439 " --> pdb=" O SER C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 453 Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'C' and resid 460 through 465 removed outlier: 3.756A pdb=" N ALA C 465 " --> pdb=" O PRO C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 478 removed outlier: 3.966A pdb=" N LEU C 471 " --> pdb=" O ASP C 467 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 477 " --> pdb=" O ALA C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 541 removed outlier: 3.702A pdb=" N LEU C 536 " --> pdb=" O GLY C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 577 Processing helix chain 'D' and resid 64 through 85 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 103 through 130 Processing helix chain 'D' and resid 149 through 160 removed outlier: 3.655A pdb=" N ILE D 153 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 168 Processing helix chain 'D' and resid 171 through 176 Processing helix chain 'D' and resid 190 through 194 removed outlier: 3.622A pdb=" N LYS D 193 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN D 194 " --> pdb=" O ASN D 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 190 through 194' Processing helix chain 'D' and resid 198 through 221 removed outlier: 4.167A pdb=" N LEU D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) Proline residue: D 206 - end of helix removed outlier: 3.570A pdb=" N ILE D 211 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Proline residue: D 213 - end of helix Processing helix chain 'D' and resid 229 through 270 removed outlier: 4.184A pdb=" N ASN D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 274 removed outlier: 3.601A pdb=" N CYS D 274 " --> pdb=" O GLU D 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 271 through 274' Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.884A pdb=" N PHE D 279 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N CYS D 281 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ASN D 282 " --> pdb=" O PHE D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 311 through 313 No H-bonds generated for 'chain 'D' and resid 311 through 313' Processing helix chain 'D' and resid 314 through 320 removed outlier: 3.681A pdb=" N VAL D 318 " --> pdb=" O TYR D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 removed outlier: 3.628A pdb=" N THR D 324 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER D 325 " --> pdb=" O VAL D 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 321 through 325' Processing helix chain 'D' and resid 326 through 344 Processing helix chain 'D' and resid 354 through 388 Processing helix chain 'D' and resid 388 through 407 removed outlier: 3.627A pdb=" N GLU D 392 " --> pdb=" O VAL D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 429 removed outlier: 3.756A pdb=" N SER D 416 " --> pdb=" O GLU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 439 removed outlier: 3.795A pdb=" N GLY D 439 " --> pdb=" O SER D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 453 Processing helix chain 'D' and resid 454 through 459 removed outlier: 3.567A pdb=" N ARG D 459 " --> pdb=" O GLU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 465 removed outlier: 4.509A pdb=" N ALA D 465 " --> pdb=" O PRO D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 478 removed outlier: 3.795A pdb=" N LEU D 471 " --> pdb=" O ASP D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 541 removed outlier: 3.682A pdb=" N LEU D 536 " --> pdb=" O GLY D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 577 removed outlier: 3.818A pdb=" N GLN D 577 " --> pdb=" O PHE D 573 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 95 removed outlier: 4.084A pdb=" N CYS A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 481 through 483 removed outlier: 4.016A pdb=" N CYS A 483 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL A 561 " --> pdb=" O CYS A 483 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE A 564 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE A 502 " --> pdb=" O PHE A 564 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 490 removed outlier: 6.391A pdb=" N VAL A 555 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 510 " --> pdb=" O THR A 554 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A 509 " --> pdb=" O CYS A 523 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'B' and resid 479 through 483 removed outlier: 3.509A pdb=" N VAL B 561 " --> pdb=" O CYS B 483 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE B 564 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE B 502 " --> pdb=" O PHE B 564 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 502 " --> pdb=" O ASP B 529 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP B 529 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 487 through 490 removed outlier: 5.990A pdb=" N TYR B 488 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA B 557 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR B 510 " --> pdb=" O THR B 554 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 92 through 94 Processing sheet with id=AA8, first strand: chain 'C' and resid 479 through 483 removed outlier: 3.853A pdb=" N CYS C 483 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C 561 " --> pdb=" O CYS C 483 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 504 " --> pdb=" O GLU C 562 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N PHE C 564 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE C 502 " --> pdb=" O PHE C 564 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 502 " --> pdb=" O ASP C 529 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP C 529 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 487 through 490 removed outlier: 6.991A pdb=" N VAL C 555 " --> pdb=" O LEU C 489 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR C 510 " --> pdb=" O THR C 554 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 92 through 95 removed outlier: 4.011A pdb=" N CYS D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 479 through 483 removed outlier: 3.508A pdb=" N VAL D 561 " --> pdb=" O CYS D 483 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N PHE D 564 " --> pdb=" O ILE D 502 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE D 502 " --> pdb=" O PHE D 564 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU D 566 " --> pdb=" O LEU D 500 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU D 500 " --> pdb=" O LEU D 566 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 502 " --> pdb=" O ASP D 529 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP D 529 " --> pdb=" O ILE D 502 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 487 through 490 removed outlier: 6.154A pdb=" N TYR D 488 " --> pdb=" O ALA D 557 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA D 557 " --> pdb=" O TYR D 488 " (cutoff:3.500A) 957 hydrogen bonds defined for protein. 2766 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: 3.09 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5293 1.34 - 1.46: 4112 1.46 - 1.58: 7615 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 17156 Sorted by residual: bond pdb=" CA ILE B 181 " pdb=" CB ILE B 181 " ideal model delta sigma weight residual 1.539 1.533 0.006 5.40e-03 3.43e+04 1.35e+00 bond pdb=" CA LYS D 193 " pdb=" CB LYS D 193 " ideal model delta sigma weight residual 1.532 1.554 -0.022 2.23e-02 2.01e+03 9.98e-01 bond pdb=" CB ASN D 486 " pdb=" CG ASN D 486 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.68e-01 bond pdb=" CB MET D 404 " pdb=" CG MET D 404 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.95e-01 bond pdb=" C GLY D 103 " pdb=" O GLY D 103 " ideal model delta sigma weight residual 1.243 1.234 0.008 9.30e-03 1.16e+04 8.35e-01 ... (remaining 17151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 23084 2.46 - 4.91: 194 4.91 - 7.37: 28 7.37 - 9.82: 1 9.82 - 12.28: 1 Bond angle restraints: 23308 Sorted by residual: angle pdb=" N ILE C 177 " pdb=" CA ILE C 177 " pdb=" C ILE C 177 " ideal model delta sigma weight residual 112.96 108.70 4.26 1.00e+00 1.00e+00 1.82e+01 angle pdb=" C TRP D 403 " pdb=" N MET D 404 " pdb=" CA MET D 404 " ideal model delta sigma weight residual 120.60 127.19 -6.59 1.60e+00 3.91e-01 1.70e+01 angle pdb=" CB MET D 404 " pdb=" CG MET D 404 " pdb=" SD MET D 404 " ideal model delta sigma weight residual 112.70 100.42 12.28 3.00e+00 1.11e-01 1.67e+01 angle pdb=" N ILE B 503 " pdb=" CA ILE B 503 " pdb=" C ILE B 503 " ideal model delta sigma weight residual 113.53 109.53 4.00 9.80e-01 1.04e+00 1.66e+01 angle pdb=" CA MET D 404 " pdb=" CB MET D 404 " pdb=" CG MET D 404 " ideal model delta sigma weight residual 114.10 120.36 -6.26 2.00e+00 2.50e-01 9.80e+00 ... (remaining 23303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 9083 17.64 - 35.28: 864 35.28 - 52.91: 164 52.91 - 70.55: 22 70.55 - 88.19: 11 Dihedral angle restraints: 10144 sinusoidal: 4068 harmonic: 6076 Sorted by residual: dihedral pdb=" CB CYS D 99 " pdb=" SG CYS D 99 " pdb=" SG CYS D 281 " pdb=" CB CYS D 281 " ideal model delta sinusoidal sigma weight residual -86.00 -25.17 -60.83 1 1.00e+01 1.00e-02 4.92e+01 dihedral pdb=" CB CYS B 99 " pdb=" SG CYS B 99 " pdb=" SG CYS B 281 " pdb=" CB CYS B 281 " ideal model delta sinusoidal sigma weight residual -86.00 -27.08 -58.92 1 1.00e+01 1.00e-02 4.64e+01 dihedral pdb=" CB CYS A 99 " pdb=" SG CYS A 99 " pdb=" SG CYS A 281 " pdb=" CB CYS A 281 " ideal model delta sinusoidal sigma weight residual -86.00 -40.09 -45.91 1 1.00e+01 1.00e-02 2.92e+01 ... (remaining 10141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1585 0.030 - 0.059: 758 0.059 - 0.089: 232 0.089 - 0.119: 86 0.119 - 0.148: 11 Chirality restraints: 2672 Sorted by residual: chirality pdb=" CB ILE D 100 " pdb=" CA ILE D 100 " pdb=" CG1 ILE D 100 " pdb=" CG2 ILE D 100 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CG LEU A 482 " pdb=" CB LEU A 482 " pdb=" CD1 LEU A 482 " pdb=" CD2 LEU A 482 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ILE D 93 " pdb=" N ILE D 93 " pdb=" C ILE D 93 " pdb=" CB ILE D 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 2669 not shown) Planarity restraints: 2912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 292 " -0.015 2.00e-02 2.50e+03 1.29e-02 4.17e+00 pdb=" CG TRP B 292 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 292 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 292 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 292 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 292 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 292 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 292 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 292 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 292 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 70 " 0.014 2.00e-02 2.50e+03 9.17e-03 2.10e+00 pdb=" CG TRP D 70 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP D 70 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP D 70 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 70 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 70 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 70 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 70 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 70 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 70 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 560 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" CD GLU A 560 " -0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU A 560 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A 560 " 0.009 2.00e-02 2.50e+03 ... (remaining 2909 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 376 2.71 - 3.26: 17829 3.26 - 3.80: 27749 3.80 - 4.35: 32905 4.35 - 4.90: 55832 Nonbonded interactions: 134691 Sorted by model distance: nonbonded pdb=" O TYR D 510 " pdb=" OG1 THR D 554 " model vdw 2.160 3.040 nonbonded pdb=" O THR A 387 " pdb=" N ARG A 389 " model vdw 2.194 3.120 nonbonded pdb=" O LYS D 193 " pdb=" NH2 ARG D 197 " model vdw 2.206 3.120 nonbonded pdb=" OH TYR A 423 " pdb=" O VAL A 561 " model vdw 2.242 3.040 nonbonded pdb=" OE1 GLN D 415 " pdb=" NH1 ARG D 418 " model vdw 2.245 3.120 ... (remaining 134686 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.880 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 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 : 0.002 0.028 17168 Z= 0.118 Angle : 0.580 12.277 23332 Z= 0.304 Chirality : 0.039 0.148 2672 Planarity : 0.003 0.036 2912 Dihedral : 13.947 88.190 6172 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.44 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.19), residues: 2072 helix: 0.82 (0.15), residues: 1320 sheet: -1.81 (0.47), residues: 120 loop : -1.76 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 438 TYR 0.013 0.001 TYR B 240 PHE 0.023 0.001 PHE D 74 TRP 0.034 0.001 TRP B 292 HIS 0.007 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00248 (17156) covalent geometry : angle 0.57947 (23308) SS BOND : bond 0.00248 ( 12) SS BOND : angle 0.71745 ( 24) hydrogen bonds : bond 0.15167 ( 957) hydrogen bonds : angle 5.60930 ( 2766) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.7182 (m-10) cc_final: 0.6971 (m-80) REVERT: A 202 ILE cc_start: 0.8676 (tp) cc_final: 0.8465 (tp) REVERT: A 283 MET cc_start: 0.7920 (mtp) cc_final: 0.7692 (mtp) REVERT: A 432 ASP cc_start: 0.7964 (t0) cc_final: 0.7530 (t0) REVERT: B 419 LYS cc_start: 0.8410 (tttt) cc_final: 0.8144 (tttt) REVERT: B 422 GLN cc_start: 0.8244 (tm-30) cc_final: 0.8006 (tm-30) REVERT: B 438 ARG cc_start: 0.8310 (ptp90) cc_final: 0.7724 (ptp90) REVERT: B 466 MET cc_start: 0.8130 (ppp) cc_final: 0.7591 (ppp) REVERT: B 479 LYS cc_start: 0.7982 (mppt) cc_final: 0.7712 (mptt) REVERT: C 202 ILE cc_start: 0.8514 (tp) cc_final: 0.8307 (tp) REVERT: C 257 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6915 (mm-30) REVERT: C 446 ARG cc_start: 0.8333 (ptm160) cc_final: 0.8011 (ttt-90) REVERT: C 530 PHE cc_start: 0.7677 (t80) cc_final: 0.7465 (t80) REVERT: D 183 ASN cc_start: 0.6587 (m-40) cc_final: 0.5468 (t0) REVERT: D 408 GLN cc_start: 0.7716 (tp40) cc_final: 0.7360 (tp40) REVERT: D 499 MET cc_start: 0.7654 (mmt) cc_final: 0.6913 (mmt) REVERT: D 502 ILE cc_start: 0.7787 (mm) cc_final: 0.7473 (mm) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.1291 time to fit residues: 59.0338 Evaluate side-chains 248 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN B 194 ASN ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.200949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121597 restraints weight = 20492.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126646 restraints weight = 9873.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129732 restraints weight = 6576.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.131233 restraints weight = 5368.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131682 restraints weight = 4891.989| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17168 Z= 0.125 Angle : 0.564 7.849 23332 Z= 0.286 Chirality : 0.040 0.163 2672 Planarity : 0.004 0.027 2912 Dihedral : 3.767 21.144 2272 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.39 % Favored : 95.22 % Rotamer: Outliers : 1.30 % Allowed : 8.10 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.19), residues: 2072 helix: 1.12 (0.15), residues: 1300 sheet: -2.01 (0.46), residues: 120 loop : -1.73 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 438 TYR 0.021 0.001 TYR C 420 PHE 0.026 0.001 PHE C 126 TRP 0.024 0.001 TRP B 292 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00277 (17156) covalent geometry : angle 0.56406 (23308) SS BOND : bond 0.00276 ( 12) SS BOND : angle 0.74891 ( 24) hydrogen bonds : bond 0.03711 ( 957) hydrogen bonds : angle 4.52644 ( 2766) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 279 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.7387 (m-10) cc_final: 0.7161 (m-80) REVERT: A 202 ILE cc_start: 0.8498 (tp) cc_final: 0.8272 (tp) REVERT: A 283 MET cc_start: 0.8009 (mtp) cc_final: 0.7719 (mtp) REVERT: A 391 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7270 (tt0) REVERT: A 425 TRP cc_start: 0.8526 (t-100) cc_final: 0.8151 (t-100) REVERT: A 432 ASP cc_start: 0.7857 (t0) cc_final: 0.7270 (t0) REVERT: A 499 MET cc_start: 0.6642 (tpp) cc_final: 0.6317 (tpp) REVERT: B 258 ARG cc_start: 0.7242 (ttm-80) cc_final: 0.6843 (ttm-80) REVERT: B 419 LYS cc_start: 0.8353 (tttt) cc_final: 0.8055 (tttt) REVERT: B 422 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7536 (tm-30) REVERT: B 426 ILE cc_start: 0.8985 (mm) cc_final: 0.8757 (mm) REVERT: B 438 ARG cc_start: 0.8271 (ptp90) cc_final: 0.7655 (ptp90) REVERT: B 466 MET cc_start: 0.8254 (ppp) cc_final: 0.7576 (ppp) REVERT: B 479 LYS cc_start: 0.8472 (mppt) cc_final: 0.8146 (mptt) REVERT: C 167 ILE cc_start: 0.7475 (tt) cc_final: 0.7266 (tt) REVERT: C 202 ILE cc_start: 0.8441 (tp) cc_final: 0.8228 (tp) REVERT: C 428 THR cc_start: 0.7880 (p) cc_final: 0.7680 (p) REVERT: D 404 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7345 (mpp) REVERT: D 408 GLN cc_start: 0.7870 (tp40) cc_final: 0.7233 (tp-100) REVERT: D 499 MET cc_start: 0.8002 (mmt) cc_final: 0.7139 (mmt) REVERT: D 502 ILE cc_start: 0.8263 (mm) cc_final: 0.8016 (mm) REVERT: D 560 GLU cc_start: 0.8867 (mp0) cc_final: 0.8644 (mp0) outliers start: 24 outliers final: 17 residues processed: 297 average time/residue: 0.1366 time to fit residues: 60.5323 Evaluate side-chains 273 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 255 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 560 GLU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 404 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 166 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 202 optimal weight: 0.0870 chunk 2 optimal weight: 0.3980 chunk 124 optimal weight: 0.6980 chunk 153 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 75 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN A 402 GLN B 194 ASN C 486 ASN D 402 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.199992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125498 restraints weight = 20608.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.126846 restraints weight = 11729.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.128148 restraints weight = 7103.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128361 restraints weight = 6798.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128631 restraints weight = 6349.454| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17168 Z= 0.105 Angle : 0.518 7.860 23332 Z= 0.261 Chirality : 0.039 0.162 2672 Planarity : 0.003 0.028 2912 Dihedral : 3.644 18.684 2272 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.91 % Favored : 95.70 % Rotamer: Outliers : 1.47 % Allowed : 10.87 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.19), residues: 2072 helix: 1.30 (0.15), residues: 1300 sheet: -2.11 (0.46), residues: 120 loop : -1.69 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 197 TYR 0.026 0.001 TYR C 420 PHE 0.025 0.001 PHE C 126 TRP 0.018 0.001 TRP D 70 HIS 0.003 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00229 (17156) covalent geometry : angle 0.51758 (23308) SS BOND : bond 0.00193 ( 12) SS BOND : angle 0.65093 ( 24) hydrogen bonds : bond 0.03315 ( 957) hydrogen bonds : angle 4.25803 ( 2766) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 283 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.7490 (m-10) cc_final: 0.7167 (m-80) REVERT: A 202 ILE cc_start: 0.8512 (tp) cc_final: 0.8286 (tp) REVERT: A 283 MET cc_start: 0.7928 (mtp) cc_final: 0.7609 (mtp) REVERT: A 359 MET cc_start: 0.7349 (mmm) cc_final: 0.7114 (mmm) REVERT: A 391 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7346 (tt0) REVERT: A 425 TRP cc_start: 0.8549 (t-100) cc_final: 0.8235 (t-100) REVERT: A 432 ASP cc_start: 0.7908 (t0) cc_final: 0.7386 (t0) REVERT: B 95 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7581 (mt0) REVERT: B 130 HIS cc_start: 0.7489 (m170) cc_final: 0.7189 (m-70) REVERT: B 258 ARG cc_start: 0.7305 (ttm-80) cc_final: 0.6874 (ttm110) REVERT: B 419 LYS cc_start: 0.8378 (tttt) cc_final: 0.8021 (tttt) REVERT: B 422 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7513 (tm-30) REVERT: B 426 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8732 (mm) REVERT: B 438 ARG cc_start: 0.8301 (ptp90) cc_final: 0.7757 (ptp90) REVERT: B 466 MET cc_start: 0.8196 (ppp) cc_final: 0.7428 (ppp) REVERT: B 499 MET cc_start: 0.6821 (ppp) cc_final: 0.5780 (ppp) REVERT: C 160 LYS cc_start: 0.8380 (ttpt) cc_final: 0.7888 (ttmm) REVERT: C 165 ASP cc_start: 0.7981 (t70) cc_final: 0.7652 (t0) REVERT: C 202 ILE cc_start: 0.8272 (tp) cc_final: 0.8014 (tp) REVERT: C 428 THR cc_start: 0.7811 (p) cc_final: 0.7562 (p) REVERT: C 438 ARG cc_start: 0.7623 (mtm180) cc_final: 0.7241 (mtm110) REVERT: C 446 ARG cc_start: 0.8426 (ptm160) cc_final: 0.8135 (ttt180) REVERT: D 359 MET cc_start: 0.7123 (mmm) cc_final: 0.6394 (mtm) REVERT: D 408 GLN cc_start: 0.7845 (tp40) cc_final: 0.7171 (tp-100) REVERT: D 494 ASP cc_start: 0.7858 (m-30) cc_final: 0.7498 (m-30) REVERT: D 499 MET cc_start: 0.8071 (mmt) cc_final: 0.7283 (mmt) REVERT: D 502 ILE cc_start: 0.8285 (mm) cc_final: 0.8053 (mm) REVERT: D 560 GLU cc_start: 0.8743 (mp0) cc_final: 0.8418 (mp0) outliers start: 27 outliers final: 14 residues processed: 298 average time/residue: 0.1352 time to fit residues: 60.1069 Evaluate side-chains 272 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 257 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 404 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 164 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN C 486 ASN D 402 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.197790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.119753 restraints weight = 20540.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124548 restraints weight = 10597.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.125250 restraints weight = 7188.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126328 restraints weight = 6458.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126418 restraints weight = 5857.268| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17168 Z= 0.122 Angle : 0.529 7.754 23332 Z= 0.265 Chirality : 0.040 0.165 2672 Planarity : 0.003 0.029 2912 Dihedral : 3.642 17.104 2272 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.96 % Favored : 95.66 % Rotamer: Outliers : 1.74 % Allowed : 13.10 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.19), residues: 2072 helix: 1.30 (0.15), residues: 1296 sheet: -2.18 (0.47), residues: 120 loop : -1.57 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 197 TYR 0.025 0.001 TYR C 420 PHE 0.025 0.001 PHE C 126 TRP 0.019 0.001 TRP D 70 HIS 0.003 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00281 (17156) covalent geometry : angle 0.52897 (23308) SS BOND : bond 0.00134 ( 12) SS BOND : angle 0.60509 ( 24) hydrogen bonds : bond 0.03243 ( 957) hydrogen bonds : angle 4.19145 ( 2766) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 268 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.7587 (m-10) cc_final: 0.7146 (m-80) REVERT: A 202 ILE cc_start: 0.8549 (tp) cc_final: 0.8286 (tp) REVERT: A 283 MET cc_start: 0.8047 (mtp) cc_final: 0.7707 (mtp) REVERT: A 359 MET cc_start: 0.7517 (mmm) cc_final: 0.7296 (mmm) REVERT: A 391 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7312 (tt0) REVERT: A 425 TRP cc_start: 0.8527 (t-100) cc_final: 0.8159 (t-100) REVERT: A 432 ASP cc_start: 0.7933 (t0) cc_final: 0.7392 (t0) REVERT: B 95 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7603 (mt0) REVERT: B 130 HIS cc_start: 0.7559 (m170) cc_final: 0.7276 (m-70) REVERT: B 258 ARG cc_start: 0.7378 (ttm-80) cc_final: 0.6267 (ttm-80) REVERT: B 419 LYS cc_start: 0.8364 (tttt) cc_final: 0.7981 (tttt) REVERT: B 422 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7487 (tm-30) REVERT: B 426 ILE cc_start: 0.8964 (mm) cc_final: 0.8696 (mm) REVERT: B 438 ARG cc_start: 0.8312 (ptp90) cc_final: 0.7766 (ptp90) REVERT: B 466 MET cc_start: 0.8228 (ppp) cc_final: 0.7397 (ppp) REVERT: B 499 MET cc_start: 0.6590 (ppp) cc_final: 0.5684 (ppp) REVERT: C 202 ILE cc_start: 0.8344 (tp) cc_final: 0.8061 (tp) REVERT: C 428 THR cc_start: 0.7761 (p) cc_final: 0.7518 (p) REVERT: C 438 ARG cc_start: 0.7636 (mtm180) cc_final: 0.7259 (mtm110) REVERT: C 446 ARG cc_start: 0.8424 (ptm160) cc_final: 0.8134 (ttt180) REVERT: D 359 MET cc_start: 0.7145 (mmm) cc_final: 0.6359 (mtm) REVERT: D 404 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7385 (mpp) REVERT: D 408 GLN cc_start: 0.7838 (tp40) cc_final: 0.7189 (tp-100) REVERT: D 426 ILE cc_start: 0.8156 (tp) cc_final: 0.7759 (tt) REVERT: D 470 MET cc_start: 0.7365 (tpt) cc_final: 0.6686 (tpp) REVERT: D 494 ASP cc_start: 0.7802 (m-30) cc_final: 0.7455 (m-30) REVERT: D 499 MET cc_start: 0.8075 (mmt) cc_final: 0.7050 (mmt) REVERT: D 502 ILE cc_start: 0.8303 (mm) cc_final: 0.8047 (mm) outliers start: 32 outliers final: 22 residues processed: 288 average time/residue: 0.1358 time to fit residues: 58.4593 Evaluate side-chains 274 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 561 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 162 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 170 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 118 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.197463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.118679 restraints weight = 20370.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.123341 restraints weight = 10086.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126214 restraints weight = 6839.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.127683 restraints weight = 5616.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.128040 restraints weight = 5121.819| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17168 Z= 0.126 Angle : 0.529 7.626 23332 Z= 0.266 Chirality : 0.039 0.148 2672 Planarity : 0.003 0.029 2912 Dihedral : 3.634 16.577 2272 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.86 % Favored : 95.75 % Rotamer: Outliers : 2.01 % Allowed : 14.51 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 2072 helix: 1.28 (0.15), residues: 1300 sheet: -2.22 (0.47), residues: 120 loop : -1.51 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 197 TYR 0.028 0.001 TYR C 420 PHE 0.024 0.001 PHE D 126 TRP 0.020 0.001 TRP D 70 HIS 0.003 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00292 (17156) covalent geometry : angle 0.52898 (23308) SS BOND : bond 0.00117 ( 12) SS BOND : angle 0.56840 ( 24) hydrogen bonds : bond 0.03196 ( 957) hydrogen bonds : angle 4.14478 ( 2766) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 264 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.7770 (m-10) cc_final: 0.7298 (m-80) REVERT: A 202 ILE cc_start: 0.8578 (tp) cc_final: 0.8298 (tp) REVERT: A 283 MET cc_start: 0.8137 (mtp) cc_final: 0.7809 (mtp) REVERT: A 359 MET cc_start: 0.7468 (mmm) cc_final: 0.7204 (mmm) REVERT: A 391 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7305 (tt0) REVERT: A 425 TRP cc_start: 0.8462 (t-100) cc_final: 0.8117 (t-100) REVERT: A 432 ASP cc_start: 0.7922 (t0) cc_final: 0.7422 (t0) REVERT: B 95 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7611 (mt0) REVERT: B 130 HIS cc_start: 0.7618 (m170) cc_final: 0.7363 (m-70) REVERT: B 240 TYR cc_start: 0.7252 (t80) cc_final: 0.6410 (t80) REVERT: B 404 MET cc_start: 0.7981 (ttm) cc_final: 0.7691 (ttm) REVERT: B 419 LYS cc_start: 0.8385 (tttt) cc_final: 0.7988 (tttt) REVERT: B 422 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7487 (tm-30) REVERT: B 426 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8691 (mm) REVERT: B 466 MET cc_start: 0.8028 (ppp) cc_final: 0.7190 (ppp) REVERT: B 499 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.5862 (ppp) REVERT: C 165 ASP cc_start: 0.8009 (t0) cc_final: 0.7668 (t70) REVERT: C 202 ILE cc_start: 0.8424 (tp) cc_final: 0.8099 (tp) REVERT: C 428 THR cc_start: 0.7739 (p) cc_final: 0.7494 (p) REVERT: C 438 ARG cc_start: 0.7681 (mtm180) cc_final: 0.7324 (mtm110) REVERT: C 446 ARG cc_start: 0.8421 (ptm160) cc_final: 0.8126 (ttt180) REVERT: D 359 MET cc_start: 0.7247 (mmm) cc_final: 0.6426 (mtm) REVERT: D 404 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7282 (mmm) REVERT: D 408 GLN cc_start: 0.7849 (tp40) cc_final: 0.7181 (tp-100) REVERT: D 426 ILE cc_start: 0.8138 (tp) cc_final: 0.7834 (tt) REVERT: D 453 CYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6340 (p) REVERT: D 470 MET cc_start: 0.7572 (tpt) cc_final: 0.6810 (tpp) REVERT: D 494 ASP cc_start: 0.7968 (m-30) cc_final: 0.7604 (m-30) REVERT: D 499 MET cc_start: 0.8006 (mmt) cc_final: 0.7210 (mmt) REVERT: D 501 PHE cc_start: 0.7950 (m-80) cc_final: 0.7379 (m-10) REVERT: D 502 ILE cc_start: 0.8473 (mm) cc_final: 0.8215 (mm) REVERT: D 560 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8441 (mm-30) outliers start: 37 outliers final: 18 residues processed: 286 average time/residue: 0.1427 time to fit residues: 61.2913 Evaluate side-chains 273 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 251 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 453 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 159 optimal weight: 0.4980 chunk 109 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 GLN C 486 ASN D 329 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.199212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.120421 restraints weight = 20611.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125154 restraints weight = 10495.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126006 restraints weight = 7194.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127319 restraints weight = 6244.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127321 restraints weight = 5741.360| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17168 Z= 0.121 Angle : 0.524 7.412 23332 Z= 0.263 Chirality : 0.039 0.156 2672 Planarity : 0.003 0.033 2912 Dihedral : 3.636 18.894 2272 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.20 % Favored : 95.42 % Rotamer: Outliers : 1.96 % Allowed : 16.41 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 2072 helix: 1.30 (0.15), residues: 1300 sheet: -2.19 (0.47), residues: 120 loop : -1.56 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 197 TYR 0.025 0.001 TYR D 423 PHE 0.024 0.001 PHE C 126 TRP 0.022 0.001 TRP D 70 HIS 0.002 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00282 (17156) covalent geometry : angle 0.52384 (23308) SS BOND : bond 0.00145 ( 12) SS BOND : angle 0.60252 ( 24) hydrogen bonds : bond 0.03163 ( 957) hydrogen bonds : angle 4.12730 ( 2766) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.7832 (m-10) cc_final: 0.7303 (m-80) REVERT: A 202 ILE cc_start: 0.8641 (tp) cc_final: 0.8365 (tp) REVERT: A 283 MET cc_start: 0.8105 (mtp) cc_final: 0.7768 (mtp) REVERT: A 359 MET cc_start: 0.7498 (mmm) cc_final: 0.7255 (mmm) REVERT: A 391 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7317 (tt0) REVERT: A 425 TRP cc_start: 0.8476 (t-100) cc_final: 0.8161 (t-100) REVERT: A 432 ASP cc_start: 0.7984 (t0) cc_final: 0.7461 (t0) REVERT: A 499 MET cc_start: 0.6719 (tpp) cc_final: 0.6174 (tpp) REVERT: A 500 LEU cc_start: 0.6857 (mp) cc_final: 0.6636 (mp) REVERT: B 95 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7607 (mt0) REVERT: B 130 HIS cc_start: 0.7577 (m170) cc_final: 0.7328 (m-70) REVERT: B 196 LEU cc_start: 0.4838 (OUTLIER) cc_final: 0.4298 (mm) REVERT: B 240 TYR cc_start: 0.7240 (t80) cc_final: 0.6370 (t80) REVERT: B 404 MET cc_start: 0.7925 (ttm) cc_final: 0.7567 (ttm) REVERT: B 419 LYS cc_start: 0.8404 (tttt) cc_final: 0.7987 (tttt) REVERT: B 422 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7448 (tm-30) REVERT: B 426 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8708 (mm) REVERT: B 438 ARG cc_start: 0.8322 (ptp90) cc_final: 0.7568 (ptp90) REVERT: B 466 MET cc_start: 0.8150 (ppp) cc_final: 0.7275 (ppp) REVERT: B 499 MET cc_start: 0.6531 (OUTLIER) cc_final: 0.5830 (ppp) REVERT: C 156 ARG cc_start: 0.8175 (tpp-160) cc_final: 0.7691 (tpp-160) REVERT: C 428 THR cc_start: 0.7750 (p) cc_final: 0.7502 (p) REVERT: C 438 ARG cc_start: 0.7737 (mtm180) cc_final: 0.7438 (mtm110) REVERT: D 183 ASN cc_start: 0.6514 (m-40) cc_final: 0.5478 (t0) REVERT: D 359 MET cc_start: 0.7250 (mmm) cc_final: 0.6470 (mtm) REVERT: D 404 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7229 (mmm) REVERT: D 408 GLN cc_start: 0.7799 (tp40) cc_final: 0.7392 (tp40) REVERT: D 426 ILE cc_start: 0.8188 (tp) cc_final: 0.7823 (tt) REVERT: D 453 CYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6396 (p) REVERT: D 470 MET cc_start: 0.7504 (tpt) cc_final: 0.6700 (tpp) REVERT: D 499 MET cc_start: 0.8179 (mmt) cc_final: 0.7354 (mmt) REVERT: D 501 PHE cc_start: 0.7880 (m-80) cc_final: 0.7332 (m-10) outliers start: 36 outliers final: 20 residues processed: 284 average time/residue: 0.1419 time to fit residues: 60.5482 Evaluate side-chains 276 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 251 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 453 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 173 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 64 optimal weight: 0.0980 chunk 196 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.198384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.119400 restraints weight = 20510.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.123947 restraints weight = 10576.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124580 restraints weight = 7286.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125931 restraints weight = 6536.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126068 restraints weight = 5871.006| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17168 Z= 0.128 Angle : 0.534 7.182 23332 Z= 0.268 Chirality : 0.040 0.159 2672 Planarity : 0.003 0.031 2912 Dihedral : 3.666 18.577 2272 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.01 % Favored : 95.61 % Rotamer: Outliers : 2.17 % Allowed : 17.01 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 2072 helix: 1.29 (0.15), residues: 1300 sheet: -2.19 (0.46), residues: 120 loop : -1.56 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 197 TYR 0.021 0.001 TYR B 133 PHE 0.024 0.001 PHE C 126 TRP 0.023 0.001 TRP D 70 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00300 (17156) covalent geometry : angle 0.53268 (23308) SS BOND : bond 0.00229 ( 12) SS BOND : angle 1.20200 ( 24) hydrogen bonds : bond 0.03178 ( 957) hydrogen bonds : angle 4.11113 ( 2766) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 262 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.7958 (m-10) cc_final: 0.7375 (m-80) REVERT: A 202 ILE cc_start: 0.8658 (tp) cc_final: 0.8372 (tp) REVERT: A 283 MET cc_start: 0.8072 (mtp) cc_final: 0.7727 (mtp) REVERT: A 359 MET cc_start: 0.7495 (mmm) cc_final: 0.7226 (mmm) REVERT: A 391 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7323 (tt0) REVERT: A 408 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7394 (mt0) REVERT: A 425 TRP cc_start: 0.8503 (t-100) cc_final: 0.8166 (t-100) REVERT: A 432 ASP cc_start: 0.7963 (t0) cc_final: 0.7435 (t0) REVERT: A 499 MET cc_start: 0.6703 (tpp) cc_final: 0.6272 (tpp) REVERT: B 95 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7653 (mt0) REVERT: B 130 HIS cc_start: 0.7566 (m170) cc_final: 0.7330 (m-70) REVERT: B 196 LEU cc_start: 0.4974 (OUTLIER) cc_final: 0.4412 (mm) REVERT: B 240 TYR cc_start: 0.7225 (t80) cc_final: 0.6321 (t80) REVERT: B 419 LYS cc_start: 0.8390 (tttt) cc_final: 0.7983 (tttt) REVERT: B 422 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7447 (tm-30) REVERT: B 426 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8700 (mm) REVERT: B 438 ARG cc_start: 0.8382 (ptp90) cc_final: 0.7689 (ptp90) REVERT: B 466 MET cc_start: 0.8186 (ppp) cc_final: 0.7304 (ppp) REVERT: B 499 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.5901 (ppp) REVERT: C 156 ARG cc_start: 0.8125 (tpp-160) cc_final: 0.7648 (tpp-160) REVERT: C 309 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.8100 (t80) REVERT: C 428 THR cc_start: 0.7806 (p) cc_final: 0.7558 (p) REVERT: C 438 ARG cc_start: 0.7768 (mtm180) cc_final: 0.7454 (mtm110) REVERT: C 446 ARG cc_start: 0.8438 (ptm160) cc_final: 0.8128 (ttt180) REVERT: D 183 ASN cc_start: 0.6552 (m-40) cc_final: 0.5494 (t0) REVERT: D 201 ILE cc_start: 0.6753 (tp) cc_final: 0.6207 (tp) REVERT: D 359 MET cc_start: 0.7270 (mmm) cc_final: 0.6479 (mtm) REVERT: D 404 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7308 (mtp) REVERT: D 408 GLN cc_start: 0.7760 (tp40) cc_final: 0.7362 (tp40) REVERT: D 426 ILE cc_start: 0.8282 (tp) cc_final: 0.7939 (tt) REVERT: D 453 CYS cc_start: 0.7455 (OUTLIER) cc_final: 0.6475 (p) REVERT: D 470 MET cc_start: 0.7542 (tpt) cc_final: 0.6710 (tpp) REVERT: D 485 GLU cc_start: 0.7951 (tt0) cc_final: 0.7054 (tm-30) REVERT: D 494 ASP cc_start: 0.7968 (m-30) cc_final: 0.7582 (m-30) REVERT: D 499 MET cc_start: 0.8121 (mmt) cc_final: 0.7362 (mmt) REVERT: D 501 PHE cc_start: 0.7617 (m-80) cc_final: 0.7194 (m-80) REVERT: D 502 ILE cc_start: 0.7540 (mm) cc_final: 0.6938 (tp) outliers start: 40 outliers final: 26 residues processed: 283 average time/residue: 0.1446 time to fit residues: 61.0837 Evaluate side-chains 284 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 251 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 309 TYR Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 453 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 173 optimal weight: 0.0030 chunk 6 optimal weight: 3.9990 chunk 118 optimal weight: 0.0470 chunk 37 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 73 optimal weight: 0.0040 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.2700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 ASN C 486 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.201195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.121669 restraints weight = 20613.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126644 restraints weight = 9973.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.129730 restraints weight = 6672.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.131343 restraints weight = 5438.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.131996 restraints weight = 4950.251| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17168 Z= 0.102 Angle : 0.524 7.616 23332 Z= 0.264 Chirality : 0.039 0.263 2672 Planarity : 0.003 0.032 2912 Dihedral : 3.624 17.183 2272 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.67 % Favored : 95.95 % Rotamer: Outliers : 1.85 % Allowed : 17.61 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.20), residues: 2072 helix: 1.42 (0.15), residues: 1300 sheet: -2.17 (0.47), residues: 120 loop : -1.53 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 477 TYR 0.029 0.001 TYR C 420 PHE 0.024 0.001 PHE D 126 TRP 0.023 0.001 TRP D 70 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00221 (17156) covalent geometry : angle 0.52301 (23308) SS BOND : bond 0.00171 ( 12) SS BOND : angle 0.95477 ( 24) hydrogen bonds : bond 0.03034 ( 957) hydrogen bonds : angle 4.05720 ( 2766) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 266 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.7976 (m-10) cc_final: 0.7443 (m-80) REVERT: A 202 ILE cc_start: 0.8663 (tp) cc_final: 0.8388 (tp) REVERT: A 283 MET cc_start: 0.8100 (mtp) cc_final: 0.7742 (mtp) REVERT: A 359 MET cc_start: 0.7393 (mmm) cc_final: 0.7125 (mmm) REVERT: A 391 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7340 (tt0) REVERT: A 408 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7446 (mt0) REVERT: A 425 TRP cc_start: 0.8487 (t-100) cc_final: 0.8165 (t-100) REVERT: A 432 ASP cc_start: 0.7937 (t0) cc_final: 0.7418 (t0) REVERT: A 499 MET cc_start: 0.6751 (tpp) cc_final: 0.6455 (tpp) REVERT: B 95 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7622 (mt0) REVERT: B 196 LEU cc_start: 0.4922 (OUTLIER) cc_final: 0.4321 (mm) REVERT: B 214 LEU cc_start: 0.5786 (OUTLIER) cc_final: 0.5583 (tt) REVERT: B 240 TYR cc_start: 0.7165 (t80) cc_final: 0.6480 (t80) REVERT: B 402 GLN cc_start: 0.8063 (tt0) cc_final: 0.7523 (tm-30) REVERT: B 419 LYS cc_start: 0.8377 (tttt) cc_final: 0.7951 (tttt) REVERT: B 422 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7436 (tm-30) REVERT: B 426 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8681 (mm) REVERT: B 438 ARG cc_start: 0.8429 (ptp90) cc_final: 0.7745 (ptp90) REVERT: B 466 MET cc_start: 0.7998 (ppp) cc_final: 0.7179 (ppp) REVERT: B 499 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.5894 (ppp) REVERT: C 156 ARG cc_start: 0.8138 (tpp-160) cc_final: 0.7722 (tpp-160) REVERT: C 309 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.7927 (t80) REVERT: C 428 THR cc_start: 0.7749 (p) cc_final: 0.7486 (p) REVERT: C 438 ARG cc_start: 0.7758 (mtm180) cc_final: 0.7528 (mtm180) REVERT: C 446 ARG cc_start: 0.8455 (ptm160) cc_final: 0.8129 (ttt180) REVERT: D 101 ASP cc_start: 0.8133 (t0) cc_final: 0.7896 (t0) REVERT: D 183 ASN cc_start: 0.6374 (m-40) cc_final: 0.5324 (t0) REVERT: D 283 MET cc_start: 0.8283 (mtp) cc_final: 0.7996 (mmm) REVERT: D 359 MET cc_start: 0.7160 (mmm) cc_final: 0.6420 (mtm) REVERT: D 404 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7315 (mtp) REVERT: D 408 GLN cc_start: 0.7719 (tp40) cc_final: 0.7285 (tp40) REVERT: D 426 ILE cc_start: 0.8212 (tp) cc_final: 0.7859 (tt) REVERT: D 453 CYS cc_start: 0.7527 (OUTLIER) cc_final: 0.6581 (p) REVERT: D 485 GLU cc_start: 0.8015 (tt0) cc_final: 0.7302 (tp30) REVERT: D 499 MET cc_start: 0.8021 (mmt) cc_final: 0.7160 (mmt) REVERT: D 501 PHE cc_start: 0.7666 (m-80) cc_final: 0.7231 (m-80) REVERT: D 502 ILE cc_start: 0.7747 (mm) cc_final: 0.7224 (tt) REVERT: D 560 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8650 (tt0) outliers start: 34 outliers final: 21 residues processed: 286 average time/residue: 0.1352 time to fit residues: 57.8986 Evaluate side-chains 278 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 249 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 309 TYR Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 453 CYS Chi-restraints excluded: chain D residue 561 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 96 optimal weight: 5.9990 chunk 48 optimal weight: 0.0270 chunk 148 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.199387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119540 restraints weight = 20648.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.124444 restraints weight = 10047.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.127400 restraints weight = 6729.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.129011 restraints weight = 5503.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.129385 restraints weight = 4996.656| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17168 Z= 0.118 Angle : 0.556 13.623 23332 Z= 0.276 Chirality : 0.040 0.254 2672 Planarity : 0.003 0.031 2912 Dihedral : 3.645 18.104 2272 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.91 % Favored : 95.70 % Rotamer: Outliers : 2.12 % Allowed : 17.93 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.19), residues: 2072 helix: 1.37 (0.15), residues: 1300 sheet: -2.18 (0.47), residues: 120 loop : -1.50 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 477 TYR 0.025 0.001 TYR C 420 PHE 0.024 0.001 PHE C 126 TRP 0.021 0.001 TRP D 70 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00278 (17156) covalent geometry : angle 0.55582 (23308) SS BOND : bond 0.00125 ( 12) SS BOND : angle 0.85863 ( 24) hydrogen bonds : bond 0.03064 ( 957) hydrogen bonds : angle 4.07348 ( 2766) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.7994 (m-10) cc_final: 0.7438 (m-80) REVERT: A 202 ILE cc_start: 0.8639 (tp) cc_final: 0.8351 (tp) REVERT: A 283 MET cc_start: 0.8090 (mtp) cc_final: 0.7724 (mtp) REVERT: A 391 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7285 (tt0) REVERT: A 397 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6058 (tmm-80) REVERT: A 408 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7448 (mt0) REVERT: A 425 TRP cc_start: 0.8513 (t-100) cc_final: 0.8130 (t-100) REVERT: A 432 ASP cc_start: 0.7920 (t0) cc_final: 0.7400 (t0) REVERT: A 499 MET cc_start: 0.6837 (tpp) cc_final: 0.6394 (tpp) REVERT: B 95 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7642 (mt0) REVERT: B 196 LEU cc_start: 0.4998 (OUTLIER) cc_final: 0.4403 (mm) REVERT: B 214 LEU cc_start: 0.5753 (OUTLIER) cc_final: 0.5544 (tt) REVERT: B 240 TYR cc_start: 0.7156 (t80) cc_final: 0.6430 (t80) REVERT: B 419 LYS cc_start: 0.8368 (tttt) cc_final: 0.7940 (tttt) REVERT: B 422 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7513 (tm-30) REVERT: B 438 ARG cc_start: 0.8358 (ptp90) cc_final: 0.7690 (ptp90) REVERT: B 466 MET cc_start: 0.8032 (ppp) cc_final: 0.7191 (ppp) REVERT: B 499 MET cc_start: 0.6618 (OUTLIER) cc_final: 0.6004 (ppp) REVERT: C 156 ARG cc_start: 0.8062 (tpp-160) cc_final: 0.7635 (tpp-160) REVERT: C 309 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7987 (t80) REVERT: C 428 THR cc_start: 0.7678 (p) cc_final: 0.7430 (p) REVERT: C 438 ARG cc_start: 0.7739 (mtm180) cc_final: 0.7433 (mtm110) REVERT: C 446 ARG cc_start: 0.8441 (ptm160) cc_final: 0.8110 (ttt180) REVERT: D 101 ASP cc_start: 0.8124 (t0) cc_final: 0.7890 (t0) REVERT: D 183 ASN cc_start: 0.6429 (m-40) cc_final: 0.5412 (t0) REVERT: D 283 MET cc_start: 0.8257 (mtp) cc_final: 0.8024 (mmm) REVERT: D 359 MET cc_start: 0.7200 (mmm) cc_final: 0.6429 (mtm) REVERT: D 404 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7422 (mtm) REVERT: D 408 GLN cc_start: 0.7721 (tp40) cc_final: 0.7319 (tp40) REVERT: D 426 ILE cc_start: 0.8242 (tp) cc_final: 0.7924 (tt) REVERT: D 453 CYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6535 (p) REVERT: D 485 GLU cc_start: 0.8063 (tt0) cc_final: 0.7350 (tp30) REVERT: D 494 ASP cc_start: 0.8202 (m-30) cc_final: 0.7804 (m-30) REVERT: D 499 MET cc_start: 0.8086 (mmt) cc_final: 0.7271 (mmt) REVERT: D 501 PHE cc_start: 0.7623 (m-80) cc_final: 0.7221 (m-80) REVERT: D 502 ILE cc_start: 0.7797 (mm) cc_final: 0.7275 (tt) outliers start: 39 outliers final: 25 residues processed: 284 average time/residue: 0.1467 time to fit residues: 61.3699 Evaluate side-chains 286 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 253 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 309 TYR Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 453 CYS Chi-restraints excluded: chain D residue 560 GLU Chi-restraints excluded: chain D residue 561 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 163 optimal weight: 10.0000 chunk 201 optimal weight: 30.0000 chunk 79 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 177 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 199 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.198638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119601 restraints weight = 20682.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124586 restraints weight = 10670.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.125680 restraints weight = 6897.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126395 restraints weight = 5965.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.126704 restraints weight = 6215.154| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17168 Z= 0.127 Angle : 0.570 14.004 23332 Z= 0.282 Chirality : 0.040 0.266 2672 Planarity : 0.003 0.033 2912 Dihedral : 3.650 18.223 2272 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.91 % Favored : 95.70 % Rotamer: Outliers : 2.07 % Allowed : 17.88 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.19), residues: 2072 helix: 1.35 (0.15), residues: 1300 sheet: -2.15 (0.47), residues: 120 loop : -1.50 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 477 TYR 0.023 0.001 TYR C 420 PHE 0.025 0.001 PHE C 126 TRP 0.022 0.001 TRP D 70 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00301 (17156) covalent geometry : angle 0.57009 (23308) SS BOND : bond 0.00128 ( 12) SS BOND : angle 0.83960 ( 24) hydrogen bonds : bond 0.03111 ( 957) hydrogen bonds : angle 4.08661 ( 2766) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 254 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8041 (m-10) cc_final: 0.7456 (m-80) REVERT: A 202 ILE cc_start: 0.8657 (tp) cc_final: 0.8364 (tp) REVERT: A 283 MET cc_start: 0.8018 (mtp) cc_final: 0.7653 (mtp) REVERT: A 359 MET cc_start: 0.7482 (mmm) cc_final: 0.7279 (mmm) REVERT: A 391 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7304 (tt0) REVERT: A 397 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6034 (tmm-80) REVERT: A 408 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7424 (mt0) REVERT: A 425 TRP cc_start: 0.8535 (t-100) cc_final: 0.8127 (t-100) REVERT: A 432 ASP cc_start: 0.7930 (t0) cc_final: 0.7407 (t0) REVERT: A 499 MET cc_start: 0.6861 (tpp) cc_final: 0.6383 (tpp) REVERT: B 95 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7527 (mt0) REVERT: B 214 LEU cc_start: 0.5752 (OUTLIER) cc_final: 0.5536 (tt) REVERT: B 240 TYR cc_start: 0.7212 (t80) cc_final: 0.6498 (t80) REVERT: B 402 GLN cc_start: 0.7985 (tt0) cc_final: 0.7498 (tm-30) REVERT: B 419 LYS cc_start: 0.8383 (tttt) cc_final: 0.7942 (tttt) REVERT: B 422 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7424 (tm-30) REVERT: B 438 ARG cc_start: 0.8369 (ptp90) cc_final: 0.7699 (ptp90) REVERT: B 466 MET cc_start: 0.8171 (ppp) cc_final: 0.7294 (ppp) REVERT: B 499 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.5954 (ppp) REVERT: C 156 ARG cc_start: 0.8034 (tpp-160) cc_final: 0.7595 (tpp-160) REVERT: C 309 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.8091 (t80) REVERT: C 428 THR cc_start: 0.7714 (p) cc_final: 0.7453 (p) REVERT: C 438 ARG cc_start: 0.7768 (mtm180) cc_final: 0.7467 (mtm110) REVERT: C 446 ARG cc_start: 0.8423 (ptm160) cc_final: 0.8100 (ttt180) REVERT: D 101 ASP cc_start: 0.8105 (t0) cc_final: 0.7902 (t0) REVERT: D 183 ASN cc_start: 0.6427 (m-40) cc_final: 0.5461 (t0) REVERT: D 359 MET cc_start: 0.7243 (mmm) cc_final: 0.6471 (mtm) REVERT: D 404 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7412 (mtm) REVERT: D 408 GLN cc_start: 0.7698 (tp40) cc_final: 0.7259 (tp40) REVERT: D 426 ILE cc_start: 0.8286 (tp) cc_final: 0.7953 (tt) REVERT: D 453 CYS cc_start: 0.7676 (OUTLIER) cc_final: 0.6649 (p) REVERT: D 485 GLU cc_start: 0.8043 (tt0) cc_final: 0.7333 (tp30) REVERT: D 499 MET cc_start: 0.8370 (mmt) cc_final: 0.7461 (mmt) REVERT: D 501 PHE cc_start: 0.7516 (m-80) cc_final: 0.7120 (m-10) REVERT: D 502 ILE cc_start: 0.7681 (mm) cc_final: 0.7144 (tt) outliers start: 38 outliers final: 26 residues processed: 277 average time/residue: 0.1441 time to fit residues: 59.4742 Evaluate side-chains 282 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 249 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 309 TYR Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 453 CYS Chi-restraints excluded: chain D residue 561 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 122 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 119 optimal weight: 0.0070 chunk 89 optimal weight: 0.9980 chunk 111 optimal weight: 0.0570 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.199722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.120126 restraints weight = 20587.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.125014 restraints weight = 10048.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.128008 restraints weight = 6742.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.129560 restraints weight = 5527.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.129888 restraints weight = 5033.794| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17168 Z= 0.113 Angle : 0.556 13.959 23332 Z= 0.276 Chirality : 0.040 0.264 2672 Planarity : 0.003 0.033 2912 Dihedral : 3.649 20.004 2272 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.81 % Favored : 95.80 % Rotamer: Outliers : 1.85 % Allowed : 18.04 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 2072 helix: 1.44 (0.15), residues: 1280 sheet: -2.11 (0.48), residues: 120 loop : -1.35 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 197 TYR 0.021 0.001 TYR C 420 PHE 0.024 0.001 PHE C 126 TRP 0.023 0.001 TRP D 70 HIS 0.005 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00260 (17156) covalent geometry : angle 0.55567 (23308) SS BOND : bond 0.00151 ( 12) SS BOND : angle 0.78804 ( 24) hydrogen bonds : bond 0.03040 ( 957) hydrogen bonds : angle 4.07673 ( 2766) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3286.34 seconds wall clock time: 57 minutes 20.31 seconds (3440.31 seconds total)